From 3a396b00675fae70541eb4a9d2e0909654b1d3bf Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 22 May 2021 18:25:06 +0200 Subject: gnu: python-genshi: Update to 0.7.5. * gnu/packages/python-web.scm (python-genshi): Update to 0.7.5. [propagated-inputs]: Add PYTHON-SIX. --- gnu/packages/python-web.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index b7411d21fa..e789f9d837 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -3926,7 +3926,7 @@ for Flask programs that are using @code{python-alembic}.") (define-public python-genshi (package (name "python-genshi") - (version "0.7.3") + (version "0.7.5") (source (origin (method git-fetch) @@ -3935,7 +3935,9 @@ for Flask programs that are using @code{python-alembic}.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "04bw7nd4wyn8ixnhik57hny2xpjjpn80k5hp6691inix5gc6rxaf")))) + (base32 "04i0caywiwrgw09grz988n15qr9lr31d9n6a529p8v80cy1fv23c")))) + (propagated-inputs + `(("python-six" ,python-six))) (build-system python-build-system) (home-page "https://genshi.edgewall.org/") (synopsis "Toolkit for generation of output for the web") -- cgit 1.4.1 From 9419f97a718904889226b28901b40334f1ddca04 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 22 May 2021 18:26:36 +0200 Subject: gnu: python-terminado: Update to 0.10.0. * gnu/packages/python-web.scm (python-terminado): Update to 0.10.0. --- gnu/packages/python-web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index e789f9d837..9815ba011b 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1749,14 +1749,14 @@ web framework, either via the basic or digest authentication schemes.") (define-public python-terminado (package (name "python-terminado") - (version "0.9.4") + (version "0.10.0") (source (origin (method url-fetch) (uri (pypi-uri "terminado" version)) (sha256 (base32 - "1glqyw97rddyzvisz8rihsn3x2nrm5xbyq82nzp3123pqbxvqzcs")))) + "1smvra3sc9sg64w49kfn5yhagshq3x55839748ck5dvxvk4hgza6")))) (build-system python-build-system) (propagated-inputs `(("python-tornado" ,python-tornado-6) -- cgit 1.4.1 From 2f97a666a564fea0fdcff00a0513aa8b4c2d60fe Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 22 May 2021 18:51:05 +0200 Subject: gnu: python-urllib3: Don't use 'package/inherit' on replacement package. * gnu/packages/python-web.scm (python-urllib3/fixed): Use regular inheritance instead of PACKAGE/INHERIT. --- gnu/packages/python-web.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 9815ba011b..72eb93541b 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2784,7 +2784,8 @@ supports url redirection and retries, and also gzip and deflate decoding.") (license license:expat))) (define python-urllib3/fixed - (package/inherit python-urllib3 + (package + (inherit python-urllib3) (version "1.26.4") (source (origin -- cgit 1.4.1 From 080770e6547132650b72711a9e1b0ce50ca4ff74 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 22 May 2021 19:17:49 +0200 Subject: gnu: python-django-statici18n: Update to 2.1.0. * gnu/packages/django.scm (python-django-statici18n): Update to 2.1.0. --- gnu/packages/django.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index debdd22d12..9080afd373 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -961,7 +961,7 @@ name is purely coincidental.") (define-public python-django-statici18n (package (name "python-django-statici18n") - (version "1.9.0") + (version "2.1.0") (home-page "https://github.com/zyegfryed/django-statici18n") (source (origin (method git-fetch) @@ -971,7 +971,7 @@ name is purely coincidental.") (file-name (git-file-name name version)) (sha256 (base32 - "1p3myp2im6c87yc05alh91jyahqws5lcw3zzdsj4dh8lx9s9cgpf")))) + "0x0xvfqd40is2ks43d65awgqkx3wk10lvdim15scvbjhkh301b6v")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases -- cgit 1.4.1 From d51b8ac9474a09b3baea4aa8cb1745d6ce9121cd Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 22 May 2021 19:46:02 +0200 Subject: gnu: Remove python2-notebook. Some of its requirements no longer support Python 2 which has left this package broken for a while. * gnu/packages/python-xyz.scm (python2-notebook): Remove variable. (python-notebook)[properties]: Remove. --- gnu/packages/python-xyz.scm | 21 --------------------- 1 file changed, 21 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index bd716f3dac..2b02efa0c4 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -11200,29 +11200,8 @@ convert an @code{.ipynb} notebook file into various static formats including: (description "The Jupyter HTML notebook is a web-based notebook environment for interactive computing.") - (properties `((python2-variant . ,(delay python2-notebook)))) (license license:bsd-3))) -(define-public python2-notebook - (let ((base (package-with-python2 - (strip-python2-variant python-notebook)))) - (package/inherit base - (native-inputs - `(("python2-mock" ,python2-mock) - ,@(package-native-inputs base))) - (arguments - (substitute-keyword-arguments (package-arguments base) - ((#:phases phases) - `(modify-phases ,phases - (add-before 'check 'disable-test-case - ;; The test requires network access to localhost. Curiously it - ;; fails with Python 2 only. Simply make the test-case return - ;; immediately. - (lambda _ - (substitute* - "notebook/services/nbconvert/tests/test_nbconvert_api.py" - (("formats = self.nbconvert_api") "return #"))))))))))) - (define-public python-widgetsnbextension (package (name "python-widgetsnbextension") -- cgit 1.4.1 From 8a0e94f69be6bbe2edf89ace385d7062f90970c1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 22 May 2021 19:48:01 +0200 Subject: gnu: Remove python2-ipython-cluster-helper. Some of its requirements no longer support Python 2 which has left this package broken for a while. * gnu/packages/python-xyz.scm (python2-ipython-cluster-helper): Remove variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2b02efa0c4..c501b65a55 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7554,9 +7554,6 @@ profile, launches a cluster and returns a view. On program exit it shuts the cluster down and deletes the throwaway profile.") (license license:expat))) -(define-public python2-ipython-cluster-helper - (package-with-python2 python-ipython-cluster-helper)) - (define-public python-traitlets (package (name "python-traitlets") -- cgit 1.4.1 From 015869d4c62c7a450b8231adf6054a7b4b28e628 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sat, 22 May 2021 21:38:48 +0300 Subject: gnu: cmdtest: Use a source file-name. * gnu/packages/check.scm (cmdtest)[source]: Add a file-name field. --- gnu/packages/check.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 08e390840c..63ed2175ef 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -430,6 +430,7 @@ a multi-paradigm automated test framework for C++ and Objective-C.") (uri (git-reference (url "git://git.liw.fi/cmdtest/") (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 "1yhcwsqcpckkq5kw3h07k0xg6infyiyzq9ni3nqphrzxis7hxjf1")))) -- cgit 1.4.1 From dac6c21623475dbd1fa9679e33649eba461dd6b2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 22 May 2021 21:56:33 +0200 Subject: gnu: zam-plugins: Update source hash. See . * gnu/packages/music.scm (zam-plugins)[source]: Update hash. --- gnu/packages/music.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 0c29deecd3..aed10632cb 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -5901,7 +5901,7 @@ audio and MIDI plugins that can also run as standalone JACK applications.") (recursive? #t))) (file-name (git-file-name name version)) (sha256 - (base32 "0bxvssqnnd7bph3w1d6xcmxradv4cqq3wyzyv1a1hfm71a0pdahs")))) + (base32 "02blg0iqich4vx5z1ahj6avkh83yqszdiq83p9jd5qwm0i4llqjq")))) (build-system gnu-build-system) (arguments `(#:tests? #f ;no "check" target -- cgit 1.4.1 From d900cbadfd03fdfca155531bf3b2f5b548582c65 Mon Sep 17 00:00:00 2001 From: Raphaël Mélotte Date: Tue, 18 May 2021 18:49:40 +0200 Subject: gnu: luakit: Update to 2.3. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/web-browsers.scm (luakit): Update to 2.3 [arguments]: Add 'set-version' phase. Signed-off-by: Ludovic Courtès --- gnu/packages/web-browsers.scm | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index af178f9092..f677d58fd6 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -231,7 +231,7 @@ features including, tables, builtin image display, bookmarks, SSL and more.") (define-public luakit (package (name "luakit") - (version "2.2") + (version "2.3") (source (origin (method git-fetch) (uri (git-reference @@ -240,7 +240,7 @@ features including, tables, builtin image display, bookmarks, SSL and more.") (file-name (git-file-name name version)) (sha256 (base32 - "0km5nxn6innzn8pfsvlkxvfj2z5g46fp6dy5bnmaklbn13mqlcrn")))) + "1khbn7dpizkznnwkw7rcfhf72dnd1nazk7dwb4rkh9i97b53mf1y")))) (inputs `(("lua-5.1" ,lua-5.1) ("gtk+" ,gtk+) @@ -254,7 +254,7 @@ features including, tables, builtin image display, bookmarks, SSL and more.") `(("pkg-config" ,pkg-config))) (build-system glib-or-gtk-build-system) (arguments - '(#:make-flags + `(#:make-flags (let ((out (assoc-ref %outputs "out"))) (list "CC=gcc" @@ -271,6 +271,10 @@ features including, tables, builtin image display, bookmarks, SSL and more.") (assoc-ref %build-inputs "lua5.1-filesystem") "/lib/lua/5.1/?.so;;")) #t)) + (add-before 'build 'set-version + (lambda _ + (setenv "VERSION_FROM_GIT" ,(package-version this-package)) + #t)) (delete 'configure) (delete 'check) (add-after 'install 'wrap -- cgit 1.4.1 From 6a54e8138bda39722c9418d4cb674f53ecc4e594 Mon Sep 17 00:00:00 2001 From: Renzo Poddighe Date: Sat, 15 May 2021 20:27:25 +0200 Subject: gnu: Add jumpapp. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/xdisorg.scm (jumpapp): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/xdisorg.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 83fefecedc..6d7794ef43 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -45,6 +45,7 @@ ;;; Copyright © 2020, 2021 Zheng Junjie <873216071@qq.com> ;;; Copyright © 2021 Nicolas Goaziou ;;; Copyright © 2021 Xinglu Chen +;;; Copyright © 2021 Renzo Poddighe ;;; ;;; This file is part of GNU Guix. ;;; @@ -2796,3 +2797,44 @@ and execute @file{.desktop} files of the Application type.") "The @command{hsetroot} command composes wallpapers for X. This package is the fork of hsetroot by Hyriand.") (license license:gpl2+))) + +(define-public jumpapp + (package + (name "jumpapp") + (version "1.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mkropat/jumpapp") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1jrk4mm42sz6ca2gkb6w3dad53d4im4shpgsq8s4vr6xpl3b43ry")))) + (build-system gnu-build-system) + (arguments `(#:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'check) + (add-before 'install 'set-prefix-in-makefile + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (substitute* "Makefile" + (("PREFIX =.*") + (string-append "PREFIX = " out "\n"))) + #true)))))) + (propagated-inputs + `(("wmctrl" ,wmctrl) + ("xdotool" ,xdotool) + ("xprop" ,xprop))) + (native-inputs + `(("pandoc" ,pandoc) + ("perl" ,perl))) + (synopsis "Run-or-raise application switcher for any X11 desktop") + (description + "Bind a key for any given application that will launch the application, +if it's not already running, or focus the application's window,if it is running. +Pressing the key again will cycle to the application's next window, +if there's more than one.") + (home-page "https://github.com/mkropat/jumpapp") + (license license:expat))) -- cgit 1.4.1 From 58b85f7f419e77930765647ffc41011c1103066e Mon Sep 17 00:00:00 2001 From: WinterHound Date: Tue, 20 Apr 2021 23:53:45 +0530 Subject: gnu: Add xdo. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/xdisorg.scm (xdo): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/xdisorg.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 6d7794ef43..bf4b062973 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -511,6 +511,39 @@ manager supports it, you can use xdotool to switch desktops, move windows between desktops, and change the number of desktops.") (license license:bsd-3))) +(define-public xdo + (package + (name "xdo") + (version "0.5.7") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/baskerville/xdo") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1h3jrygcjjbavdbkpx2hscsf0yf97gk487lzjdlvymd7dxdv9hy9")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no tests + #:make-flags + (list (string-append "CC=" ,(cc-for-target)) + (string-append "PREFIX=" %output)) + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (inputs + `(("libxcb" ,libxcb) + ("xcb-util-wm" ,xcb-util-wm) + ("xcb-util" ,xcb-util))) + (home-page "https://github.com/baskerville/xdo") + (synopsis "Small X utility to perform elementary actions on windows") + (description + "Apply the given action to the given windows. If no window IDs and no +options are given, the action applies to the focused window.") + (license license:bsd-2))) + (define-public xeyes (package (name "xeyes") -- cgit 1.4.1 From d49402ab45486347cddfd000951a69f0c872cfda Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Sat, 22 May 2021 20:45:09 +0100 Subject: gnu: cl-trivial-features: Update to 1.0. * gnu/packages/lisp-xyz.scm (sbcl-trivial-features): Update to 1.0. [arguments]: Add comment about disabled tests. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 46 ++++++++++++++++++++++++---------------------- 1 file changed, 24 insertions(+), 22 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 8163fbdecf..4a1e9064d5 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -1360,29 +1360,31 @@ utilities that make it even easier to manipulate text in Common Lisp. It has (sbcl-package->ecl-package sbcl-cl-strings)) (define-public sbcl-trivial-features - ;; No release since 2014. - (let ((commit "870d03de0ed44067963350936856e17ee725153e")) - (package - (name "sbcl-trivial-features") - (version (git-version "0.8" "1" commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/trivial-features/trivial-features") - (commit commit))) - (file-name (git-file-name "trivial-features" version)) - (sha256 - (base32 "14pcahr8r2j3idhyy216zyw8jnj1dnrx0qbkkbdqkvwzign1ah4j")))) - (build-system asdf-build-system/sbcl) - (arguments - '(#:asd-files '("trivial-features.asd") - #:tests? #f)) - (home-page "https://cliki.net/trivial-features") - (synopsis "Ensures consistency of @code{*FEATURES*} in Common Lisp") - (description "Trivial-features ensures that @code{*FEATURES*} is + (package + (name "sbcl-trivial-features") + (version "1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/trivial-features/trivial-features") + (commit (string-append "v" version)))) + (file-name (git-file-name "trivial-features" version)) + (sha256 + (base32 "0jsqah1znzqilxnw5vannb083ayk0d7phkackqzwwqkyg5hpn6pq")))) + (build-system asdf-build-system/sbcl) + (arguments + '(#:asd-files '("trivial-features.asd") + ;; FIXME: Tests disabled because of a circular dependency between + ;; trivial-features and cffi. + #:tests? #f)) + ;; (native-inputs + ;; `(("cffi" ,sbcl-cffi))) + (home-page "https://cliki.net/trivial-features") + (synopsis "Ensures consistency of @code{*FEATURES*} in Common Lisp") + (description "Trivial-features ensures that @code{*FEATURES*} is consistent across multiple Common Lisp implementations.") - (license license:expat)))) + (license license:expat))) (define-public cl-trivial-features (sbcl-package->cl-source-package sbcl-trivial-features)) -- cgit 1.4.1 From 9351b2a48145a690484ff38ace0ccb828c204c09 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 22 May 2021 21:33:53 +0200 Subject: gnu: squashfs-tools: Prepare for GCC 10. * gnu/packages/compression.scm (squashfs-tools)[source](modules, snippet): New fields. --- gnu/packages/compression.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 746a496c90..c1996edbec 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -863,7 +863,15 @@ time for compression ratio.") "squashfs" version ".tar.gz")) (sha256 (base32 - "0zmhvczscqz0mzh4b9m8m42asq14db0a6lc8clp5ljq5ybrv70d9")))) + "0zmhvczscqz0mzh4b9m8m42asq14db0a6lc8clp5ljq5ybrv70d9")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Fix build with -fno-common (default in GCC 10). + ;; Remove for squashfs-tools > 4.4. + (substitute* "squashfs-tools/mksquashfs.h" + (("struct cache \\*bwriter_buffer" all) + (string-append "extern " all))))))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no check target -- cgit 1.4.1 From dbcf2b61b1f48cbe84d51873f4e4de60897b914c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 23 May 2021 14:07:34 +0200 Subject: gnu: Fix erroneous uses of 'package/inherit'. These packages use a different source/version from the inherited package, and thus should not inherit replacements. * gnu/packages/check.scm (googletest-1.8, python-pytest-runner-2): Use record inheritance instead of PACKAGE/INHERIT. * gnu/packages/crates-io.scm (rust-bindgen-0.49, rust-bytes-0.4, rust-colored-1.9.1, rust-difference-1, rust-docopt-0.8, rust-html5ever-0.23, rust-http-0.1, rust-http-body-0.1, rust-loom-0.2, rust-loom-0.1, rust-pulldown-cmark-0.0.8, rust-ring-0.13, rust-rustls-0.12, rust-sct-0.3, rust-term-0.2, rust-untrusted-0.6, rust-webpki-0.18, rust-webpki-roots-0.17, rust-webpki-roots-0.14): Likewise. * gnu/packages/emacs.scm (emacs-next, emacs-next-pgtk, guile-emacs): Likewise. * gnu/packages/guile.scm (guile-2.2.4): Likewise. * gnu/packages/maths.scm (hdf5-1.10, hdf5-1.12): Likewise. * gnu/packages/protobuf.scm (protobuf-3.6, protobuf-3.5, python-protobuf-3.6): Likewise. * gnu/packages/python-web.scm (python2-html2text): Likewise. * gnu/packages/python-xyz.scm (python-pygments/fixed, python2-numpy, python2-urwid, python2-markdown, python2-fonttools): Likewise. * gnu/packages/racket.scm (racket): Likewise. * gnu/packages/sequoia.scm (sequoia4pEp): Likewise. --- gnu/packages/check.scm | 8 +++---- gnu/packages/crates-io.scm | 57 ++++++++++++++++++++++++++++++--------------- gnu/packages/emacs.scm | 9 ++++--- gnu/packages/guile.scm | 4 ++-- gnu/packages/maths.scm | 6 +++-- gnu/packages/protobuf.scm | 10 ++++---- gnu/packages/python-web.scm | 3 ++- gnu/packages/python-xyz.scm | 18 +++++++------- gnu/packages/racket.scm | 4 ++-- gnu/packages/sequoia.scm | 3 ++- 10 files changed, 76 insertions(+), 46 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 63ed2175ef..7b20d863e6 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -697,8 +697,8 @@ generation.") (license license:bsd-3))) (define-public googletest-1.8 - (package/inherit - googletest + (package + (inherit googletest) (version "1.8.1") (source (origin (method git-fetch) @@ -1188,8 +1188,8 @@ contacting the real http server.") ;; python-bleach 3.1.0 requires this ancient version of pytest-runner. ;; Remove once no longer needed. (define-public python-pytest-runner-2 - (package/inherit - python-pytest-runner + (package + (inherit python-pytest-runner) (version "2.12.2") (source (origin (method url-fetch) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 313c57e90f..318b2c695b 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -4416,7 +4416,8 @@ bindings to C and C++ libraries.") ("rust-shlex" ,rust-shlex-0.1)))))) (define-public rust-bindgen-0.49 - (package/inherit rust-bindgen-0.50 + (package + (inherit rust-bindgen-0.50) (name "rust-bindgen") (version "0.49.4") (source @@ -5949,7 +5950,8 @@ little-endian.") (("rust-serde" ,rust-serde-1)))))) (define-public rust-bytes-0.4 - (package/inherit rust-bytes-0.5 + (package + (inherit rust-bytes-0.5) (name "rust-bytes") (version "0.4.12") (source @@ -7660,7 +7662,8 @@ colors.") (license license:mpl2.0))) (define-public rust-colored-1.9.1 - (package/inherit rust-colored-1 + (package + (inherit rust-colored-1) (name "rust-colored") (version "1.9.1") (source @@ -11575,7 +11578,8 @@ Diesel.") (license license:expat))) (define-public rust-difference-1 - (package/inherit rust-difference-2 + (package + (inherit rust-difference-2) (name "rust-difference") (version "1.0.0") (source @@ -12123,7 +12127,8 @@ from macros.") (license (list license:expat license:unlicense)))) (define-public rust-docopt-0.8 - (package/inherit rust-docopt-1 + (package + (inherit rust-docopt-1) (name "rust-docopt") (version "0.8.3") (source @@ -18312,7 +18317,8 @@ Hash-based Message Authentication Code algorithm} for SHA1.") ("rust-typed-arena" ,rust-typed-arena-1)))))) (define-public rust-html5ever-0.23 - (package/inherit rust-html5ever-0.24 + (package + (inherit rust-html5ever-0.24) (name "rust-html5ever") (version "0.23.0") (source @@ -18387,7 +18393,8 @@ requests and responses.") (license (list license:asl2.0 license:expat)))) (define-public rust-http-0.1 - (package/inherit rust-http-0.2 + (package + (inherit rust-http-0.2) (name "rust-http") (version "0.1.17") (source @@ -18454,7 +18461,8 @@ HTTP request or response body.") ("rust-http" ,rust-http-0.2)))))) (define-public rust-http-body-0.1 - (package/inherit rust-http-body-0.3 + (package + (inherit rust-http-body-0.3) (name "rust-http-body") (version "0.1.0") (source @@ -22410,7 +22418,8 @@ explosion.") ("rust-serde-json" ,rust-serde-json-1)))))) (define-public rust-loom-0.2 - (package/inherit rust-loom-0.3 + (package + (inherit rust-loom-0.3) (name "rust-loom") (version "0.2.13") (source @@ -22432,7 +22441,8 @@ explosion.") ("rust-serde-json" ,rust-serde-json-1)))))) (define-public rust-loom-0.1 - (package/inherit rust-loom-0.3 + (package + (inherit rust-loom-0.3) (name "rust-loom") (version "0.1.1") (source @@ -30534,7 +30544,8 @@ compliant email address validation.") ("rust-getopts" ,rust-getopts-0.2)))))) (define-public rust-pulldown-cmark-0.0.8 - (package/inherit rust-pulldown-cmark-0.4 + (package + (inherit rust-pulldown-cmark-0.4) (name "rust-pulldown-cmark") (version "0.0.8") (source @@ -33150,7 +33161,8 @@ functionality as retain but gives mutable borrow to the predicate.") ("rust-cc" ,rust-cc-1)))))) (define-public rust-ring-0.13 - (package/inherit rust-ring-0.16 + (package + (inherit rust-ring-0.16) (name "rust-ring") (version "0.13.5") (source @@ -35111,7 +35123,8 @@ rustc compiler.") ("rust-webpki" ,rust-webpki-0.18)))))) (define-public rust-rustls-0.12 - (package/inherit rust-rustls-0.16 + (package + (inherit rust-rustls-0.16) (name "rust-rustls") (version "0.12.0") (source @@ -36158,7 +36171,8 @@ Pwrite traits from the scroll crate.") ("rust-untrusted" ,rust-untrusted-0.6)))))) (define-public rust-sct-0.3 - (package/inherit rust-sct-0.6 + (package + (inherit rust-sct-0.6) (name "rust-sct") (version "0.3.0") (source @@ -41958,7 +41972,8 @@ template language.") ("rust-winapi" ,rust-winapi-0.2)))))) (define-public rust-term-0.2 - (package/inherit rust-term-0.4 + (package + (inherit rust-term-0.4) (name "rust-term") (version "0.2.14") (source @@ -47060,7 +47075,8 @@ untrusted inputs in Rust.") (license license:isc))) (define-public rust-untrusted-0.6 - (package/inherit rust-untrusted-0.7 + (package + (inherit rust-untrusted-0.7) (name "rust-untrusted") (version "0.6.2") (source @@ -48681,7 +48697,8 @@ Verification.") (("rust-base64" ,rust-base64-0.9)))))) (define-public rust-webpki-0.18 - (package/inherit rust-webpki-0.21 + (package + (inherit rust-webpki-0.21) (name "rust-webpki") (version "0.18.1") (source @@ -48767,7 +48784,8 @@ with webpki.") (base32 "1d4ss607rgi9pj01zzqa13c1p3m35z314yh6lmjaj4kzvwv5gkci")))))) (define-public rust-webpki-roots-0.17 - (package/inherit rust-webpki-roots-0.18 + (package + (inherit rust-webpki-roots-0.18) (name "rust-webpki-roots") (version "0.17.0") (source @@ -48818,7 +48836,8 @@ with webpki.") ("rust-webpki" ,rust-webpki-0.18)))))) (define-public rust-webpki-roots-0.14 - (package/inherit rust-webpki-roots-0.18 + (package + (inherit rust-webpki-roots-0.18) (name "rust-webpki-roots") (version "0.14.0") (source diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 5316d25151..1a2b98bec2 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -305,7 +305,8 @@ languages.") (define-public emacs-next (let ((commit "2ea34662c20f71d35dd52a5ed996542c7386b9cb") (revision "0")) - (package/inherit emacs + (package + (inherit emacs) (name "emacs-next") (version (git-version "28.0.50" revision commit)) (source @@ -326,7 +327,8 @@ languages.") (define-public emacs-next-pgtk (let ((commit "ae18c8ec4f0ef37c8c9cda473770ff47e41291e2") (revision "1")) - (package/inherit emacs-next + (package + (inherit emacs-next) (name "emacs-next-pgtk") (version (git-version "28.0.50" revision commit)) (source @@ -450,7 +452,8 @@ editor (with wide ints)" ) (define-public guile-emacs (let ((commit "41120e0f595b16387eebfbf731fff70481de1b4b") (revision "0")) - (package/inherit emacs + (package + (inherit emacs) (name "guile-emacs") (version (git-version "0.0.0" revision commit)) (source (origin diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 74c0709ea4..5de4f68093 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -269,8 +269,8 @@ without requiring the source code to be rewritten.") (define-deprecated guile-2.2/bug-fix guile-2.2) (define-public guile-2.2.4 - (package/inherit - guile-2.2 + (package + (inherit guile-2.2) (version "2.2.4") (source (origin (inherit (package-source guile-2.2)) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 8cd64e7697..5062cc0347 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1230,7 +1230,8 @@ extremely large and complex data collections.") "https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING")))) (define-public hdf5-1.10 - (package/inherit hdf5-1.8 + (package + (inherit hdf5-1.8) (version "1.10.7") (source (origin @@ -1249,7 +1250,8 @@ extremely large and complex data collections.") (patches (search-patches "hdf5-config-date.patch")))))) (define-public hdf5-1.12 - (package/inherit hdf5-1.8 + (package + (inherit hdf5-1.8) (version "1.12.0") (source (origin diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm index 995d543059..857adf1703 100644 --- a/gnu/packages/protobuf.scm +++ b/gnu/packages/protobuf.scm @@ -123,7 +123,8 @@ internal RPC protocols and file formats.") ;; Tensorflow requires version 3.6 specifically. (define-public protobuf-3.6 - (package/inherit protobuf + (package + (inherit protobuf) (version "3.6.1") (source (origin (method url-fetch) @@ -136,8 +137,8 @@ internal RPC protocols and file formats.") ;; The 3.5 series are the last versions that do not require C++ 11. (define-public protobuf-3.5 - (package/inherit - protobuf + (package + (inherit protobuf) (version "3.5.1") (source (origin (method url-fetch) @@ -289,7 +290,8 @@ structured data.") ;; For tensorflow. (define-public python-protobuf-3.6 - (package/inherit python-protobuf + (package + (inherit python-protobuf) (name "python-protobuf") (version (package-version protobuf-3.6) ) (source diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 72eb93541b..4468a9b8cd 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -707,7 +707,8 @@ Swartz.") (define-public python2-html2text (let ((base (package-with-python2 python-html2text))) - (package/inherit base + (package + (inherit base) ;; This is the last version with support for Python 2. (version "2019.8.11") (source (origin diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c501b65a55..5a3c6b670e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3980,7 +3980,8 @@ text styles of documentation.") (properties `((python2-variant . ,(delay python2-pygments)))))) (define python-pygments/fixed - (package/inherit python-pygments + (package + (inherit python-pygments) (version "2.7.4") (source (origin @@ -4969,8 +4970,8 @@ capabilities.") (define-public python2-numpy (let ((numpy (package-with-python2 (strip-python2-variant python-numpy)))) - (package/inherit - numpy + (package + (inherit numpy) (version "1.16.5") (source (origin (method url-fetch) @@ -8087,7 +8088,8 @@ features useful for text console applications.") (define-public python2-urwid (let ((base (package-with-python2 (strip-python2-variant python-urwid)))) - (package/inherit base + (package + (inherit base) (version "2.1.0") (source (origin @@ -9528,8 +9530,8 @@ markdown_py is also provided to convert Markdown files to HTML.") ;; Markdown 3.2 dropped support for Python 2. (define-public python2-markdown (let ((base (package-with-python2 (strip-python2-variant python-markdown)))) - (package/inherit - base + (package + (inherit base) (version "3.1.1") (source (origin (method url-fetch) @@ -9697,8 +9699,8 @@ from an XML-based format.") ;; Fonttools 4.x dropped support for Python 2, so stick with 3.x here. (define-public python2-fonttools (let ((base (package-with-python2 (strip-python2-variant python-fonttools)))) - (package/inherit - base + (package + (inherit base) (version "3.44.0") (source (origin (method url-fetch) diff --git a/gnu/packages/racket.scm b/gnu/packages/racket.scm index 18af14b2ec..be33270b30 100644 --- a/gnu/packages/racket.scm +++ b/gnu/packages/racket.scm @@ -173,8 +173,8 @@ DrRacket IDE, are not included.") (define-public racket - (package/inherit - racket-minimal + (package + (inherit racket-minimal) (name "racket") (version (package-version racket-minimal)) ; needed for origin uri to work (source diff --git a/gnu/packages/sequoia.scm b/gnu/packages/sequoia.scm index cb1e2a4872..c83926ef6c 100644 --- a/gnu/packages/sequoia.scm +++ b/gnu/packages/sequoia.scm @@ -221,7 +221,8 @@ with OpenPGP data.") (define-public sequoia4pEp ;; Currently pEp Engine requires sequoia in not-so-current version - (package/inherit sequoia + (package + (inherit sequoia) (name "sequoia") (version "0.15.0-pEp") (source -- cgit 1.4.1 From 250a216cdc2d5425ee0053f3e614d54e0fb6aa90 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 23 May 2021 14:20:34 +0200 Subject: gnu: OpenSSL: Replace with 1.1.1k [fixes CVE-2021-3449 and CVE-2021-3450]. * gnu/packages/tls.scm (openssl-1.1.1k): New variable. (openssl)[replacement]: New field. --- gnu/packages/tls.scm | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 1a4e3dc258..174438ad87 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -9,7 +9,7 @@ ;;; Copyright © 2016, 2017, 2018 Nikita ;;; Copyright © 2016 Hartmut Goebel ;;; Copyright © 2017 Ricardo Wurmus -;;; Copyright © 2017, 2018, 2019, 2020 Marius Bakke +;;; Copyright © 2017, 2018, 2019, 2020, 2021 Marius Bakke ;;; Copyright © 2017–2019, 2021 Tobias Geerinckx-Rice ;;; Copyright © 2017 Rutger Helling ;;; Copyright © 2018 Clément Lassieur @@ -289,6 +289,7 @@ required structures.") (package (name "openssl") (version "1.1.1j") + (replacement openssl-1.1.1k) (source (origin (method url-fetch) (uri (list (string-append "https://www.openssl.org/source/openssl-" @@ -422,6 +423,25 @@ required structures.") (license license:openssl) (home-page "https://www.openssl.org/"))) +;; Replacement package to fix CVE-2021-3449 and CVE-2021-3450. +(define openssl-1.1.1k + (package + (inherit openssl) + (version "1.1.1k") + (source (origin + (method url-fetch) + (uri (list (string-append "https://www.openssl.org/source/openssl-" + version ".tar.gz") + (string-append "ftp://ftp.openssl.org/source/" + "openssl-" version ".tar.gz") + (string-append "ftp://ftp.openssl.org/source/old/" + (string-trim-right version char-set:letter) + "/openssl-" version ".tar.gz"))) + (patches (search-patches "openssl-1.1-c-rehash-in.patch")) + (sha256 + (base32 + "1rdfzcrxy9y38wqdw5942vmdax9hjhgrprzxm42csal7p5shhal9")))))) + (define-public openssl-1.0 (package (inherit openssl) -- cgit 1.4.1 From a9f84f93b45db712b3bd30943361a267cb85cf79 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 23 May 2021 14:23:18 +0200 Subject: gnu: libx11: Update replacement to 1.7.1 [fixes CVE-2021-31535]. * gnu/packages/xorg.scm (libx11/fixed): Update to 1.7.1. --- gnu/packages/xorg.scm | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index dea4f8e304..1b9dfed34b 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -11,7 +11,7 @@ ;;; Copyright © 2016 Alex Kost ;;; Copyright © 2016 David Craven ;;; Copyright © 2016, 2017 John Darrington -;;; Copyright © 2017, 2018, 2019, 2020 Marius Bakke +;;; Copyright © 2017, 2018, 2019, 2020, 2021 Marius Bakke ;;; Copyright © 2017, 2018, 2019 Rutger Helling ;;; Copyright © 2017, 2020 Arun Isaac ;;; Copyright © 2018–2021 Tobias Geerinckx-Rice @@ -5523,17 +5523,14 @@ draggable titlebars and borders.") (define-public libx11/fixed (package (inherit libx11) - (version "1.6.12") + (version "1.7.1A") (source (origin (method url-fetch) - (uri (string-append - "mirror://xorg/individual/lib/libX11-" - version - ".tar.bz2")) + (uri "mirror://xorg/individual/lib/libX11-1.7.1.tar.bz2") (sha256 (base32 - "1ivfzl1qwk8zh7gc0m5vb58gdxz11jwg7w3d356w16j1d5s2427i")))))) + "0isxad59hvdwggbxqqjjjg3zmih9xiq4d9mdsnqbyb2nmbg46kp6")))))) ;; packages of height 5 in the propagated-inputs tree -- cgit 1.4.1 From 030bdbf141eefa725735d4fe04e2ef5763a14f24 Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Sun, 16 May 2021 16:08:32 +0200 Subject: gnu: notmuch: Update to 0.32.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/mail.scm (notmuch): Update to 0.32.1. [arguments]<#:phases>: Don’t return #t at the end of the phase, this won’t be necessary once core-update gets merged. Signed-off-by: Marius Bakke --- gnu/packages/mail.scm | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 8cb233812f..ded60cdc2c 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1331,14 +1331,14 @@ invoking @command{notifymuch} from the post-new hook.") (define-public notmuch (package (name "notmuch") - (version "0.31.4") + (version "0.32.1") (source (origin (method url-fetch) (uri (string-append "https://notmuchmail.org/releases/notmuch-" version ".tar.xz")) (sha256 (base32 - "0magnyjjhhv11nwcm2596hdxszrj61y69i0hmwqdc3v6cxjvcqc6")))) + "0586d13ssygapjdri4cl25wzywivwsbxpjm6xlgxj6f9ii7clix7")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build gnu-build-system) @@ -1354,8 +1354,7 @@ invoking @command{notifymuch} from the post-new hook.") (add-after 'unpack 'patch-notmuch-lib.el (lambda _ (substitute* "emacs/notmuch-lib.el" - (("/bin/sh") (which "sh"))) - #t)) + (("/bin/sh") (which "sh"))))) (replace 'configure (lambda* (#:key outputs #:allow-other-keys) (setenv "CC" "gcc") @@ -1372,15 +1371,13 @@ invoking @command{notifymuch} from the post-new hook.") ;; and try removing this for notmuch versions > 0.31. (lambda _ (substitute* "test/T356-protected-headers.sh" - (("\\$NOTMUCH_GMIME_X509_CERT_VALIDITY") "0")) - #t)) + (("\\$NOTMUCH_GMIME_X509_CERT_VALIDITY") "0")))) (add-before 'check 'prepare-test-environment (lambda _ (setenv "TEST_CC" "gcc") ;; Patch various inline shell invocations. (substitute* (find-files "test" "\\.sh$") - (("/bin/sh") (which "sh"))) - #t)) + (("/bin/sh") (which "sh"))))) (add-after 'install 'make-autoloads (assoc-ref emacs:%standard-phases 'make-autoloads))))) (native-inputs -- cgit 1.4.1 From 1c4144a159b4eec005af545b2701ee838a781a2c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 15:06:00 +0200 Subject: gnu: ois: Update to 1.5.1. * gnu/packages/game-development.scm (ois): Update to 1.5.1. --- gnu/packages/game-development.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index 52541196b3..62b8c6cdb1 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -1488,7 +1488,7 @@ painted with a mouse.") (define-public ois (package (name "ois") - (version "1.5") + (version "1.5.1") (source (origin (method git-fetch) @@ -1497,7 +1497,7 @@ painted with a mouse.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0g8krgq5bdx2rw7ig0xva4kqv4x815672i7z6lljp3n8847wmypa")))) + (base32 "0nkh0zrsbyv47c0i0vhdna3jsnvs69pb1svg75avxw6z7kwskgla")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ; no test suite -- cgit 1.4.1 From b83a8c7d9d55c45992107a2806f070eec44de89f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 15:11:45 +0200 Subject: gnu: filezilla: Update to 3.54.1. * gnu/packages/ftp.scm (filezilla): Update to 3.54.1. --- gnu/packages/ftp.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm index 4ee96125fd..880eaee9f6 100644 --- a/gnu/packages/ftp.scm +++ b/gnu/packages/ftp.scm @@ -220,14 +220,14 @@ output. (define-public filezilla (package (name "filezilla") - (version "3.53.1") + (version "3.54.1") (source (origin (method url-fetch) (uri (string-append "https://download.filezilla-project.org/client/" "FileZilla_" version "_src.tar.bz2")) (sha256 - (base32 "0ygpqfzj5ms1pd46fpfya1y1jl4w2kmaa7plf8n6fm7cxbr78s35")))) + (base32 "0smayigsk8hjplk7pm6dd80r1dnhr4f6xzp3n1p1ss5v2ff1jfkh")))) (build-system gnu-build-system) (arguments ;; Don't let filezilla phone home to check for updates. -- cgit 1.4.1 From f72e2d216b2d28bfba368431a9738204e0450b52 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 16:49:42 +0200 Subject: gnu: slurm: Update to 20.11.7. * gnu/packages/parallel.scm (slurm): Update to 20.11.7. --- gnu/packages/parallel.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm index 17e2a7f7fe..ffca2defbf 100644 --- a/gnu/packages/parallel.scm +++ b/gnu/packages/parallel.scm @@ -138,7 +138,7 @@ execution is also possible.") (define-public slurm (package (name "slurm") - (version "20.11.3") + (version "20.11.7") (source (origin (method url-fetch) (uri (string-append @@ -146,7 +146,7 @@ execution is also possible.") version ".tar.bz2")) (sha256 (base32 - "1s70x6yh60sx63dgmp5rlhq8jcz7kxv9pk8gbs9v1jg8zps5h5bk")) + "1fdjihg1x7ks5l77yjv14a4mg6r0v8c3zk1dcxkhrhq3n4dc9nbs")) (modules '((guix build utils))) (snippet '(begin -- cgit 1.4.1 From ba31fbb1632cdfeed6c9cff807268359ef88b279 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 12:25:04 +0200 Subject: gnu: cava: Update to 0.7.4. * gnu/packages/audio.scm (cava): Update to 0.7.4. --- gnu/packages/audio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 2f05a26e41..cbd25192a0 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -4314,7 +4314,7 @@ representations.") (define-public cava (package (name "cava") - (version "0.7.3") + (version "0.7.4") (source (origin (method git-fetch) (uri (git-reference @@ -4323,7 +4323,7 @@ representations.") (file-name (git-file-name name version)) (sha256 (base32 - "04j5hb29hivcbk542sfsx9m57dbnj2s6qpvy9fs488zvgjbgxrai")))) + "1mziklmqifhnb4kg9ia2r56r8wjn6xp40bkpf484hsgqvnrccl86")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) -- cgit 1.4.1 From d289a60770c8e4449439858158c28e84a053c3b0 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 12:50:07 +0200 Subject: gnu: nvc: Update to 1.5.1. * gnu/packages/fpga.scm (nvc): Update to 1.5.1. [arguments]: Hopefully re-enable #:parallel-build?s. --- gnu/packages/fpga.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/fpga.scm b/gnu/packages/fpga.scm index 809a807467..380a09d7f6 100644 --- a/gnu/packages/fpga.scm +++ b/gnu/packages/fpga.scm @@ -432,7 +432,7 @@ a hardware description and verification language. ") (define-public nvc (package (name "nvc") - (version "1.5.0") + (version "1.5.1") (source (origin (method git-fetch) (uri (git-reference @@ -441,11 +441,10 @@ a hardware description and verification language. ") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0dd1xany6qhh2qsfw8ba0ky7y86h19yr4hlk0r5i2bvwsg4355v9")))) + "0m1zhcqhgz5fajz98ky5zdv8g8gvk9caghqfpbv8q3mzdzahcsx5")))) (build-system gnu-build-system) (arguments - `(#:parallel-build? #f ; https://github.com/nickg/nvc/issues/409 - #:configure-flags + `(#:configure-flags '("--enable-vhpi") #:phases (modify-phases %standard-phases -- cgit 1.4.1 From 755d494cbd9446628be3b255c1e2122bb547e9d2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 12:53:10 +0200 Subject: gnu: butt: Update to 0.1.30. * gnu/packages/audio.scm (butt): Update to 0.1.30. --- gnu/packages/audio.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index cbd25192a0..dda1159f98 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -5166,14 +5166,14 @@ while still staying in time.") (define-public butt (package (name "butt") - (version "0.1.29") + (version "0.1.30") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/butt/butt/butt-" version "/butt-" version ".tar.gz")) (sha256 (base32 - "0nbz0z4d7krvhmnwn10594gwc61gn2dlb5fazmynjfisrfdswqlg")))) + "1dfspdh3f18lpp7asxpj63b9zfpvazi7shgrdacg17gd42ycayq5")))) (build-system gnu-build-system) (arguments `(#:phases @@ -5210,7 +5210,7 @@ while still staying in time.") version "_manual.pdf")) (sha256 (base32 - "1hhgdhdg5s86hjcbwh856gcd3kcch0i5xgi3i3v02zz3xmzl7gg3")))))) + "1w3krh7f2v5vdz18hqycnpn0qv1x6xl6pa1najgp4jbfisjc1mn8")))))) (home-page "https://danielnoethen.de/butt/") (synopsis "Audio streaming tool") (description "Butt is a tool to stream audio to a ShoutCast or -- cgit 1.4.1 From 6c7dc0bad197a4f6dd621b1b54b545a31d19eac2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 22:38:58 +0200 Subject: gnu: butt: Add snippet. * gnu/packages/audio.scm (butt)[source]: Add snippet. --- gnu/packages/audio.scm | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index dda1159f98..2afb37175d 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -5173,7 +5173,11 @@ while still staying in time.") version "/butt-" version ".tar.gz")) (sha256 (base32 - "1dfspdh3f18lpp7asxpj63b9zfpvazi7shgrdacg17gd42ycayq5")))) + "1dfspdh3f18lpp7asxpj63b9zfpvazi7shgrdacg17gd42ycayq5")) + (modules '((guix build utils))) + (snippet + '(substitute* "src/butt.cpp" + ((".*zica.*") ""))))) (build-system gnu-build-system) (arguments `(#:phases -- cgit 1.4.1 From da671c16f26a6f581aca3d3e9633bb4c92e57454 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 10:06:44 +0200 Subject: gnu: abook: Fix typo in description. * gnu/packages/mail.scm (abook)[description]: Fix typo. --- gnu/packages/mail.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index ded60cdc2c..a8f4e0ed88 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -207,10 +207,10 @@ `(("ncurses" ,ncurses) ("readline" ,readline))) (home-page "https://abook.sourceforge.io/") - (synopsis "Text-based addressbook") + (synopsis "Text-based address book") (description - "Abook is a text-based addressbook program designed to use with Mutt mail -client.") + "Abook is a text-based address book program designed to use with the Mutt +mail client.") (license license:gpl2))) (define-public anubis -- cgit 1.4.1 From 97cb3cf25a43e172c57907c80156412122495900 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 18:06:50 +0200 Subject: gnu: parallel: Update to 20210522. * gnu/packages/parallel.scm (parallel): Update to 20210522. --- gnu/packages/parallel.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm index ffca2defbf..d950fa9014 100644 --- a/gnu/packages/parallel.scm +++ b/gnu/packages/parallel.scm @@ -57,14 +57,14 @@ (define-public parallel (package (name "parallel") - (version "20210422") + (version "20210522") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/parallel/parallel-" version ".tar.bz2")) (sha256 - (base32 "1s4ynlsh5fr5vxcf5xm45fcfyzp62zclzjq5b7rbwrs4chxnlgmy")))) + (base32 "1qdgywilyy2vy8lcl7f5qa7cm0b2ddnwwx9n8xcfbv9wj0z3wrpg")))) (build-system gnu-build-system) (arguments `(#:phases -- cgit 1.4.1 From ada6f396e4f6c75859e3d191f0f8362aa91a1761 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 11:25:57 +0200 Subject: gnu: hddtemp: Update to 0.4.3. * gnu/packages/disk.scm (hddtemp): Update to 0.4.3. [source, home-page]: Use a maintained fork/continuation. [arguments]: Add a new 'delete-autogen.sh phase. Adjust the 'install-db phase to install the bundled hddtemp.db. [inputs]: Remove old hddtemp.db. [native-inputs]: Add autoconf, automake, and gettext. f hddtemp --- gnu/packages/disk.scm | 46 +++++++++++++++++++++++++--------------------- 1 file changed, 25 insertions(+), 21 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm index 006cb8e301..84996f9bc4 100644 --- a/gnu/packages/disk.scm +++ b/gnu/packages/disk.scm @@ -1144,15 +1144,18 @@ of choice for all light thinking Unix addicts!") (define-public hddtemp (package (name "hddtemp") - (version "0.3-beta15") - (source (origin - (method url-fetch) - (uri (string-append "mirror://savannah/hddtemp/hddtemp-" - version - ".tar.bz2")) - (sha256 - (base32 - "0nzgg4nl8zm9023wp4dg007z6x3ir60rwbcapr9ks2al81c431b1")))) + ;; advertises the project as + ;; ‘orphaned/unmaintained’. Use a maintained fork/continuation. + (version "0.4.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vitlav/hddtemp") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "04kylb2ka0jimi238zpfq1yii2caidpmj3ck51rvxz03y5lpq8fw")))) (build-system gnu-build-system) (arguments `(#:configure-flags (list (string-append @@ -1161,19 +1164,20 @@ of choice for all light thinking Unix addicts!") "/share/hddtemp/hddtemp.db")) #:phases (modify-phases %standard-phases + (add-before 'bootstrap 'delete-autogen.sh + (lambda _ + ;; The default 'bootstrap phase works better. + (delete-file "autogen.sh"))) (add-after 'install 'install-db - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((target (string-append (assoc-ref outputs "out") - "/share/hddtemp/hddtemp.db"))) - (mkdir-p (dirname target)) - (copy-file (assoc-ref inputs "db") target))))))) - (inputs - `(("db" ,(origin - (method url-fetch) - (uri "mirror://savannah/hddtemp/hddtemp.db") - (sha256 - (base32 "1fr6qgns6qv7cr40lic5yqwkkc7yjmmgx8j0z6d93csg3smzhhya")))))) - (home-page "https://savannah.nongnu.org/projects/hddtemp/") + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (install-file "data/hddtemp.db" + (string-append out "/share/hddtemp")))))))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("gettext" ,gettext-minimal))) + (home-page "https://github.com/vitlav/hddtemp") (synopsis "Report the temperature of hard drives from S.M.A.R.T. information") (description "@command{hddtemp} is a small utility that gives you the temperature of your hard drive by reading S.M.A.R.T. information (for drives -- cgit 1.4.1 From 5c49c38d9a6e9d8a60a41a6feaedb95e40c1264f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 11:28:09 +0200 Subject: gnu: diffoscope: Update to 175. * gnu/packages/diffoscope.scm (diffoscope): Update to 175. --- gnu/packages/diffoscope.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm index b74b9d1b1a..21c78ae6f0 100644 --- a/gnu/packages/diffoscope.scm +++ b/gnu/packages/diffoscope.scm @@ -72,7 +72,7 @@ (define-public diffoscope (package (name "diffoscope") - (version "174") + (version "175") (source (origin (method git-fetch) (uri (git-reference @@ -81,7 +81,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "16nvcvvps2gxr0b9wbfilrn4397cqkcm716zvhlx5hsbq6w6cx08")))) + "1qzdi9110mdm5af4nq1nwx9b1hrin9a1v3vhnxwrkyb7j0mvcg7v")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases -- cgit 1.4.1 From 0dcb822bf6c891b40ff570059dfb0ae661da389a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 11:44:14 +0200 Subject: gnu: exfatprogs: Update to 1.1.2. * gnu/packages/file-systems.scm (exfatprogs): Update to 1.1.2. --- gnu/packages/file-systems.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm index ad721017b5..c64c0df727 100644 --- a/gnu/packages/file-systems.scm +++ b/gnu/packages/file-systems.scm @@ -477,7 +477,7 @@ from the bcachefs-tools package. It is meant to be used in initrds.") (define-public exfatprogs (package (name "exfatprogs") - (version "1.1.1") + (version "1.1.2") (source (origin (method git-fetch) @@ -486,7 +486,7 @@ from the bcachefs-tools package. It is meant to be used in initrds.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1zl3w5w2mzyggizc4dsiln0pa013f8sf5dxmm5wflplpfm6k4brk")))) + (base32 "19pbybgbfnvjb3n944ihrn1r8ch4dm8dr0d44d6w7p63dcp372xy")))) (build-system gnu-build-system) (arguments `(#:configure-flags -- cgit 1.4.1 From 45dd728510646a6f3017a6e5780ecc217f05152b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 12:49:17 +0200 Subject: gnu: freeipmi: Update to 1.6.8. * gnu/packages/freeipmi.scm (freeipmi): Update to 1.6.8. --- gnu/packages/freeipmi.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/freeipmi.scm b/gnu/packages/freeipmi.scm index eb10b509c9..acd527fcee 100644 --- a/gnu/packages/freeipmi.scm +++ b/gnu/packages/freeipmi.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013 Ludovic Courtès ;;; Copyright © 2015, 2016, 2017, 2020, 2021 Efraim Flashner -;;; Copyright © 2019, 2020 Tobias Geerinckx-Rice +;;; Copyright © 2019–2021 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -28,14 +28,14 @@ (define-public freeipmi (package (name "freeipmi") - (version "1.6.7") + (version "1.6.8") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/freeipmi/freeipmi-" version ".tar.gz")) (sha256 (base32 - "1gyyx99q02p3v2nqm3h53mkjd33l0hrapwg4alg6qr9k74qik1dv")))) + "0w8af1i57szmxl9vfifwwyal7xh8aixz2l9487wvy6yckqk6m92a")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("--disable-static"))) -- cgit 1.4.1 From cbaa8e0454426d1fd4452103e6bb1f14cef28d43 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 11:16:41 +0200 Subject: gnu: python-django-compressor: Update to 2.4.12.4.1. * gnu/packages/django.scm (python-django-compressor): Update to 2.4.12.4.1. --- gnu/packages/django.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index 9080afd373..fa67e7412a 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -1120,14 +1120,13 @@ forms using your favorite CSS framework, without writing template code.") (define-public python-django-compressor (package (name "python-django-compressor") - (version "2.4") + (version "2.4.1") (source (origin (method url-fetch) (uri (pypi-uri "django_compressor" version)) (sha256 - (base32 - "0kx7bclfa0sxlsz6ka70zr9ra00lks0hmv1kc99wbanx6xhirvfj")))) + (base32 "1q0m0hfg7sqmj5km924g4dgy3nx51aszzsprlp6gsin10mv0fn1k")))) (build-system python-build-system) (arguments '(#:phases -- cgit 1.4.1 From 55244601d76b31082ab3c7f555d333d7cb106e89 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 11:43:50 +0200 Subject: gnu: retroarch: Update to 1.9.3. * gnu/packages/emulators.scm (retroarch): Update to 1.9.3. --- gnu/packages/emulators.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index 30cd2daf55..47dae86b51 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -1314,7 +1314,7 @@ as RetroArch.") (define-public retroarch (package (name "retroarch") - (version "1.9.2") + (version "1.9.3") (source (origin (method git-fetch) @@ -1323,7 +1323,7 @@ as RetroArch.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0zrry2zwknzsrrz8r6rl1iy9hmiv4dwjmf61aidx3xwxby3g82qg")) + (base32 "01ssacnq5sl9221476df95dgry5m1z5mnlk3l3dh3rrg0qr4nvv3")) (patches (search-patches "retroarch-LIBRETRO_DIRECTORY.patch")))) (build-system gnu-build-system) -- cgit 1.4.1 From 363095f296bb49d4a43603e273706ae33ee061ac Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 13:43:56 +0200 Subject: gnu: ltris: Update to 1.2.3. * gnu/packages/games.scm (ltris): Update to 1.2.3. [arguments]: Remove unnecessary #:configure-flags. --- gnu/packages/games.scm | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 24e487a2b8..6f07cd3aa9 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -1836,19 +1836,17 @@ Chess). It is similar to standard chess but this variant is far more complicate (define-public ltris (package (name "ltris") - (version "1.2.1") + (version "1.2.3") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/lgames/ltris/" "ltris-" version ".tar.gz")) (sha256 - (base32 "0959vvxh5xnxzpdv7i67lpd2b6ghx69z65ldnclj1z6llyfzfs7q")))) + (base32 "1a2m17jwkyar8gj07bn5jk01j2ps4vvc48z955jjjsh67q2svi0f")))) (build-system gnu-build-system) (arguments - '(;; The code in LTris uses traditional GNU semantics for inline functions - #:configure-flags '("CFLAGS=-fgnu89-inline") - #:phases + '(#:phases (modify-phases %standard-phases (add-after 'set-paths 'set-sdl-paths (lambda* (#:key inputs #:allow-other-keys) -- cgit 1.4.1 From d694018daca526b8a743faf45839e5a44ada7490 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 15:04:52 +0200 Subject: gnu: libetonyek: Update to 0.1.10. * gnu/packages/libreoffice.scm (libetonyek): Update to 0.1.10. --- gnu/packages/libreoffice.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index 4218168cd2..e03047c3fd 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -453,14 +453,14 @@ CorelDRAW documents of all versions.") (define-public libetonyek (package (name "libetonyek") - (version "0.1.9") + (version "0.1.10") (source (origin (method url-fetch) (uri (string-append "http://dev-www.libreoffice.org/src/" name "/" name "-" version ".tar.xz")) (sha256 (base32 - "0jhsbdimiyijdqriy0zzkjjgc4wi6fjimhdg4mdybrlwg7l7f5p6")))) + "16hy60ws29pb4pz3z5l4920yn9hnk2vlij0xfs5qi1w4drd46c5l")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-mdds=1.5"))) -- cgit 1.4.1 From aa65bba301b66b9cc7557255b567df5e35fbabe8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 15:05:30 +0200 Subject: gnu: libmediaart: Update to 1.9.5. * gnu/packages/gnome.scm (libmediaart): Update to 1.9.5. [arguments]: Use meson-next. --- gnu/packages/gnome.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index be458c07bb..4934ae0cc3 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -1407,7 +1407,7 @@ and implementation of UPnP A/V profiles.") (define-public libmediaart (package (name "libmediaart") - (version "1.9.4") + (version "1.9.5") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -1415,8 +1415,10 @@ and implementation of UPnP A/V profiles.") name "-" version ".tar.xz")) (sha256 (base32 - "0gc10imyabk57ar54m0qzms0x9dnmkymhkzyk8w1aj3y4lby0yx5")))) - (build-system gnu-build-system) + "1mlw1qgj8nkd9ll6b6h54r1gfdy3zp8a8xqz7qfyfaj85jjgbph7")))) + (build-system meson-build-system) + (arguments + `(#:meson ,meson-next)) (native-inputs `(("glib:bin" ,glib "bin") ("pkg-config" ,pkg-config))) -- cgit 1.4.1 From b40090bc6fabfc6af17fe1cef2519cbe9bfbc5fa Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 15:05:48 +0200 Subject: gnu: mm-common: Update to 1.0.3. * gnu/packages/gnome.scm (mm-common): Update to 1.0.3. [arguments]: Use meson-0.55. --- gnu/packages/gnome.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 4934ae0cc3..7e0ee6d314 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -1108,7 +1108,7 @@ freedesktop.org desktop notification specification.") (define-public mm-common (package (name "mm-common") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/mm-common/" @@ -1116,10 +1116,11 @@ freedesktop.org desktop notification specification.") "mm-common-" version ".tar.xz")) (sha256 (base32 - "07b4s5ckcz9q5gwx8vchim19mhfgl8wysqwi30pndks3m4zrzad2")))) + "1x8yvjy0yg17qyhmqws8xh2k8dvzrhpwqz7j1cfwzalrb1i9c5g8")))) (build-system meson-build-system) (arguments - `(#:phases + `(#:meson ,meson-0.55 + #:phases (modify-phases %standard-phases (add-after 'unpack 'patch (lambda* (#:key inputs #:allow-other-keys) -- cgit 1.4.1 From 36d2e48c303d2ba7dc80722939353ba754378957 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 15:11:57 +0200 Subject: gnu: lmdb: Update to 0.9.29. * gnu/packages/databases.scm (lmdb): Update to 0.9.29. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index d18fb89188..cead8c0e5a 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2383,7 +2383,7 @@ database.") (define-public lmdb (package (name "lmdb") - (version "0.9.28") + (version "0.9.29") (source (origin (method git-fetch) @@ -2392,7 +2392,7 @@ database.") (commit (string-append "LMDB_" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "012a8bs49cswsnzw7k4piis5b6dn4by85w7a7mai9i04xcjyy9as")))) + (base32 "0airps4cd0d91nbgy7hgvifa801snxwxzwxyr6pdv61plsi7h8l3")))) (build-system gnu-build-system) (arguments `(#:test-target "test" -- cgit 1.4.1 From ec81488b93ca9a9af6487e422eeeaf998e5bc505 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 23 May 2021 16:50:32 +0200 Subject: gnu: md4c: Update to 0.4.8. * gnu/packages/markup.scm (md4c): Update to 0.4.8. --- gnu/packages/markup.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/markup.scm b/gnu/packages/markup.scm index 695eed67b1..368976bfde 100644 --- a/gnu/packages/markup.scm +++ b/gnu/packages/markup.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015 David Thompson ;;; Copyright © 2016, 2019 Efraim Flashner ;;; Copyright © 2017 Nikita -;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice +;;; Copyright © 2017–2021 Tobias Geerinckx-Rice ;;; Copyright © 2020 Marius Bakke ;;; Copyright © 2020 EuAndreh ;;; Copyright © 2021 Noisytoot @@ -284,7 +284,7 @@ and smu is that smu doesn't support reference style links.") (define-public md4c (package (name "md4c") - (version "0.4.7") + (version "0.4.8") (source (origin (method git-fetch) @@ -293,7 +293,7 @@ and smu is that smu doesn't support reference style links.") (commit (string-append "release-" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0m3202zzjvw4k7jw66z1qi3cbisxzvplq5alkygpifvhzm81gwwx")))) + (base32 "12pdh4rfjc3b0cblj5nz3jksr2376lx8ay0vw5dwa1s97q09pczq")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) (home-page "https://github.com/mity/md4c/") -- cgit 1.4.1 From 169cbd808aa712a355173609fe309ef1b83140fa Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 20 May 2021 20:45:00 +0200 Subject: gnu: Respect the root file-system's CHECK? field. * gnu/build/linux-boot.scm (mount-root-file-system): Take a new #:CHECK? keyword argument. Add it to the docstring. Conditionally call CHECK-FILE-SYSTEM. (boot-system): Adjust its only caller to pass the 's CHECK? option through, if available. --- gnu/build/linux-boot.scm | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/build/linux-boot.scm b/gnu/build/linux-boot.scm index f20eeaac9f..7d1b3ee835 100644 --- a/gnu/build/linux-boot.scm +++ b/gnu/build/linux-boot.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès -;;; Copyright © 2016, 2017, 2019, 2020 Tobias Geerinckx-Rice +;;; Copyright © 2016, 2017, 2019–2021 Tobias Geerinckx-Rice ;;; Copyright © 2017 Mathieu Othacehe ;;; Copyright © 2019 Guillaume Le Vaillant ;;; @@ -411,11 +411,13 @@ the last argument of `mknod'." (filter-map string->number (scandir "/proc"))))) (define* (mount-root-file-system root type - #:key volatile-root? (flags 0) options) + #:key volatile-root? (flags 0) options + check?) "Mount the root file system of type TYPE at device ROOT. If VOLATILE-ROOT? is true, mount ROOT read-only and make it an overlay with a writable tmpfs using the kernel built-in overlayfs. FLAGS and OPTIONS indicates the options to use -to mount ROOT, and behave the same as for the `mount' procedure." +to mount ROOT, and behave the same as for the `mount' procedure. +If CHECK? is true, first run ROOT's fsck tool (if any) non-interactively." (if volatile-root? (begin @@ -436,7 +438,8 @@ to mount ROOT, and behave the same as for the `mount' procedure." (mount "none" "/root" "overlay" 0 "lowerdir=/real-root,upperdir=/rw-root/upper,workdir=/rw-root/work")) (begin - (check-file-system root type) + (when check? + (check-file-system root type)) (mount root "/root" type flags options))) ;; Make sure /root/etc/mtab is a symlink to /proc/self/mounts. @@ -600,7 +603,10 @@ upon error." root-fs-type #:volatile-root? volatile-root? #:flags root-fs-flags - #:options root-options) + #:options root-options + #:check? (if root-fs + (file-system-check? root-fs) + #t)) (mount "none" "/root" "tmpfs")) ;; Mount the specified file systems. -- cgit 1.4.1 From 5b76cdae9dfae44318a56d6b442cc91abd719882 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 24 May 2021 00:23:19 +0200 Subject: gnu: qutebrowser: Update to 2.2.2. * gnu/packages/web-browsers.scm (qutebrowser): Update to 2.2.2. --- gnu/packages/web-browsers.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index f677d58fd6..b6e0e23357 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -487,7 +487,7 @@ interface.") (define-public qutebrowser (package (name "qutebrowser") - (version "2.2.1") + (version "2.2.2") (source (origin (method url-fetch) @@ -495,7 +495,7 @@ interface.") "qutebrowser/releases/download/v" version "/" "qutebrowser-" version ".tar.gz")) (sha256 - (base32 "0vr6xpjy93w4i0x408vvs9xl497sjah51lxdk4awnx2gfg3acz14")))) + (base32 "11vjp20gzmdjj09b7wxzn7ar6viih0bk76y618yqsyqqkffylmbq")))) (build-system python-build-system) (native-inputs `(("python-attrs" ,python-attrs))) ; for tests -- cgit 1.4.1 From 2bd09dd47f2b97803cf36425f6efb4262bcdd218 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 24 May 2021 01:03:16 +0200 Subject: gnu: surf: Update to 2.1. * gnu/packages/suckless.scm (surf): Update to 2.1. [inputs]: Add gcr. --- gnu/packages/suckless.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/suckless.scm b/gnu/packages/suckless.scm index 7e297eb9ae..f4bf01c5df 100644 --- a/gnu/packages/suckless.scm +++ b/gnu/packages/suckless.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2015 Leo Famulari ;;; Copyright © 2016 Eric Bavier ;;; Copyright © 2017 Alex Griffin -;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice +;;; Copyright © 2018–2021 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -270,15 +270,14 @@ drawing.") (define-public surf (package (name "surf") - (version "2.0") + (version "2.1") (source (origin (method url-fetch) (uri (string-append "https://dl.suckless.org/surf/surf-" version ".tar.gz")) (sha256 - (base32 - "07cmajyafljigy10d21kkyvv5jf3hxkx06pz3rwwk3y3c9x4rvps")))) + (base32 "0mrj0kp01bwrgrn4v298g81h6zyq64ijsg790di68nm21f985rbj")))) (build-system glib-or-gtk-build-system) (arguments `(#:tests? #f ; no tests @@ -297,6 +296,7 @@ drawing.") #t))))) (inputs `(("dmenu" ,dmenu) + ("gcr" ,gcr) ("glib-networking" ,glib-networking) ("gsettings-desktop-schemas" ,gsettings-desktop-schemas) ("webkitgtk" ,webkitgtk) -- cgit 1.4.1 From b95fbb510db87576d9a54e4264618b6f6f259b05 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 24 May 2021 02:02:14 +0200 Subject: gnu: whois: Update to 5.5.9. * gnu/packages/networking.scm (whois): Update to 5.5.9. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 6292241007..7f399640b2 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1380,7 +1380,7 @@ and up to 1 Mbit/s downstream.") (define-public whois (package (name "whois") - (version "5.5.8") + (version "5.5.9") (source (origin (method git-fetch) @@ -1389,7 +1389,7 @@ and up to 1 Mbit/s downstream.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "12lhl2q1pa1qkbv0l1cpy8hn4wh5i99bqc68rlm4f7jyqlj2l82r")))) + (base32 "0l9dhyciylh14lqw8j5mrk0y2hl95cnj8pyvvabbgwxpsdn0yvbb")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no test suite -- cgit 1.4.1 From 88c8a910ea916d9dfad412f478f57227488446f9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 24 May 2021 02:02:24 +0200 Subject: gnu: frrouting: Update to 7.5.17.5.1. * gnu/packages/networking.scm (frrouting): Update to 7.5.17.5.1. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 7f399640b2..8bcaa98fbb 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -3569,7 +3569,7 @@ A very simple IM client working over the DHT. (define-public frrouting (package (name "frrouting") - (version "7.5") + (version "7.5.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/FRRouting/frr/releases/" @@ -3577,7 +3577,7 @@ A very simple IM client working over the DHT. ".tar.xz")) (sha256 (base32 - "1a27wvxmc51sr0kchy0hjfpv19imlgrr3s9k48lik9k01g71yrdr")))) + "1r7gh5h27ii7d1d0z0x48wx7hs8vvympv3gqvy3cwzg05q5vk9xs")))) (build-system gnu-build-system) (inputs `(("c-ares" ,c-ares) -- cgit 1.4.1 From 22d4c2e452a61f7d6d01e130619bb4d6f71756c7 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 24 May 2021 02:07:43 +0200 Subject: gnu: hangups: Update to 0.4.14. * gnu/packages/messaging.scm (hangups): Update to 0.4.14. --- gnu/packages/messaging.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 59c154b9f7..413e41c4c1 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -2404,13 +2404,13 @@ QMatrixClient project.") (define-public hangups (package (name "hangups") - (version "0.4.13") + (version "0.4.14") (source (origin (method url-fetch) (uri (pypi-uri "hangups" version)) (sha256 - (base32 "015g635vnrxk5lf9n80rdcmh6chv8kmla1k2j7m1iijijs519ngn")))) + (base32 "15qbbafcrdkx73xz9y30qa3d8nj6mgrp2m41749i5nn1qywmikk8")))) (build-system python-build-system) (arguments `(#:phases -- cgit 1.4.1 From 162fa6bd595898e29791d142fbd77170fbb1de0e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 24 May 2021 02:07:57 +0200 Subject: gnu: libsignal-protocol-c: Update to 2.3.3. * gnu/packages/messaging.scm (libsignal-protocol-c): Update to 2.3.3. --- gnu/packages/messaging.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 413e41c4c1..b326b68952 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -478,7 +478,7 @@ your private keys, no previous conversation is compromised.") (define-public libsignal-protocol-c (package (name "libsignal-protocol-c") - (version "2.3.2") + (version "2.3.3") (source (origin (method git-fetch) (uri (git-reference @@ -487,7 +487,7 @@ your private keys, no previous conversation is compromised.") (file-name (git-file-name name version)) (sha256 (base32 - "1qj2w4csy6j9jg1jy66n1qwysx7hgjywk4n35hlqcnh1kpa14k3p")))) + "0z5p03vk15i6h870azfjgyfgxhv31q2vq6rfhnybrnkxq2wqzwhk")))) (arguments `(;; Required for proper linking and for tests to run. #:configure-flags '("-DBUILD_SHARED_LIBS=on" "-DBUILD_TESTING=1"))) -- cgit 1.4.1 From cf105d9021688ad47acf5b729d6006569c7a9874 Mon Sep 17 00:00:00 2001 From: Leo Prikler Date: Mon, 24 May 2021 01:37:24 +0200 Subject: gnu: font-sarasa-gothic: Update to 0.31.2. * gnu/packages/fonts.scm (font-sarasa-gothic): Update to 0.31.2. --- gnu/packages/fonts.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index 32c4187337..c2280565ab 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -1387,7 +1387,7 @@ programming. Iosevka is completely generated from its source code.") (define-public font-sarasa-gothic (package (name "font-sarasa-gothic") - (version "0.12.7") + (version "0.31.2") (source (origin (method url-fetch) @@ -1395,7 +1395,7 @@ programming. Iosevka is completely generated from its source code.") "/releases/download/v" version "/sarasa-gothic-ttc-" version ".7z")) (sha256 - (base32 "09v65k00g8m953s6riz9xjzb2jgr6v5pdhcllalzzl7c1cn2xl3k")))) + (base32 "0p67qyhm266s6q17islqvwch807fy5slgp2symrl0z665vp6hycj")))) (build-system font-build-system) (arguments `(#:phases (modify-phases %standard-phases -- cgit 1.4.1 From ac95609208c0afe55d68bf42993ccb9b58ad44ce Mon Sep 17 00:00:00 2001 From: Solene Rapenne Date: Sun, 23 May 2021 13:14:44 +0200 Subject: gnu: services: Add missing wireguard related exports. * gnu/services/vpn.scm: Export 'wireguard-peer-public-key' and 'wireguard-peer-keep-alive'. Signed-off-by: Guillaume Le Vaillant --- gnu/services/vpn.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/services/vpn.scm b/gnu/services/vpn.scm index 6fbe20a849..2bcbf76727 100644 --- a/gnu/services/vpn.scm +++ b/gnu/services/vpn.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2017 Clément Lassieur ;;; Copyright © 2017 Mathieu Othacehe ;;; Copyright © 2021 Guillaume Le Vaillant +;;; Copyright © 2021 Solene Rapenne ;;; ;;; This file is part of GNU Guix. ;;; @@ -48,6 +49,8 @@ wireguard-peer-name wireguard-peer-endpoint wireguard-peer-allowed-ips + wireguard-peer-public-key + wireguard-peer-keep-alive wireguard-configuration wireguard-configuration? @@ -526,7 +529,6 @@ is truncated and rewritten every minute.") (openvpn-remote-configuration ,openvpn-remote-configuration-fields)) 'openvpn-client-configuration)) - ;;; ;;; Wireguard. ;;; -- cgit 1.4.1 From 029a3fe46b6549c17085f661bb7b934d7ca0fa3e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 24 May 2021 11:10:26 +0300 Subject: gnu: python-nltk-3.4: Add missing input. * gnu/packages/python-xyz.scm (python-nltk-3.4)[propagated-inputs]: Add python-six. --- gnu/packages/python-xyz.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5a3c6b670e..e011d37e91 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15484,7 +15484,8 @@ reasoning, wrappers for natural language processing libraries.") (method url-fetch) (uri (pypi-uri "nltk" version ".zip")) (sha256 - (base32 "153x2clrnigs74jdgnn3qmljdjj4gprmvpdvh49i18ls4m8mbm5y")))))) + (base32 "153x2clrnigs74jdgnn3qmljdjj4gprmvpdvh49i18ls4m8mbm5y")))) + (propagated-inputs `(("python-six" ,python-six))))) (define-public python2-nltk (package-with-python2 python-nltk)) -- cgit 1.4.1 From 67ac4348d4f4631b65201f66e0ba56f54143ad1b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 24 May 2021 11:11:34 +0300 Subject: gnu: python-nltk: Add missing inputs. * gnu/packages/python-xyz.scm (python-nltk)[propagated-inputs]: Add python-click, python-joblib, python-regex, python-tqdm. --- gnu/packages/python-xyz.scm | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e011d37e91..954536b283 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15463,6 +15463,11 @@ extracting firmware images") '(;; The tests require some extra resources to be downloaded. ;; TODO Try packaging these resources. #:tests? #f)) + (propagated-inputs + `(("python-click" ,python-click) + ("python-joblib" ,python-joblib) + ("python-regex" ,python-regex) + ("python-tqdm" ,python-tqdm))) (native-inputs `(("unzip" ,unzip))) (home-page "http://nltk.org/") -- cgit 1.4.1 From 4ea6161046e664470b036f4692ea115e33ef6003 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 24 May 2021 16:13:35 +0300 Subject: gnu: python-matplotlib: Don't hardcode python version. * gnu/packages/python-xyz.scm (python-matplotlib)[arguments]: In custom 'install-jquery-ui phase programmatically get the version of python. --- gnu/packages/python-xyz.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 954536b283..25f986e9b6 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5563,8 +5563,11 @@ convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc. #t)) (add-before 'install 'install-jquery-ui (lambda* (#:key outputs inputs #:allow-other-keys) - (let ((dir (string-append (assoc-ref outputs "out") - "/lib/python3.7/site-packages/matplotlib/backends/web_backend/"))) + (let* ((python-version (python-version + (assoc-ref inputs "python"))) + (dir (string-append (assoc-ref outputs "out") + "/lib/python" python-version "/site-packages" + "/matplotlib/backends/web_backend/"))) (mkdir-p dir) (invoke "unzip" (assoc-ref inputs "jquery-ui") -- cgit 1.4.1 From 0befeed292885601e36769533521a01fe84b6bfe Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 24 May 2021 12:01:20 -0400 Subject: gnu: linux-libre: Update to 5.12.6. * gnu/packages/linux.scm (linux-libre-5.12-version): Update to 5.12.6. (linux-libre-5.12-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 83ae36f0c8..26e9d1e268 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -356,7 +356,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernels. That is, the most recently released major ;; versions that are still supported upstream. -(define-public linux-libre-5.12-version "5.12.5") +(define-public linux-libre-5.12-version "5.12.6") (define deblob-scripts-5.12 (linux-libre-deblob-scripts linux-libre-5.12-version @@ -364,7 +364,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1qp25fd4wgjyk7dzdq9yirm1z5w68sd1p3wv8lch8259i51gwjnf"))) (define-public linux-libre-5.12-pristine-source (let ((version linux-libre-5.12-version) - (hash (base32 "1x39sdswww4j8zr54wpjzy9dia52kihs11xwljxcnz8pck0vwja0"))) + (hash (base32 "1cdxda5mgdi5dky6hvrq2727rrlw9lnzf30kf3lbiikjybvlqw2b"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.12))) -- cgit 1.4.1 From 2e3c8a5371fc134e0aa366c2ff6ff365f032eab8 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 24 May 2021 12:01:51 -0400 Subject: gnu: linux-libre 5.10: Update to 5.10.39. * gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.39. (linux-libre-5.10-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 26e9d1e268..fc0c0ce1ce 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -372,7 +372,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; -(define-public linux-libre-5.10-version "5.10.38") +(define-public linux-libre-5.10-version "5.10.39") (define deblob-scripts-5.10 (linux-libre-deblob-scripts linux-libre-5.10-version @@ -380,7 +380,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0hh27ccqimagr3aij7ygwikxw66y63sqwd0xlf49bhpjd090r9a7"))) (define-public linux-libre-5.10-pristine-source (let ((version linux-libre-5.10-version) - (hash (base32 "0bzipgnfvd5w70rv1x6g81iwknn2qskw92p2bpyiks7r52qmmwij"))) + (hash (base32 "057nnfkbm69ji80rx9lqgmvqsv74x9lcaq3kfs0k91cpr8asaf2p"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.10))) -- cgit 1.4.1 From 443d3c6a00df0c5417360457cdab82982a7cffa9 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 24 May 2021 12:02:16 -0400 Subject: gnu: linux-libre 5.4: Update to 5.4.121. * gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.121. (linux-libre-5.4-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index fc0c0ce1ce..a0bca87d93 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -385,7 +385,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.10))) -(define-public linux-libre-5.4-version "5.4.120") +(define-public linux-libre-5.4-version "5.4.121") (define deblob-scripts-5.4 (linux-libre-deblob-scripts linux-libre-5.4-version @@ -393,7 +393,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1xghbbnaisjd0k1klbyn1p7r6r4x5a1bpmkm56a3gh2zvw4s7mj8"))) (define-public linux-libre-5.4-pristine-source (let ((version linux-libre-5.4-version) - (hash (base32 "0q08q6q2l9k04p8a0vvbnhwfp4yiags8s6wc9dnac0fhd4y3gl1q"))) + (hash (base32 "0prparsdyi8n3cfq3vbhn5var2xcw5dglscxqny19qcplgy2g4wx"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.4))) -- cgit 1.4.1 From 2fca4acdf6942ce9fbaf3580dda4e5fa7cabd2f2 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 24 May 2021 12:02:31 -0400 Subject: gnu: linux-libre 4.19: Update to 4.19.191. * gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.191. (linux-libre-4.19-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a0bca87d93..66e1daf38c 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -398,7 +398,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.4))) -(define-public linux-libre-4.19-version "4.19.190") +(define-public linux-libre-4.19-version "4.19.191") (define deblob-scripts-4.19 (linux-libre-deblob-scripts linux-libre-4.19-version @@ -406,7 +406,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1jiaw0as1ippkrjdpd52657w5mz9qczg3y2hlra7m9k0xawwiqlf"))) (define-public linux-libre-4.19-pristine-source (let ((version linux-libre-4.19-version) - (hash (base32 "0pf8py0id0r8wzr5050bik1sbhl8gsznnr5bvcmrs4jkhpp2m73g"))) + (hash (base32 "1jd97rzv900mnyzps4xmf6k166zrg391vcrbmr5zvcway5qbn9mm"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.19))) -- cgit 1.4.1 From 9a57cac2a09aa592b29eaba8738c32a585efd82c Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 24 May 2021 12:16:56 -0400 Subject: gnu: linux-libre 4.14: Update to 4.14.233. * gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.233. (linux-libre-4.14-pristine-source): Update hash. (deblob-scripts-4.14): Update hash. --- gnu/packages/linux.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 66e1daf38c..f5e2a4b1fc 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -411,15 +411,15 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.19))) -(define-public linux-libre-4.14-version "4.14.232") +(define-public linux-libre-4.14-version "4.14.233") (define deblob-scripts-4.14 (linux-libre-deblob-scripts linux-libre-4.14-version - (base32 "091jk9jkn9jf39bxpc7395bhcb7p96nkg3a8047380ki06lnfxh6") + (base32 "07afckszdm4pq008i6ij0pxpw2rpgi5q931nxh6dxcczpicvwbc9") (base32 "1qij18inijj6c3ma8hv98yjagnzxdxyn134da9fd23ky8q6hbvky"))) (define-public linux-libre-4.14-pristine-source (let ((version linux-libre-4.14-version) - (hash (base32 "0sa3sz7bznlhijd0iwv37nyrrnw34iq6dq1bqr6cj2wpyrhr7h8x"))) + (hash (base32 "0sqikz8cvrjfs46mcqx9gbdfkpdims0m5xxxzwr5vcfph5rdvj26"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.14))) -- cgit 1.4.1 From 19f0fafa77771eaaace3060b6feea62771b9c787 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 24 May 2021 12:17:43 -0400 Subject: gnu: linux-libre 4.9: Update to 4.9.269. * gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.269. (linux-libre-4.9-pristine-source): Update hash. (deblob-scripts-4.9): Update hash. --- gnu/packages/linux.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index f5e2a4b1fc..26485c1451 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -424,15 +424,15 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.14))) -(define-public linux-libre-4.9-version "4.9.268") +(define-public linux-libre-4.9-version "4.9.269") (define deblob-scripts-4.9 (linux-libre-deblob-scripts linux-libre-4.9-version - (base32 "1wvldzlv7q2xdbadas87dh593nxr4a8p5n0f8zpm72lja6w18hmg") + (base32 "1w8cb8w1cpcwswc3rxq6vwjafw6yy0igib34rrm93ag5h6inncfv") (base32 "0fxajshb75siq39lj5h8xvhdj8lcmddkslwlyj65rhlwk6g2r4b2"))) (define-public linux-libre-4.9-pristine-source (let ((version linux-libre-4.9-version) - (hash (base32 "0aknrlf5q0dsqib8c9klmf5c60dy7hg2zksb020qvyrp077gcrjv"))) + (hash (base32 "1pnggwc9i6hka21vvl4yd9pd38hpnym9z56m4mhl970ijl4zywbr"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.9))) -- cgit 1.4.1 From 173156167b0ca920216f2aee4ff0e6c947407265 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 24 May 2021 12:19:17 -0400 Subject: gnu: linux-libre 4.4: Update to 4.4.269. * gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.269. (linux-libre-4.4-pristine-source): Update hash. (deblob-scripts-4.4): Update hash. --- gnu/packages/linux.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 26485c1451..affc3066c0 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -437,15 +437,15 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.9))) -(define-public linux-libre-4.4-version "4.4.268") +(define-public linux-libre-4.4-version "4.4.269") (define deblob-scripts-4.4 (linux-libre-deblob-scripts linux-libre-4.4-version - (base32 "0x2j1i88am54ih2mk7gyl79g25l9zz4r08xhl482l3fvjj2irwbw") + (base32 "1lid4k7g947yi3hcjj0lz0fnssawbph3jsy67vrv57l5imrhv3zs") (base32 "0hhin1jpfkd6nwrb6xqxjzl3hdxy4pn8a15hy2d3d83yw6pflbsf"))) (define-public linux-libre-4.4-pristine-source (let ((version linux-libre-4.4-version) - (hash (base32 "1srk08kaxq5jjlqx804cgjffhcsrdkv3idh8ipagl6v2w4kas5v8"))) + (hash (base32 "0qx5zwi2ijwv9jwhs4cz91z7yxy6nd0g8ryzrlg1ar2xyk8w4yh4"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.4))) -- cgit 1.4.1 From 9b4f9039e8b2ac4087b1d714e7987c2a1d4e8c4c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 23 May 2021 19:06:30 +0200 Subject: gnu: HYPRE: Update source and home page URLs. * gnu/packages/maths.scm (hypre)[source]: Change to new repository home. [home-page]: Follow redirect. --- gnu/packages/maths.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 5062cc0347..ee0a69bbd7 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4613,7 +4613,7 @@ set.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/LLNL/hypre") + (url "https://github.com/hypre-space/hypre") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -4699,7 +4699,8 @@ set.") '("HYPRE_usr_manual" "HYPRE_ref_manual"))) #t)))))) - (home-page "http://www.llnl.gov/casc/hypre/") + (home-page "https://computing.llnl.gov/projects\ +/hypre-scalable-linear-solvers-multigrid-methods") (synopsis "Library of solvers and preconditioners for linear equations") (description "HYPRE is a software library of high performance preconditioners and -- cgit 1.4.1 From 488fc3d2e6e0a3d5fc4fe747587cf831989ece58 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 24 May 2021 19:27:16 +0200 Subject: gnu: python-breathe: Update to 4.30.0. * gnu/packages/sphinx.scm (python-breathe): Update to 4.30.0. [propagated-inputs]: Remove PYTHON-SIX. --- gnu/packages/sphinx.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm index 4aeed10f30..14bc3f5a79 100644 --- a/gnu/packages/sphinx.scm +++ b/gnu/packages/sphinx.scm @@ -606,18 +606,17 @@ and several other projects.") (define-public python-breathe (package (name "python-breathe") - (version "4.22.1") + (version "4.30.0") (source (origin (method url-fetch) (uri (pypi-uri "breathe" version)) (sha256 (base32 - "0snk538xv60z4vfhl3f7v5g658za7257hddkg07cknkn33k6cjvf")))) + "055h95fkdld7s49878fqjx1nri1drj1czc184vrb7i60mf2yqg9n")))) (build-system python-build-system) (propagated-inputs `(("python-docutils" ,python-docutils) - ("python-six" ,python-six) ("python-sphinx" ,python-sphinx))) (home-page "https://github.com/michaeljones/breathe") (synopsis "ReStructuredText and Sphinx bridge to Doxygen") -- cgit 1.4.1 From 3aea1433f110c4c0acb75920b10c92de92996adb Mon Sep 17 00:00:00 2001 From: Björn Höfling Date: Tue, 25 May 2021 01:15:08 +0200 Subject: gnu: python2-shapely: Remove package. * gnu/packages/python-xyz.scm (python2-shapely): Delete variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 25f986e9b6..770beb0336 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -861,9 +861,6 @@ module and then similar looking characters are removed.") and function call return values in a human-readable way.") (license license:asl2.0))) -(define-public python2-shapely - (package-with-python2 python-shapely)) - (define-public python-clyent (package (name "python-clyent") -- cgit 1.4.1 From e47b7a73becbee8b513a65b76337438d4909b449 Mon Sep 17 00:00:00 2001 From: Solene Rapenne Date: Mon, 24 May 2021 10:36:00 +0200 Subject: gnu: i2pd: update to 2.38.0. * gnu/packages/i2p.scm (i2pd): Update to 2.38.0. Signed-off-by: Efraim Flashner --- gnu/packages/i2p.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/i2p.scm b/gnu/packages/i2p.scm index 5698e6362c..7b9b1e13ee 100644 --- a/gnu/packages/i2p.scm +++ b/gnu/packages/i2p.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2019 Jakob L. Kreuze ;;; Copyright © 2020 Tobias Geerinckx-Rice +;;; Copyright © 2021 Solene Rapenne ;;; ;;; This file is part of GNU Guix. ;;; @@ -30,7 +31,7 @@ (define-public i2pd (package (name "i2pd") - (version "2.36.0") + (version "2.38.0") (source (origin (method git-fetch) @@ -39,7 +40,7 @@ (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0gx7y0vrg9lsl7m1r6c8xyyqmaqn900kms4g0941g0gd5zdb0mvz")))) + (base32 "1a35grcfw5a9dsj0rnm2i86fjf4px96xbnjj3hkril7hv5jvl37k")))) (build-system cmake-build-system) (inputs `(("boost" ,boost) ("miniupnpc" ,miniupnpc) -- cgit 1.4.1 From e52c64cb04f1cf52611b2f8fd2660675a6829db4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 25 May 2021 09:00:33 +0300 Subject: gnu: i2pd: Reflow package definition. * gnu/packages/i2p.scm (i2pd): Reflow package definition. --- gnu/packages/i2p.scm | 66 +++++++++++++++++++++++++++------------------------- 1 file changed, 34 insertions(+), 32 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/i2p.scm b/gnu/packages/i2p.scm index 7b9b1e13ee..4da58087e7 100644 --- a/gnu/packages/i2p.scm +++ b/gnu/packages/i2p.scm @@ -42,38 +42,40 @@ (sha256 (base32 "1a35grcfw5a9dsj0rnm2i86fjf4px96xbnjj3hkril7hv5jvl37k")))) (build-system cmake-build-system) - (inputs `(("boost" ,boost) - ("miniupnpc" ,miniupnpc) - ("openssl" ,openssl) - ("zlib" ,zlib))) - (arguments '(#:configure-flags - (let ((source (assoc-ref %build-inputs "source"))) - (list (string-append "-S" source "/build") - "-DWITH_PCH=OFF" - "-DWITH_STATIC=OFF" - "-DWITH_UPNP=ON" - "-DWITH_LIBRARY=ON" - "-DBUILD_SHARED_LIBS=ON" - "-DWITH_BINARY=ON")) - #:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key - (make-flags '()) - (parallel-tests? #t) - #:allow-other-keys) - (let ((source (assoc-ref %build-inputs "source"))) - (copy-recursively (string-append source "/tests") - "./tests") - (with-directory-excursion "tests" - (substitute* "Makefile" - (("../libi2pd/") (string-append source "/libi2pd/"))) - (apply invoke "make" "all" - `(,@(if parallel-tests? - `("-j" ,(number->string - (parallel-job-count))) - '()) - ,@make-flags))))))))) + (inputs + `(("boost" ,boost) + ("miniupnpc" ,miniupnpc) + ("openssl" ,openssl) + ("zlib" ,zlib))) + (arguments + '(#:configure-flags + (let ((source (assoc-ref %build-inputs "source"))) + (list (string-append "-S" source "/build") + "-DWITH_PCH=OFF" + "-DWITH_STATIC=OFF" + "-DWITH_UPNP=ON" + "-DWITH_LIBRARY=ON" + "-DBUILD_SHARED_LIBS=ON" + "-DWITH_BINARY=ON")) + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key + (make-flags '()) + (parallel-tests? #t) + #:allow-other-keys) + (let ((source (assoc-ref %build-inputs "source"))) + (copy-recursively (string-append source "/tests") + "./tests") + (with-directory-excursion "tests" + (substitute* "Makefile" + (("../libi2pd/") (string-append source "/libi2pd/"))) + (apply invoke "make" "all" + `(,@(if parallel-tests? + `("-j" ,(number->string + (parallel-job-count))) + '()) + ,@make-flags))))))))) (home-page "https://i2pd.website/") (synopsis "Router for an end-to-end encrypted and anonymous internet") (description "i2pd is a client for the anonymous I2P network, upon which -- cgit 1.4.1 From a0b31909f482c7a3d1ee8f7f1a3595a33db38a92 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 25 May 2021 09:06:51 +0300 Subject: gnu: i2pd: Allow skipping tests. * gnu/packages/i2p.scm (i2pd)[arguments]: Adjust custom 'check phase to honor --without-tests flag. --- gnu/packages/i2p.scm | 25 ++++++++++++++----------- 1 file changed, 14 insertions(+), 11 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/i2p.scm b/gnu/packages/i2p.scm index 4da58087e7..1a9958c8d0 100644 --- a/gnu/packages/i2p.scm +++ b/gnu/packages/i2p.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2019 Jakob L. Kreuze ;;; Copyright © 2020 Tobias Geerinckx-Rice ;;; Copyright © 2021 Solene Rapenne +;;; Copyright © 2021 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -61,21 +62,23 @@ (modify-phases %standard-phases (replace 'check (lambda* (#:key + tests? (make-flags '()) (parallel-tests? #t) #:allow-other-keys) (let ((source (assoc-ref %build-inputs "source"))) - (copy-recursively (string-append source "/tests") - "./tests") - (with-directory-excursion "tests" - (substitute* "Makefile" - (("../libi2pd/") (string-append source "/libi2pd/"))) - (apply invoke "make" "all" - `(,@(if parallel-tests? - `("-j" ,(number->string - (parallel-job-count))) - '()) - ,@make-flags))))))))) + (when tests? + (copy-recursively (string-append source "/tests") + "./tests") + (with-directory-excursion "tests" + (substitute* "Makefile" + (("../libi2pd/") (string-append source "/libi2pd/"))) + (apply invoke "make" "all" + `(,@(if parallel-tests? + `("-j" ,(number->string + (parallel-job-count))) + '()) + ,@make-flags)))))))))) (home-page "https://i2pd.website/") (synopsis "Router for an end-to-end encrypted and anonymous internet") (description "i2pd is a client for the anonymous I2P network, upon which -- cgit 1.4.1 From 03eb0b1be2cfedd0d9a66fef0edc53a17f7653a5 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 25 May 2021 09:17:37 +0300 Subject: gnu: infamous-plugins: Fix build. Reported by Thorsten Wilms . Fixes * gnu/packages/audio.scm (infamous-plugins)[arguments]: Add phase to restore compatibility with packaged lv2. --- gnu/packages/audio.scm | 6 ++++++ 1 file changed, 6 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 2afb37175d..f0858d25d7 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1041,6 +1041,12 @@ generators of mostly elementary and occasionally exotic nature.") (lambda _ (substitute* (find-files "." "CMakeLists.txt") (("-msse2 -mfpmath=sse") "")) + #t)) + (add-after 'unpack 'fix-build-with-newer-lv2 + (lambda _ + ;; https://github.com/ssj71/infamousPlugins/commit/4c7275b1fa8ea3296446421cbd29ec2df66588c0 + (substitute* (find-files "src" ".*\\.cxx") + (("_LV2UI_Descriptor") "LV2UI_Descriptor")) #t))))) (inputs `(("cairo" ,cairo) -- cgit 1.4.1 From fa4dae68c4560fafba0046433da425b055d5e1d0 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 25 May 2021 09:20:20 +0300 Subject: gnu: infamous-plugins: Update to 0.3.0. * gnu/packages/audio.scm (infamous-plugins): Update to 0.3.0. --- gnu/packages/audio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index f0858d25d7..5e30ed296d 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1022,7 +1022,7 @@ generators of mostly elementary and occasionally exotic nature.") (define-public infamous-plugins (package (name "infamous-plugins") - (version "0.2.04") + (version "0.3.0") (source (origin (method git-fetch) (uri (git-reference @@ -1031,7 +1031,7 @@ generators of mostly elementary and occasionally exotic nature.") (file-name (git-file-name name version)) (sha256 (base32 - "0hmqk80w4qxq09iag7b7srf2g0wigkyhzq0ywxvhz2iz0hq9k0dh")))) + "1r72agk5nxf5k0mghcc2j90z43j5d9i7rqjmf49jfyqnd443isip")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; there are no tests -- cgit 1.4.1 From a5c2e0dc4eee1a4319d2dfc1562e38fff76123a5 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Sat, 22 May 2021 14:30:15 +0200 Subject: ci: Add derivation inputs. * gnu/ci.scm (derivation->job): Add the derivation inputs to the job association list. --- gnu/ci.scm | 3 +++ 1 file changed, 3 insertions(+) (limited to 'gnu') diff --git a/gnu/ci.scm b/gnu/ci.scm index 8d3590bcdc..c5de25e70e 100644 --- a/gnu/ci.scm +++ b/gnu/ci.scm @@ -92,6 +92,9 @@ MAX-SILENT-TIME and TIMEOUT are build options passed to the daemon when building the derivation." `((#:job-name . ,name) (#:derivation . ,(derivation-file-name drv)) + (#:inputs . ,(map (compose derivation-file-name + derivation-input-derivation) + (derivation-inputs drv))) (#:outputs . ,(filter-map (lambda (res) (match res -- cgit 1.4.1 From 0e007842c9ab3021160596a0de14a2ef1b94acb2 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Sun, 23 May 2021 21:09:14 +0100 Subject: gnu: Add cl-arnesi. * gnu/packages/lisp-xyz.scm (sbcl-arnesi, ecl-arnesi, cl-arnesi): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 52 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 4a1e9064d5..3f4b0ff136 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -16847,3 +16847,55 @@ building block for higher level libraries.") (define-public ecl-json-streams (sbcl-package->ecl-package sbcl-json-streams)) + +(define-public sbcl-arnesi + (let ((commit "1e7dc4cb2cad8599113c7492c78f4925e839522e") + (revision "1")) + (package + (name "sbcl-arnesi") + (version (git-version "2.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/AccelerationNet/arnesi") + (commit commit))) + (file-name (git-file-name "arnesi" version)) + (sha256 + (base32 "0jgj2xgd1gq6rf8ia43lkmbrbxnp8rgs053br9azfa25ygk3ikbh")))) + (build-system asdf-build-system/sbcl) + (arguments + ;; FIXME: (Sharlatan-20210523T190315+0100): Tests failed on + ;; special-lisp-var-rebount-in/cc + ;; + ;; ; processing (TEST SPECIAL-LISP-VAR-REBOUND-IN/CC ...) + ;; ; wrote .../sbcl/arnesi/t/call-cc-tmp5GEXGEG5.fasl + ;; ; compilation finished in 0:00:00.028 + ;; Unhandled SIMPLE-ERROR in thread + ;; #: + ;; Sorry, No walker for the special operater DECLARE defined. + ;; + ;; Backtrace for: # + ;; 0: (SB-DEBUG::DEBUGGER-DISABLED-HOOK # # :QUIT T) + ;; + `(#:tests? #f)) + (native-inputs + `(("fiveam" ,sbcl-fiveam))) + (inputs + `(("cl-ppcre" ,sbcl-cl-ppcre) + ("collectors" ,sbcl-collectors) + ("swank" ,sbcl-slime-swank))) + (home-page "https://github.com/AccelerationNet/arnesi") + (synopsis "Common Lisp utility suite") + (description + "ARNESI is Common Lisp utilities library similar to ALEXANDRIA, ANAPHORA +or GOLDEN-UTILS.") + (license license:bsd-3)))) + +(define-public ecl-arnesi + (sbcl-package->ecl-package sbcl-arnesi)) + +(define-public cl-arnesi + (sbcl-package->cl-source-package sbcl-arnesi)) -- cgit 1.4.1 From 16342832c522796a19d209b0159fcb3fb0d9bc71 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Sun, 23 May 2021 21:12:03 +0100 Subject: gnu: Add cl-gettext. * gnu/packages/lisp-xyz.scm (sbcl-gettext, ecl-gettext, cl-gettext): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 3f4b0ff136..5ccf3e37e9 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -16899,3 +16899,38 @@ or GOLDEN-UTILS.") (define-public cl-arnesi (sbcl-package->cl-source-package sbcl-arnesi)) + +(define-public sbcl-gettext + (let ((commit "a432020cbad99fc22cbe6bb9aa8a83a35000d7aa") + (revision "1")) + (package + (name "sbcl-gettext") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rotatef/gettext") + (commit commit))) + (file-name (git-file-name "gettext" version)) + (sha256 + (base32 "1pzhamgni6k5hi6bbvlb3dm659pcllrrr3vhhn3rpjn238zxg5ar")))) + (build-system asdf-build-system/sbcl) + (native-inputs + `(("stefil" ,sbcl-stefil))) + (inputs + `(("flexi-streams" ,sbcl-flexi-streams) + ("split-sequence" ,sbcl-split-sequence) + ("yacc" ,sbcl-cl-yacc))) + (home-page "https://github.com/rotatef/gettext") + (synopsis "Common Lisp implementation of Gettext") + (description + "This package provides GNU @code{gettext} completely implemented in +Common Lisp without any C library bindings.") + (license license:lgpl3+)))) + +(define-public ecl-gettext + (sbcl-package->ecl-package sbcl-gettext)) + +(define-public cl-gettext + (sbcl-package->cl-source-package sbcl-gettext)) -- cgit 1.4.1 From 77bd1b5be0cfebdd3c6fbc55658c473cf43f2832 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Sun, 23 May 2021 21:14:32 +0100 Subject: gnu: Add cl-parser-combinators. * gnu/packages/lisp-xyz.scm (sbcl-parser-combinators, ecl-parser-combinators, cl-parser-combinators): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 5ccf3e37e9..b2adb9d37b 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -16934,3 +16934,45 @@ Common Lisp without any C library bindings.") (define-public cl-gettext (sbcl-package->cl-source-package sbcl-gettext)) + +(define-public sbcl-parser-combinators + (let ((commit "9c7569a4f6af5e60c0d3a51d9c15c16d1714c845") + (revision "1")) + (package + (name "sbcl-parser-combinators") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Ramarren/cl-parser-combinators") + (commit commit))) + (file-name (git-file-name "parser-combinators" version)) + (sha256 + (base32 "1k49vha5xm2cklayzpqwg73n4v93xwsbs5in6342pkkiimnidhs8")))) + (build-system asdf-build-system/sbcl) + (arguments + ;; FIXME: (Sharlatan-20210523T184237+0100): Tests require `femlisp', which + ;; is quite chunky not packaged system yet, enable them when it's packed. + `(#:tests? #f + #:test-asd-file "parser-combinators-tests.asd")) + ;; (native-inputs + ;; `(("hu.dwim.stefil" ,sbcl-hu.dwim.stefil) + ;; ("infix" ,sbcl-femlisp))) + (inputs + `(("alexandria" ,sbcl-alexandria) + ("cl-containers" ,sbcl-cl-containers) + ("cl-ppcre" ,sbcl-cl-ppcre) + ("iterate" ,sbcl-iterate))) + (home-page "https://github.com/Ramarren/cl-parser-combinators") + (synopsis "Parser combinators in Common Lisp") + (description + "PARSER-COMBINATORS is a library implementing monadic parser +combinators in Common Lisp, similar in concept to Haskell Parsec system.") + (license license:bsd-3)))) + +(define-public ecl-parser-combinators + (sbcl-package->ecl-package sbcl-parser-combinators)) + +(define-public cl-parser-combinators + (sbcl-package->cl-source-package sbcl-parser-combinators)) -- cgit 1.4.1 From 7af6a356bbb3bd690b42f479a5a336b3091acff3 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Sun, 23 May 2021 21:17:56 +0100 Subject: gnu: Add cl-locale. * gnu/packages/lisp-xyz.scm (sbcl-cl-locale, ecl-cl-locale, cl-locale): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 49 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index b2adb9d37b..0bfc14af26 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -16976,3 +16976,52 @@ combinators in Common Lisp, similar in concept to Haskell Parsec system.") (define-public cl-parser-combinators (sbcl-package->cl-source-package sbcl-parser-combinators)) + +(define-public sbcl-cl-locale + (let ((commit "0a36cc0dcf5e0a8c8bf97869cd6199980ca25eec") + (revision "1")) + (package + (name "sbcl-cl-locale") + (version (git-version "0.1.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/fukamachi/cl-locale") + (commit commit))) + (file-name (git-file-name "cl-locale" version)) + (sha256 + (base32 "1rhannhpsw1yg1fpflam483a3w9qb1izgyvmnmiddv3dn4qsmn9p")))) + (build-system asdf-build-system/sbcl) + (arguments + ;; FIXME: (Sharlatan-20210523T190658+0100): All tests passed ok but + ;; successfully failed in the end: + ;; + ;; Summary: + ;; All 1 file passed. + ;; Unhandled ASDF/FIND-COMPONENT:MISSING-DEPENDENCY + ;; in thread #: + ;; Component CL-LOCALE-ASD::CL-LOCALE-TEST not found, required by + ;; # + ;; + `(#:tests? #f)) + (native-inputs + `(("prove" ,sbcl-prove) + ("flexi-streams" ,sbcl-flexi-streams))) + (inputs + `(("anaphora" ,sbcl-anaphora) + ("arnesi" ,sbcl-arnesi) + ("cl-annot" ,sbcl-cl-annot) + ("cl-syntax" ,sbcl-cl-syntax))) + (home-page "https://github.com/fukamachi/cl-locale") + (synopsis "Internalization library for Common Lisp") + (description + "This package provides a Common Lisp translation library similar to +CL-I18N and CL-L10N.") + (license license:llgpl)))) + +(define-public ecl-cl-locale + (sbcl-package->ecl-package sbcl-cl-locale)) + +(define-public cl-locale + (sbcl-package->cl-source-package sbcl-cl-locale)) -- cgit 1.4.1 From a0dcb1aa8f03d2b4702c9dc31d21d4e0e1090122 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Sun, 23 May 2021 21:20:13 +0100 Subject: gnu: Add cl-slice. * gnu/packages/lisp-xyz.scm (sbcl-cl-slice, ecl-cl-slice, cl-slice): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 0bfc14af26..1aa63c0ab4 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -17025,3 +17025,37 @@ CL-I18N and CL-L10N.") (define-public cl-locale (sbcl-package->cl-source-package sbcl-cl-locale)) + +(define-public sbcl-cl-slice + (let ((commit "c531683f287216aebbb0affbe090611fa1b5d697") + (revision "1")) + (package + (name "sbcl-cl-slice") + (version (git-version "0.1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tpapp/cl-slice") + (commit commit))) + (file-name (git-file-name "cl-slice" version)) + (sha256 + (base32 "1ybznf4y5lda6bn163jcvj281qzhm24dfcwhbgxmm5n6f27gdccl")))) + (build-system asdf-build-system/sbcl) + (native-inputs + `(("clunit" ,sbcl-clunit))) + (inputs + `(("alexandria" ,sbcl-alexandria) + ("anaphora" ,sbcl-anaphora) + ("let-plus" ,sbcl-let-plus))) + (home-page "https://github.com/tpapp/cl-slice") + (synopsis "Array slices for Common Lisp") + (description + "This package provides a DSL for array slices in Common Lisp.") + (license license:expat)))) + +(define-public ecl-cl-slice + (sbcl-package->ecl-package sbcl-cl-slice)) + +(define-public cl-slice + (sbcl-package->cl-source-package sbcl-cl-slice)) -- cgit 1.4.1 From 3a89ff123a52059743d48f6c3428fc436b4d397a Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Sun, 23 May 2021 21:26:49 +0100 Subject: gnu: Add cl-djula. * gnu/packages/lisp-xyz.scm: (sbcl-djula, ecl-djula, cl-djula): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 46 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 1aa63c0ab4..eb431cab11 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -17059,3 +17059,49 @@ CL-I18N and CL-L10N.") (define-public cl-slice (sbcl-package->cl-source-package sbcl-cl-slice)) + +(define-public sbcl-djula + (let ((commit "5df7af35a21503d468a878fc6029caa527a7d204") + (revision "1")) + (package + (name "sbcl-djula") + (version (git-version "0.2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mmontone/djula") + (commit commit))) + (file-name (git-file-name "djula" version)) + (sha256 + (base32 "1lk2ypm3sacf60h96a7hv9jwjlxkl4k40yzdalmqdg548vrd1jjm")))) + (build-system asdf-build-system/sbcl) + (native-inputs + `(("fiveam" ,sbcl-fiveam))) + (inputs + `(("access" ,sbcl-access) + ("alexandria" ,sbcl-alexandria) + ("anaphora" ,sbcl-anaphora) + ("babel" ,sbcl-babel) + ("cl-locale" ,sbcl-cl-locale) + ("cl-ppcre" ,sbcl-cl-ppcre) + ("cl-slice" ,sbcl-cl-slice) + ("closer-mop" ,sbcl-closer-mop) + ("gettext" ,sbcl-gettext) + ("iterate" ,sbcl-iterate) + ("local-time" ,sbcl-local-time) + ("parser-combinators" ,sbcl-parser-combinators) + ("split-sequence" ,sbcl-split-sequence) + ("trivial-backtrace" ,sbcl-trivial-backtrace))) + (home-page "https://mmontone.github.io/djula/") + (synopsis "Common Lisp port of the Django templating language") + (description + "This package provides a Common Lisp templating system based on Python +Django with a syntax similar to Python Jinja2.") + (license license:expat)))) + +(define-public ecl-djula + (sbcl-package->ecl-package sbcl-djula)) + +(define-public cl-djula + (sbcl-package->cl-source-package sbcl-djula)) -- cgit 1.4.1 From 6602d89a14d80b13373996a05d3c10b1ad251188 Mon Sep 17 00:00:00 2001 From: Alexandr Vityazev Date: Thu, 20 May 2021 15:01:49 +0000 Subject: gnu: emasc-geiser: Update to 0.16. * gnu/packages/emacs-xyz (emacs-geiser): Update to 0.16. [patches]: Remove. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index cc843bfb78..6783e621bb 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -221,7 +221,7 @@ (define-public emacs-geiser (package (name "emacs-geiser") - (version "0.13") + (version "0.16") (source (origin (method git-fetch) @@ -230,9 +230,7 @@ (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0bwjcfmcyv6z0i5ivqirgcibxdkrlf5vyxcbj7k8dk7flwg1fpd9")) - (patches - (search-patches "emacs-geiser-autoload-activate-implementation.patch")))) + (base32 "18gx7ak2ldpmqbimnq221dn2qg7qwm5n1mj6ajymwkgvqwcrsl2r")))) (build-system emacs-build-system) (arguments '(#:phases -- cgit 1.4.1 From 68b6ea55918e7965b5ec34db749e969d8d22b735 Mon Sep 17 00:00:00 2001 From: Alexandr Vityazev Date: Thu, 20 May 2021 14:58:07 +0000 Subject: gnu: emacs-geiser-guile: Update to 0.17. * gnu/packages/emacs-xyz (emacs-geiser-guile): Update to 0.17. [patches]: Remove. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 6783e621bb..23a52edecb 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -269,7 +269,7 @@ e.g. emacs-geiser-guile for Guile.") (define-public emacs-geiser-guile (package (name "emacs-geiser-guile") - (version "0.13") + (version "0.17") (source (origin (method git-fetch) @@ -278,9 +278,7 @@ e.g. emacs-geiser-guile for Guile.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0w264pjwlxna31260ll6gd0n77jlynhzf3h2dws5wr7jflns5mbc")) - (patches (search-patches - "emacs-geiser-guile-auto-activate.patch")))) + (base32 "0iw23nlgqppf6f00ly50m8lq85n9mv244pw3whxv0hynfjxr2ic0")))) (build-system emacs-build-system) (arguments '(#:include (cons "^src/" %default-include) -- cgit 1.4.1 From 3c52c96ca2828c580986a72944c60ae10b6024c3 Mon Sep 17 00:00:00 2001 From: Alexandr Vityazev Date: Thu, 20 May 2021 14:58:14 +0000 Subject: gnu: Remove unnecessary patches for emacs-geiser. * gnu/packages/patches/emacs-geiser-autoload-activate-implementation.patch: * gnu/packages/patches/emacs-geiser-guile-auto-activate.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Apply file removal. Signed-off-by: Nicolas Goaziou --- gnu/local.mk | 2 -- ...s-geiser-autoload-activate-implementation.patch | 26 ----------------- .../patches/emacs-geiser-guile-auto-activate.patch | 34 ---------------------- 3 files changed, 62 deletions(-) delete mode 100644 gnu/packages/patches/emacs-geiser-autoload-activate-implementation.patch delete mode 100644 gnu/packages/patches/emacs-geiser-guile-auto-activate.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 9dac7ea152..b0df9d582d 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -972,8 +972,6 @@ dist_patch_DATA = \ %D%/packages/patches/emacs-exec-path.patch \ %D%/packages/patches/emacs-exwm-fix-fullscreen-states.patch \ %D%/packages/patches/emacs-fix-scheme-indent-function.patch \ - %D%/packages/patches/emacs-geiser-guile-auto-activate.patch \ - %D%/packages/patches/emacs-geiser-autoload-activate-implementation.patch \ %D%/packages/patches/emacs-ignore-empty-xim-styles.patch \ %D%/packages/patches/emacs-json-reformat-fix-tests.patch \ %D%/packages/patches/emacs-highlight-stages-add-gexp.patch \ diff --git a/gnu/packages/patches/emacs-geiser-autoload-activate-implementation.patch b/gnu/packages/patches/emacs-geiser-autoload-activate-implementation.patch deleted file mode 100644 index 47d513b3a3..0000000000 --- a/gnu/packages/patches/emacs-geiser-autoload-activate-implementation.patch +++ /dev/null @@ -1,26 +0,0 @@ -From 9fd3174cead8bfa17a8413bffa38362853d71a02 Mon Sep 17 00:00:00 2001 -From: jao -Date: Mon, 5 Apr 2021 23:06:56 +0100 -Subject: [PATCH] autoload geiser activate implementation - ---- - elisp/geiser.el | 3 +++ - readme.org | 4 ++-- - 2 files changed, 5 insertions(+), 2 deletions(-) - -diff --git a/elisp/geiser.el b/elisp/geiser.el -index 887b8da..96c1dd6 100644 ---- a/elisp/geiser.el -+++ b/elisp/geiser.el -@@ -104,6 +104,9 @@ - ;;;###autoload - (autoload 'geiser-mode--maybe-activate "geiser-mode") - -+;;;###autoload -+(autoload 'geiser-activate-implementation "geiser-impl") -+ - ;;;###autoload - (mapc (lambda (group) - (custom-add-load group (symbol-name group)) --- -GitLab diff --git a/gnu/packages/patches/emacs-geiser-guile-auto-activate.patch b/gnu/packages/patches/emacs-geiser-guile-auto-activate.patch deleted file mode 100644 index 44837f90df..0000000000 --- a/gnu/packages/patches/emacs-geiser-guile-auto-activate.patch +++ /dev/null @@ -1,34 +0,0 @@ -From 93ef7101fdfcc7eac6f465b4b9788c384a323c14 Mon Sep 17 00:00:00 2001 -From: jao -Date: Mon, 5 Apr 2021 20:17:50 +0100 -Subject: [PATCH] fix: auto-activate guile implementation - ---- - geiser-guile.el | 4 ++++ - 1 file changed, 4 insertions(+) - -diff --git a/geiser-guile.el b/geiser-guile.el -index 340442b..deeb76f 100644 ---- a/geiser-guile.el -+++ b/geiser-guile.el -@@ -25,6 +25,7 @@ - (require 'geiser-syntax) - (require 'geiser-custom) - (require 'geiser-repl) -+(require 'geiser-impl) - (require 'geiser-base) - (require 'geiser-eval) - (require 'geiser-edit) -@@ -474,6 +475,9 @@ it spawn a server thread." - - (geiser-impl--add-to-alist 'regexp "\\.scm$" 'guile t) - -+;;;###autoload -+(geiser-activate-implementation 'guile) -+ - ;;;###autoload - (autoload 'run-guile "geiser-guile" "Start a Geiser Guile REPL." t) - --- -GitLab - -- cgit 1.4.1 From 7c1065030d5632ee5d83086df4014b80c3b6f8c2 Mon Sep 17 00:00:00 2001 From: Solene Rapenne via Guix-patches via Date: Sat, 22 May 2021 22:35:31 +0200 Subject: gnu: lagrange: Update to 1.4.2. * gnu/packages/web-browsers.scm (lagrange): Update to 1.4.2. Signed-off-by: Nicolas Goaziou --- gnu/packages/web-browsers.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index b6e0e23357..a8e77f8c7e 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -722,7 +722,7 @@ key-bindings (Emacs, vi, CUA), and is fully configurable in Common Lisp.") (define-public lagrange (package (name "lagrange") - (version "1.3.4") + (version "1.4.2") (source (origin (method url-fetch) @@ -730,7 +730,7 @@ key-bindings (Emacs, vi, CUA), and is fully configurable in Common Lisp.") (string-append "https://git.skyjake.fi/skyjake/lagrange/releases/" "download/v" version "/lagrange-" version ".tar.gz")) (sha256 - (base32 "108b8a9vdmf846v7p30fs9z0b68w3naifixnia0ra54ssxjvy0h6")))) + (base32 "1gnivksxxw2k0kx7fsyrwrxffl67dph2b9w9hsv9id6x89k6dwh2")))) (build-system cmake-build-system) (arguments `(#:tests? #false)) ;no tests -- cgit 1.4.1 From ae88e30a0f8403e781f8b01262766cdc46b1018a Mon Sep 17 00:00:00 2001 From: David Dashyan Date: Tue, 25 May 2021 00:39:32 +0300 Subject: gnu: Add emacs-geiser-racket. * gnu/packages/emacs-xyz.scm (emacs-geiser-racket): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 44 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 23a52edecb..6ace04a88f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -186,6 +186,7 @@ #:use-module (gnu packages package-management) #:use-module (gnu packages perl) #:use-module (gnu packages pdf) + #:use-module (gnu packages racket) #:use-module (gnu packages ruby) #:use-module (gnu packages rust-apps) #:use-module (gnu packages scheme) @@ -357,6 +358,49 @@ using geiser.") a generic Scheme interaction mode for the GNU Emacs editor.") (license license:expat))) +(define-public emacs-geiser-racket + (package + (name "emacs-geiser-racket") + (version "0.16") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/emacs-geiser/racket.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1aqsvmk1hi7kc3j4h8xlza7c6rwm71v98fv5wpw8kmyj9vsp49wx")))) + (build-system emacs-build-system) + (arguments + '(#:include (cons "^src/" %default-include) + #:phases + (modify-phases %standard-phases + (add-after 'make-autoloads 'patch-autoloads + (lambda* (#:key outputs #:allow-other-keys) + (substitute* (string-append + (elpa-directory (assoc-ref outputs "out")) + "/geiser-racket-autoloads.el") + ;; Activating implementations fails when Geiser is not yet + ;; loaded, so let's defer that until it is. + (("\\(geiser-activate-implementation .*\\)" all) + (string-append + "(eval-after-load 'geiser-impl '" all ")")) + (("\\(geiser-implementation-extension .*\\)" all) + (string-append + "(eval-after-load 'geiser-impl '" all ")"))) + #t))))) + (inputs + `(("racket" ,racket))) + (propagated-inputs + `(("geiser" ,emacs-geiser))) + (home-page "https://nongnu.org/geiser/") + (synopsis "Racket support for Geiser") + (description + "This package adds support for the Racket implementation to Geiser, +a generic Scheme interaction mode for the GNU Emacs editor.") + (license license:bsd-3))) + (define-public emacs-vc-hgcmd (package (name "emacs-vc-hgcmd") -- cgit 1.4.1 From f820315ddd92c4c8516b0ee168993b95de076c11 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 25 May 2021 11:37:26 +0200 Subject: gnu: emacs-xyz.scm: Add missing copyright line. --- gnu/packages/emacs-xyz.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 6ace04a88f..4959949cb3 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -98,6 +98,7 @@ ;;; Copyright © 2021 Simon Tournier ;;; Copyright © 2021 Eugene Klimov ;;; Copyright © 2021 Zheng Junjie <873216071@qq.com> +;;; Copyright © 2021 David Dashyan ;;; ;;; This file is part of GNU Guix. ;;; -- cgit 1.4.1 From b1bbeeafb42381ff30f3ec75cd02fba8d4f519a9 Mon Sep 17 00:00:00 2001 From: Solene Rapenne via Guix-patches via Date: Mon, 24 May 2021 10:34:14 +0200 Subject: gnu: openttd-engine: Update to 1.11.2. * gnu/packages/games.scm (openttd-engine): Update to 1.11.2. [build-system]: Switch to CMake. [arguments]: Enable tests. (openttd)[arguments]<#:configure-flags>: Use CMake flags. <#:phases>: Remove `configure'. Copy assets file before check step to enable tests. Signed-off-by: Nicolas Goaziou --- gnu/packages/games.scm | 51 +++++++++++++++----------------------------------- 1 file changed, 15 insertions(+), 36 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 6f07cd3aa9..c7e6097bd4 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -61,6 +61,7 @@ ;;; Copyright © 2021 Greg Hogan ;;; Copyright © 2021 David Pflug ;;; Copyright © 2021 Felix Gruber +;;; Copyright © 2021 Solene Rapenne ;;; ;;; This file is part of GNU Guix. ;;; @@ -4315,35 +4316,15 @@ world}, @uref{http://evolonline.org, Evol Online} and (define openttd-engine (package (name "openttd-engine") - (version "1.10.3") + (version "1.11.2") (source (origin (method url-fetch) (uri (string-append "https://cdn.openttd.org/openttd-releases/" version "/openttd-" version "-source.tar.xz")) (sha256 (base32 - "0fxmfz1mm95a2x0rnzfff9wb8q57w0cvsdd0z7agdcbyakph25n1")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; no "check" target - #:phases - (modify-phases %standard-phases - ;; The build process fails if the configure script is passed the - ;; option "--enable-fast-install". - (replace 'configure - (lambda* (#:key inputs outputs (configure-flags '()) - #:allow-other-keys) - (let ((out (assoc-ref outputs "out")) - (lzo (assoc-ref inputs "lzo"))) - (apply invoke "./configure" - (string-append "--prefix=" out) - ;; Provide the "lzo" path. - (string-append "--with-liblzo2=" - lzo "/lib/liblzo2.a") - ;; Put the binary in 'bin' instead of 'games'. - "--binary-dir=bin" - configure-flags))))))) - (native-inputs `(("pkg-config" ,pkg-config))) + "0v9f93lsdcv3ia28y8iihx9nj9zp6fpf5hkdrpl4ypw159d97fhg")))) + (build-system cmake-build-system) (inputs `(("allegro" ,allegro) ("fontconfig" ,fontconfig) @@ -4510,19 +4491,17 @@ Transport Tycoon Deluxe.") (name "openttd") (arguments `(#:configure-flags - (list (string-append "--with-midi=" (assoc-ref %build-inputs "timidity++") - "/bin/timidity")) - ,@(substitute-keyword-arguments (package-arguments openttd-engine) - ((#:phases phases) - `(modify-phases ,phases - (add-after 'install 'install-data - (lambda* (#:key inputs outputs #:allow-other-keys) - (for-each - (lambda (input) - (copy-recursively (assoc-ref inputs input) - (assoc-ref outputs "out"))) - (list "opengfx" "openmsx" "opensfx")) - #t))))))) + (let* ((out (assoc-ref %outputs "out"))) + (list (string-append "-DCMAKE_INSTALL_BINDIR=" out "/bin"))) + #:phases + (modify-phases %standard-phases + (add-before 'check 'install-data + (lambda* (#:key inputs outputs #:allow-other-keys) + (for-each + (lambda (input) + (copy-recursively (assoc-ref inputs input) + (assoc-ref outputs "out"))) + (list "opengfx" "openmsx" "opensfx"))))))) (inputs `(("timidity++" ,timidity++) ,@(package-inputs openttd-engine))) -- cgit 1.4.1 From a443181d7b6fcefa0e4cc32a078949fd6c7648c0 Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Tue, 25 May 2021 10:47:36 +0200 Subject: gnu: emacs-vertico: Update to 0.11. * gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 0.11. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 4959949cb3..da2754aa5e 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -28040,7 +28040,7 @@ and preferred services can easily be configured.") (define-public emacs-vertico (package (name "emacs-vertico") - (version "0.10") + (version "0.11") (source (origin (method git-fetch) @@ -28049,7 +28049,7 @@ and preferred services can easily be configured.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0am7d29gni7irbwsv3zc9cpk12f6pyys06zlpj506wj2d21v36la")))) + (base32 "0vx23csk1nsrcazifwjxchqdmp3qbg2mwbvkqxn134g89qi8pqkw")))) (build-system emacs-build-system) (native-inputs `(("texinfo" ,texinfo))) -- cgit 1.4.1 From a68cca64cd92b36d6f5e887d43f591f356e0a237 Mon Sep 17 00:00:00 2001 From: nixo Date: Tue, 25 May 2021 09:02:41 +0200 Subject: gnu: Add kanatest. * gnu/packages/education.scm (kanatest): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/education.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index 0986d2a19e..1f39e2afd2 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -9,6 +9,7 @@ ;;; Copyright © 2020 Guy Fleury Iteriteka ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2020 Prafulla Giri +;;; Copyright © 2021 Nicolò Balzarotti ;;; ;;; This file is part of GNU Guix. ;;; @@ -727,6 +728,43 @@ languages and keyboard layouts, and typing statistics are used to dynamically adjust the level of difficulty.") (license license:gpl2))) +(define-public kanatest + ;; Latest release tarball is 0.4.8, which is really old and does not build + ;; commit on sourceforge are not tagged, we take the latest + (let ((commit "860e790a35f547cc96669f805d371a5ba3d8daff") + (revision "0")) + (package + (name "kanatest") + (version (git-version "0.4.10" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.code.sf.net/p/kanatest/code") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0dz63m9p4ggzw0yb309qmgnl664qb5q268vaa3i9v0i8qsl66d78")))) + (build-system gnu-build-system) + (native-inputs + `(("gettext" ,gettext-minimal) ; for msgfmt + ("pkg-config" ,pkg-config))) + (inputs + `(("libxml2" ,libxml2) + ("gtk+" ,gtk+))) + (home-page "https://kanatest.sourceforge.io/") + (synopsis "Hiragana and Katakana simple flashcard tool") + (description "Kanatest is a Japanese kana (Hiragana and Katakana) simple +flashcard tool. + +During test the Kanatest displays randomly selected kana char (respecting mode +and lesson) and waits for user answer expected as romaji equivalent. This +process continues until all questions will be answered or all questions will +be answered correctly (depends on options). At the end of test a short info +about drilling time and correctness ratio is displayed. The results are +stored and user can review his performance in any time.") + (license license:gpl2+)))) + (define-public anki (package (name "anki") -- cgit 1.4.1 From a154048d980ada9b7dcc35e35cbe75056a0cd756 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 25 May 2021 12:25:40 +0200 Subject: gnu: emacs-shell-command+: Update to 2.2.0. * gnu/packages/emacs-xyz.scm (emacs-shell-command+): Update to 2.2.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index da2754aa5e..886320cc34 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -27351,13 +27351,13 @@ Features: (define-public emacs-shell-command+ (package (name "emacs-shell-command+") - (version "2.1.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "shell-command+-" version ".tar")) (sha256 - (base32 "1jyrnv89989bi03m5h8dj0cllsw3rvyxkiyfrh9v6gpxjwfy8lmq")))) + (base32 "1ms2xk7xfgd3ngwm90hnmlxwpvyb167bislc2wr3ilfrirbbw476")))) (build-system emacs-build-system) (home-page "http://elpa.gnu.org/packages/shell-command+.html") (synopsis "Extended Emacs @code{shell-command}") -- cgit 1.4.1 From bc13e794763991e1883751bfdb1e7a48195cba97 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 25 May 2021 13:50:26 +0200 Subject: gnu: Add perl-const-fast. * gnu/packages/perl.scm (perl-const-fast): New variable. --- gnu/packages/perl.scm | 28 +++++++++++++++++++++++++++- 1 file changed, 27 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index d35508112f..0e18c73138 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -9,7 +9,7 @@ ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner ;;; Copyright © 2016 Nikita ;;; Copyright © 2016 Alex Sassmannshausen -;;; Copyright © 2016, 2018, 2020 Roel Janssen +;;; Copyright © 2016, 2018, 2020, 2021 Roel Janssen ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2016, 2020 Jan (janneke) Nieuwenhuizen ;;; Copyright © 2017 Raoul J.P. Bonnal @@ -1918,6 +1918,32 @@ of the style used by the Git version control system.") and writing of @code{.ini}-style configuration files.") (license (package-license perl)))) +(define-public perl-const-fast + (package + (name "perl-const-fast") + (version "0.014") + (source + (origin + (method url-fetch) + (uri (string-append + "mirror://cpan/authors/id/L/LE/LEONT/" + "Const-Fast-" version ".tar.gz")) + (sha256 + (base32 + "1nwlldgrx86yn7y6a53cqgvzm2ircsvxg1addahlcy6510x9a1gq")))) + (inputs + `(("perl-module-build-tiny" ,perl-module-build-tiny) + ("perl-test-fatal" ,perl-test-fatal))) + ;; Needed for tests. + (native-inputs + `(("perl-sub-exporter-progressive" ,perl-sub-exporter-progressive))) + (build-system perl-build-system) + (home-page "https://metacpan.org/release/Const-Fast") + (synopsis "Facility for creating read-only scalars, arrays, and hashes") + (description "This package provides prodecures to create read-only +scalars, arrays, and hashes.") + (license (package-license perl)))) + (define-public perl-context-preserve (package (name "perl-context-preserve") -- cgit 1.4.1 From 414e41de64e0e8aeb380ff7c9e4b0a0420cf630b Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Tue, 25 May 2021 13:55:42 +0200 Subject: gnu: cuirass: Update to 1.0.0-18.b1abb44. * gnu/packages/ci.scm (cuirass): Update to 1.0.0-18.b1abb44. --- gnu/packages/ci.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm index c850d37b47..28dd9ada2b 100644 --- a/gnu/packages/ci.scm +++ b/gnu/packages/ci.scm @@ -73,8 +73,8 @@ (file-name (string-append name "-" version "-checkout"))))))) (define-public cuirass - (let ((commit "31fd4d4fe107d86f5e202510e177726a1f49e828") - (revision "17")) + (let ((commit "b1abb4438b99fa4f5b0fcc0052015e69209e1ea0") + (revision "18")) (package (name "cuirass") (version (git-version "1.0.0" revision commit)) @@ -87,7 +87,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "08phqr0sfi6hkzrqhqsh9ri9434sd41qg1b5vijbadgsj1ql33rw")))) + "0iadm1qlg8535yzs1sw1v1iszlfdd42nrzfh4s7kbwvf28ksh4a3")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build utils) -- cgit 1.4.1 From 906cdbd4f93b346f4982617ad29e0ab396baac49 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 25 May 2021 13:55:51 +0200 Subject: gnu: Add perl-data-uuid. * gnu/packages/perl.scm (perl-data-uuid): New variable. --- gnu/packages/perl.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 0e18c73138..47d64e2f68 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -2508,6 +2508,27 @@ generating unique ids. These ids are coded with a Base62 system to make them short and handy (e.g. to use it as part of a URL).") (license (package-license perl)))) +(define-public perl-data-uuid + (package + (name "perl-data-uuid") + (version "1.226") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://cpan/authors/id/R/RJ/RJBS/" + "Data-UUID-" version ".tar.gz")) + (sha256 + (base32 + "0lv4k4ibxwkw7zz9hw97s34za9nvjxb4kbmgmx5sj4fll3zmfg89")))) + (build-system perl-build-system) + (home-page "https://metacpan.org/release/Data-UUID") + (synopsis "Universally Unique Identifiers generator") + (description "@code{Data::UUID} provides a framework for generating +Universally Unique Identifiers (UUIDs), also known as Globally Unique +Identifiers (GUIDs). A UUID is 128 bits long, and is guaranteed to be +different from all other UUIDs/GUIDs generated until 3400 CE.") + (license (package-license perl)))) + (define-public perl-data-dump (package (name "perl-data-dump") -- cgit 1.4.1 From fe578ee51a823151caf0b83eaf6a5701067626f8 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 25 May 2021 14:08:34 +0200 Subject: gnu: Add perl-extutils-manifest. * gnu/packages/perl.scm (perl-extutils-manifest): New variable. --- gnu/packages/perl.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 47d64e2f68..dd5d64da1b 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -4226,6 +4226,27 @@ and alternative installers with the `installler` option. But it's written in only about 40% as many lines of code and with zero non-core dependencies.") (license (package-license perl)))) +(define-public perl-extutils-manifest + (package + (name "perl-extutils-manifest") + (version "1.73") + (source (origin + (method url-fetch) + (uri (string-append + "https://cpan.metacpan.org/authors/id/E/ET/ETHER/" + "ExtUtils-Manifest-" version ".tar.gz")) + (sha256 + (base32 + "1y5siyw9sbxq6kdmsjfsx0mrbqb6xr8kmniwli7xc6hbmhyhcp6w")))) + (build-system perl-build-system) + (home-page "https://metacpan.org/release/ExtUtils-Manifest") + (synopsis "Utilities to write and check a MANIFEST file") + (description "This package contains functions to manipulate a MANIFEST +file. The package exports no functions by default. The following are exported +on request: mkmanifest, manifind, manicheck, filecheck, fullcheck, skipcheck, +maniread, maniskip, manicopy, maniadd.") + (license (package-license perl)))) + (define-public perl-extutils-installpaths (package (name "perl-extutils-installpaths") -- cgit 1.4.1 From 5bfb84b8cff02e07cf5a403ba3e2bc9729de565c Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 25 May 2021 14:19:09 +0200 Subject: gnu: Add perl-log-message. * gnu/packages/perl.scm (perl-log-message): New variable. --- gnu/packages/perl.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index dd5d64da1b..8b8709ee3b 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -5830,6 +5830,29 @@ logging mechanism.") @code{Log::Any} adapter using @code{Log::Log4perl} for logging.") (license (package-license perl)))) +(define-public perl-log-message + (package + (name "perl-log-message") + (version "0.08") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://cpan/authors/id/B/BI/BINGOS/Log-Message-" + version ".tar.gz")) + (sha256 + (base32 + "0ipyk7zbvz31kf3mj5ahwi2cbcfy54s8387hx4cd29mg5bb7ssdx")))) + (build-system perl-build-system) + (home-page "https://metacpan.org/release/Log-Message") + (synopsis "Powerful and flexible message logging mechanism") + (description "This package enables you to do generic message logging +throughout programs and projects. Every message will be logged with +stacktraces, timestamps and so on. You can use built-in handlers +immediately, or after the fact when you inspect the error stack. It +is highly configurable and let's you even provide your own handlers +for dealing with messages.") + (license (package-license perl)))) + (define-public perl-log-log4perl (package (name "perl-log-log4perl") -- cgit 1.4.1 From ac30a53c6a3195f2122040f709670544d45715bd Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 25 May 2021 14:20:07 +0200 Subject: gnu: Add perl-log-message-simple * gnu/packages/perl.scm (perl-log-message-simple): New variable. --- gnu/packages/perl.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 8b8709ee3b..e3a43446c2 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -5853,6 +5853,29 @@ is highly configurable and let's you even provide your own handlers for dealing with messages.") (license (package-license perl)))) +(define-public perl-log-message-simple + (package + (name "perl-log-message-simple") + (version "0.10") + (source + (origin + (method url-fetch) + (uri (string-append + "mirror://cpan/authors/id/B/BI/BINGOS/Log-Message-Simple-" + version ".tar.gz")) + (sha256 + (base32 + "15nxi935nfrf8dkdrgvcrf2qlai4pbz03yj8sja0n9mcq2jd24ma")))) + (build-system perl-build-system) + (inputs + `(("perl-log-message" ,perl-log-message))) + (home-page "https://metacpan.org/release/Log-Message-Simple") + (synopsis "Simplified interface to @code{Log::Message}") + (description "This package provides a simplified frontend to +@code{Log::Message}, offering most common use for logging, and easy access to +the stack (in both raw and pretty-printable form).") + (license (package-license perl)))) + (define-public perl-log-log4perl (package (name "perl-log-log4perl") -- cgit 1.4.1 From dc851004816ce70b5bb12fdf684efa544b7ef3a2 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 25 May 2021 14:31:06 +0200 Subject: gnu: Add perl-set-intervaltree. * gnu/packages/perl.scm (perl-set-intervaltree): New variable. --- gnu/packages/perl.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index e3a43446c2..7d3a5f7010 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -8895,6 +8895,27 @@ collector.") (description "Set::Infinite is a set theory module for infinite sets.") (license (package-license perl)))) +(define-public perl-set-intervaltree + (package + (name "perl-set-intervaltree") + (version "0.12") + (source + (origin + (method url-fetch) + (uri (string-append + "mirror://cpan/authors/id/S/SL/SLOYD/Set-IntervalTree-" + version ".tar.gz")) + (sha256 + (base32 "0jf3vdmdgxx6a9xrfwnbbs9g37i1i6qhfg5qwln8x5i280701m3g")))) + (build-system perl-build-system) + (native-inputs + `(("perl-extutils-cppguess" ,perl-extutils-cppguess))) + (home-page "https://metacpan.org/release/Set-IntervalTree") + (synopsis "Perform range-based lookups on sets of ranges") + (description "This package provides an efficient mechanism to look up +ranges in Interval Trees.") + (license (package-license perl)))) + (define-public perl-set-intspan (package (name "perl-set-intspan") -- cgit 1.4.1 From c942e17c296c319704d0a78698a1987583250c68 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 25 May 2021 15:37:05 +0300 Subject: gnu: qhull: Link binaries to shared library. This drops the package size by nearly 60%. * gnu/packages/maths.scm (qhull)[arguments]: Add configure-flag to link binaries to shared library. --- gnu/packages/maths.scm | 2 ++ 1 file changed, 2 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index ee0a69bbd7..d0ca2f4647 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -247,6 +247,8 @@ programming languages.") (base32 "0zlbhg0lb6j60188c2xhcrvviskr079552icjldqhy1jhgmxghmm")))) (build-system cmake-build-system) + (arguments + `(#:configure-flags '("-DLINK_APPS_SHARED=ON"))) (synopsis "Calculate convex hulls and related structures") (description "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi -- cgit 1.4.1 From d2a8b72b2ffe6ec743ddcdb82dfe4b96204b2b3a Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Tue, 25 May 2021 15:15:44 +0200 Subject: gnu: cuirass: Update to 1.0.0-19.e1382f0. * gnu/packages/ci.scm (cuirass): Update to 1.0.0-19.e1382f0. --- gnu/packages/ci.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm index 28dd9ada2b..1f08fdef15 100644 --- a/gnu/packages/ci.scm +++ b/gnu/packages/ci.scm @@ -73,8 +73,8 @@ (file-name (string-append name "-" version "-checkout"))))))) (define-public cuirass - (let ((commit "b1abb4438b99fa4f5b0fcc0052015e69209e1ea0") - (revision "18")) + (let ((commit "e1382f0303d282017aa5d68f0e870863070f28c0") + (revision "19")) (package (name "cuirass") (version (git-version "1.0.0" revision commit)) @@ -87,7 +87,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0iadm1qlg8535yzs1sw1v1iszlfdd42nrzfh4s7kbwvf28ksh4a3")))) + "0kxackclmcqi44xi1pwnm65c05wkp1z6aid2qzkw7sxc1j24iaw2")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build utils) -- cgit 1.4.1 From 0ffac75ece4f22a8595e19b8a375791e87d365aa Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 25 May 2021 16:25:35 +0300 Subject: gnu: qhull: Build position independent. * gnu/packages/maths.scm (qhull)[arguments]: Add configure-flag to build code position independent. --- gnu/packages/maths.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index d0ca2f4647..3d7248417b 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -248,7 +248,8 @@ programming languages.") "0zlbhg0lb6j60188c2xhcrvviskr079552icjldqhy1jhgmxghmm")))) (build-system cmake-build-system) (arguments - `(#:configure-flags '("-DLINK_APPS_SHARED=ON"))) + `(#:configure-flags '("-DLINK_APPS_SHARED=ON" + "-DCMAKE_POSITION_INDEPENDENT_CODE=ON"))) (synopsis "Calculate convex hulls and related structures") (description "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi -- cgit 1.4.1 From d366557b7b7e6b981e33eb162eb7b1e0550d9f59 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 25 May 2021 12:42:55 -0400 Subject: gnu: nginx: Update to 1.21.0 [fixes CVE-2021-23017]. * gnu/packages/web.scm (nginx, nginx-documentation): Update to 1.21.0. --- gnu/packages/web.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 5bf417c7e1..30216911ce 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -368,14 +368,14 @@ the same, being completely separated from the Internet.") ;; ’stable’ and recommends that “in general you deploy the NGINX mainline ;; branch at all times” (https://www.nginx.com/blog/nginx-1-6-1-7-released/) ;; Consider updating the nginx-documentation package together with this one. - (version "1.19.10") + (version "1.21.0") (source (origin (method url-fetch) (uri (string-append "https://nginx.org/download/nginx-" version ".tar.gz")) (sha256 (base32 - "121d11693d6dbim3lh64hrqi66z129z30cvcrpbnm631yl7jkl78")))) + "0w87zhm5nfx88x9hj6drrvm5f3m02kzbjp39x1lsglrbmi5jl6gy")))) (build-system gnu-build-system) (inputs `(("libxml2" ,libxml2) ("libxslt" ,libxslt) @@ -466,9 +466,9 @@ and as a proxy to reduce the load on back-end HTTP or mail servers.") (define-public nginx-documentation ;; This documentation should be relevant for the current nginx package. - (let ((version "1.19.10") - (revision 2708) - (changeset "f8686d85df53")) + (let ((version "1.21.0") + (revision 2726) + (changeset "a7a36efd10af")) (package (name "nginx-documentation") (version (simple-format #f "~A-~A-~A" version revision changeset)) @@ -480,7 +480,7 @@ and as a proxy to reduce the load on back-end HTTP or mail servers.") (file-name (string-append name "-" version)) (sha256 (base32 - "00b0dkpblw3m2cwbbzv3miw47c0m3s0dvh1xy0hihkggy7mqv2r2")))) + "1fl7rkbfdd26c78h85x4w3kas16rpj4pxzjhc071qvx7znwgm2pn")))) (build-system gnu-build-system) (arguments '(#:tests? #f ; no test suite -- cgit 1.4.1 From 458126a2370706a35cf6a272b2c7a988c75ab375 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 25 May 2021 16:29:42 -0400 Subject: gnu: Add rsync 3.2.3. * gnu/packages/rsync.scm (rsync-next): New variable. --- gnu/packages/rsync.scm | 41 ++++++++++++++++++++++++++++++++++++++++- 1 file changed, 40 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/rsync.scm b/gnu/packages/rsync.scm index 37b15663b9..59460f1324 100644 --- a/gnu/packages/rsync.scm +++ b/gnu/packages/rsync.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2016 Mark H Weaver ;;; Copyright © 2017, 2019 Efraim Flashner ;;; Copyright © 2018, 2021 Tobias Geerinckx-Rice -;;; Copyright © 2019 Leo Famulari +;;; Copyright © 2019, 2021 Leo Famulari ;;; Copyright © 2020 Vincent Legoll ;;; ;;; This file is part of GNU Guix. @@ -26,6 +26,7 @@ #:use-module (gnu packages acl) #:use-module (gnu packages base) #:use-module (gnu packages compression) + #:use-module (gnu packages digest) #:use-module (gnu packages perl) #:use-module (gnu packages popt) #:use-module ((guix licenses) #:prefix license:) @@ -68,6 +69,44 @@ files in the destination.") (license license:gpl3+) (home-page "https://rsync.samba.org/"))) +(define-public rsync-next + (package + (name "rsync") + (version "3.2.3") + (source (origin + (method url-fetch) + (uri (string-append "https://rsync.samba.org/ftp/rsync/src/rsync-" + version ".tar.gz")) + (sha256 + (base32 + "03p5dha9g9krq61mdbcrjkpz5nglri0009ks2vs9k97f9i83rk5y")))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags + ;; The bundled copies are preferred by default. + (list "--without-included-zlib" + "--without-included-popt" + ;; Avoid these dependencies for now. + "--disable-lz4" + "--disable-openssl" + "--disable-zstd"))) + (native-inputs + `(("perl" ,perl))) + (inputs + `(("acl" ,acl) + ("popt" ,popt) + ("xxhash" ,xxhash) + ("zlib" ,zlib))) + (synopsis "Remote (and local) file copying tool") + (description + "Rsync is a fast and versatile file copying tool. It can copy locally, +to/from another host over any remote shell, or to/from a remote rsync daemon. +Its delta-transfer algorithm reduces the amount of data sent over the network +by sending only the differences between the source files and the existing +files in the destination.") + (license license:gpl3+) + (home-page "https://rsync.samba.org/"))) + (define-public librsync (package (name "librsync") -- cgit 1.4.1 From 189311660bab43952c4bd266317d892dc5fae5ce Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 09:13:08 +0200 Subject: gnu: Add r-aneufinderdata. * gnu/packages/bioconductor.scm (r-aneufinderdata): New variable. --- gnu/packages/bioconductor.scm | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 45e31a5760..b4ea90592b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus -;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen +;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017 Efraim Flashner @@ -934,6 +934,22 @@ datasets which are derived from the Allen Brain Atlas: All datasets are restricted to protein coding genes.") (license license:gpl2+))) +(define-public r-aneufinderdata + (package + (name "r-aneufinderdata") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AneuFinderData" version 'experiment)) + (sha256 + (base32 + "02vb3kmza5hv8bc424fdmfif608xvpdb759w8882kac8izpv29ks")))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/AneuFinderData/") + (synopsis "Data package for @code{AneuFinder}") + (description "This package contains data used by @code{AneuFinder}.") + (license license:artistic2.0))) + (define-public r-arrmdata (package (name "r-arrmdata") -- cgit 1.4.1 From b84ead8c045f7921131dc66ab85ee1db3113607a Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 09:13:54 +0200 Subject: gnu: Add r-aneufinder. * gnu/packages/bioconductor.scm (r-aneufinder): New variable. --- gnu/packages/bioconductor.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b4ea90592b..02bfe21f7d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -950,6 +950,48 @@ All datasets are restricted to protein coding genes.") (description "This package contains data used by @code{AneuFinder}.") (license license:artistic2.0))) +(define-public r-aneufinder + (package + (name "r-aneufinder") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AneuFinder" version)) + (sha256 + (base32 + "1j2n6i3ja63i98y1mbb8ndn6cn2a0pw97zz6al4myycnv55w49j3")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (propagated-inputs + `(("r-genomicranges" ,r-genomicranges) + ("r-aneufinderdata" ,r-aneufinderdata) + ("r-ecp" ,r-ecp) + ("r-foreach" ,r-foreach) + ("r-doparallel" ,r-doparallel) + ("r-biocgenerics" ,r-biocgenerics) + ("r-s4vectors" ,r-s4vectors) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-bamsignals" ,r-bamsignals) + ("r-dnacopy" ,r-dnacopy) + ("r-biostrings" ,r-biostrings) + ("r-genomicalignments" ,r-genomicalignments) + ("r-ggplot2" ,r-ggplot2) + ("r-reshape2" ,r-reshape2) + ("r-ggdendro" ,r-ggdendro) + ("r-ggrepel" ,r-ggrepel) + ("r-reordercluster" ,r-reordercluster) + ("r-mclust" ,r-mclust) + ("r-cowplot" ,r-cowplot))) + (home-page "https://bioconductor.org/packages/AneuFinder/") + (synopsis "Copy number variation analysis in single-cell-sequencing data") + (description "This package implements functions for copy number variant +calling, plotting, export and analysis from whole-genome single cell +sequencing data.") + (license license:artistic2.0))) + (define-public r-arrmdata (package (name "r-arrmdata") -- cgit 1.4.1 From b1fee8a00318f4cf2cb3f854edc70f5c000ab71f Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 09:29:01 +0200 Subject: gnu: Add r-spp. * gnu/packages/bioinformatics.scm (r-spp): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9c77d66a35..bcc9f5bef2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8108,6 +8108,30 @@ sequence motif occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.") (license license:gpl3+))) +(define-public r-spp + (package + (name "r-spp") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (cran-uri "spp" version)) + (sha256 + (base32 + "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w")))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-catools" ,r-catools) + ("r-rcpp" ,r-rcpp) + ("r-rsamtools" ,r-rsamtools))) + (home-page "https://cran.r-project.org/web/packages/spp/") + (synopsis "ChIP-Seq processing pipeline") + (description "This package provides tools for analysis of ChIP-seq and +other functional sequencing data.") + (license license:gpl2))) + (define-public r-genomation (package (name "r-genomation") -- cgit 1.4.1 From af163badb409872b4c676ccb2274694ae892cc40 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 09:34:37 +0200 Subject: gnu: Add r-phantompeakqualtools. * gnu/packages/bioinformatics.scm (r-phantompeakqualtools): New variable. --- gnu/packages/bioinformatics.scm | 47 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bcc9f5bef2..074ff8046f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8132,6 +8132,53 @@ reference point and sorted by a user defined feature.") other functional sequencing data.") (license license:gpl2))) +(define-public r-phantompeakqualtools + (package + (name "r-phantompeakqualtools") + (version "1.2.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kundajelab/phantompeakqualtools") + (commit "8d2b2d18c686d894ef5908b37da7adf72a07ef42"))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "00anrvcwsp02d98qhj1xpj85644h2pp4kfzq6dgbmwmdr6jvy7p4")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests. + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((script (string-append (assoc-ref outputs "out") + "/share/scripts"))) + (install-file "run_spp.R" script))))))) + (inputs + `(("r" ,r-minimal))) + (propagated-inputs + `(("r-catools" ,r-catools) + ("r-snow" ,r-snow) + ("r-snowfall" ,r-snowfall) + ("r-bitops" ,r-bitops) + ("r-rsamtools" ,r-rsamtools) + ("r-spp" ,r-spp) + ("gawk" ,gawk) + ("samtools" ,samtools) + ("boost" ,boost) + ("gzip" ,gzip))) + (home-page "https://github.com/kundajelab/phantompeakqualtools") + (synopsis "Informative enrichment for ChIP-seq data") + (description "This package computes informative enrichment and quality +measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be +used to obtain robust estimates of the predominant fragment length or +characteristic tag shift values in these assays.") + (license license:bsd-3))) + (define-public r-genomation (package (name "r-genomation") -- cgit 1.4.1 From 9048e7f3b4d53a61050a8c1f0d47f7a1f637478f Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 09:42:01 +0200 Subject: gnu: Add r-bsgenome-btaurus-ucsc-bostau8. * gnu/packages/bioconductor.scm (r-bsgenome-btaurus-ucsc-bostau8): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 02bfe21f7d..24b0e6a2fa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -103,6 +103,29 @@ analysis.") database, assembled using data from REACTOME.") (license license:cc-by4.0))) +(define-public r-bsgenome-btaurus-ucsc-bostau8 + (package + (name "r-bsgenome-btaurus-ucsc-bostau8") + (version "1.4.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome.Btaurus.UCSC.bosTau8" + version 'annotation)) + (sha256 + (base32 + "16wjy1aw9nvx03r7w8yh5w7sw3pn8i9nczd0n0728l6nnyqxlsz6")))) + (properties + `((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome))) + (home-page + "https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/") + (synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)") + (description "This package provides the full genome sequences for Bos +taurus (UCSC version bosTau8).") + (license license:artistic2.0))) + (define-public r-bsgenome-celegans-ucsc-ce6 (package (name "r-bsgenome-celegans-ucsc-ce6") -- cgit 1.4.1 From 3f2a4b098039bd374c76d524223de3c6c475f23e Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 09:52:12 +0200 Subject: gnu: Add r-pvclust. * gnu/packages/cran.scm (r-pvclust): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8709cd21fa..949c74f0e8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2894,6 +2894,26 @@ attaching it. This is a key part of the @code{devtools} package as it allows you to rapidly iterate while developing a package.") (license license:gpl3))) +(define-public r-pvclust + (package + (name "r-pvclust") + (version "2.2-0") + (source (origin + (method url-fetch) + (uri (cran-uri "pvclust" version)) + (sha256 + (base32 + "0082icm54k2yq60k06qpr92a626k39j2jr0046lva4ylmhxqb4kq")))) + (build-system r-build-system) + (home-page "https://github.com/shimo-lab/pvclust") + (synopsis + "Hierarchical clustering with P-values via multiscale bootstrap resampling") + (description "This package provides an implementation of multiscale bootstrap +resampling for assessing the uncertainty in hierarchical cluster analysis. It +provides an AU (approximately unbiased) P-value as well as a BP (bootstrap probability) +value for each cluster in a dendrogram.") + (license license:gpl2+))) + (define-public r-rcpp (package (name "r-rcpp") -- cgit 1.4.1 From 5aa68a9408e7af7dfb38abf48e499788fb7b0f82 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 10:00:51 +0200 Subject: gnu: Add r-model4you. * gnu/packages/cran.scm (r-model4you): New variable. --- gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 949c74f0e8..b8417ec974 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1157,6 +1157,36 @@ the embedded @code{RapidXML} C++ library.") ;; 'rapidxml' which is Boost. (license (list license:gpl3 license:bsd-2 license:boost1.0)))) +(define-public r-model4you + (package + (name "r-model4you") + (version "0.9-7") + (source (origin + (method url-fetch) + (uri (cran-uri "model4you" version)) + (sha256 + (base32 + "0pni9v3nradvy8sp2m07903vc7z610xrh426lf19dxss12kgrfi8")))) + (build-system r-build-system) + (propagated-inputs + `(("r-formula" ,r-formula) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-partykit" ,r-partykit) + ("r-sandwich" ,r-sandwich) + ("r-survival" ,r-survival))) + (home-page "https://cran.r-project.org/web/packages/model4you/") + (synopsis "Stratified and personalised models based on trees and forests") + (description + "This package provides procedures for model-based trees for subgroup +analyses in clinical trials and model-based forests for the estimation and +prediction of personalised treatment effects. Currently partitioning of linear +models, @code{lm()}, generalised linear models, @code{glm()}, and +Weibull models, @code{survreg()}, are supported. Advanced plotting functionality is +supported for the trees and a test for parameter heterogeneity is provided for +the personalised models.") + (license license:gpl2+))) + (define-public r-modelr (package (name "r-modelr") -- cgit 1.4.1 From 94b8ad4490707369146eddd79d4f543238b4978e Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 10:21:32 +0200 Subject: gnu: Add r-chipseeker. * gnu/packages/bioconductor.scm (r-chipseeker): New variable. --- gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 24b0e6a2fa..3359ce16cb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1055,6 +1055,54 @@ from Illumina 450k methylation arrays.") chromstaR package.") (license license:gpl3))) +(define-public r-chipseeker + (package + (name "r-chipseeker") + (version "1.26.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ChIPseeker" version)) + (sha256 + (base32 + "1r197qwsriap6s6nb2p9j3521pjs2f0lgyzvppvlxj1531sa6g6z")))) + (build-system r-build-system) + (inputs + `(("r-knitr" ,r-knitr))) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocgenerics" ,r-biocgenerics) + ("r-boot" ,r-boot) + ("r-enrichplot" ,r-enrichplot) + ("r-iranges" ,r-iranges) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-ggplot2" ,r-ggplot2) + ("r-gplots" ,r-gplots) + ("r-gtools" ,r-gtools) + ("r-dplyr" ,r-dplyr) + ("r-plotrix" ,r-plotrix) + ("r-dplyr" ,r-dplyr) + ("r-magrittr" ,r-magrittr) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-txdb-hsapiens-ucsc-hg19-knowngene" + ,r-txdb-hsapiens-ucsc-hg19-knowngene))) + (home-page "https://www.bioconductor.org/packages/ChIPseeker/") + (synopsis + "ChIPseeker for ChIP peak Annotation, Comparison, and Visualization") + (description "This package implements functions to retrieve the nearest +genes around the peak, annotate genomic region of the peak, statstical methods +for estimate the significance of overlap among ChIP peak data sets, and +incorporate GEO database for user to compare the own dataset with those +deposited in database. The comparison can be used to infer cooperative +regulation and thus can be used to generate hypotheses. Several visualization +functions are implemented to summarize the coverage of the peak experiment, +average profile and heatmap of peaks binding to TSS regions, genomic +annotation, distance to TSS, and overlap of peaks or genes.") + (license license:artistic2.0))) + (define-public r-genelendatabase (package (name "r-genelendatabase") -- cgit 1.4.1 From 63962f9b6cb0358d091b9b97b66d348e865229e2 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 26 May 2021 10:29:22 +0200 Subject: gnu: Add minimodem. * gnu/packages/radio.scm (minimodem): New variable. --- gnu/packages/radio.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 6b2c3eb387..72f0618313 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -1927,3 +1927,32 @@ spectrum waterfall. It supports at least the following models: @end itemize\n") (license (list license:expat license:gpl3))))) + +(define-public minimodem + (package + (name "minimodem") + (version "0.24") + (source + (origin + (method url-fetch) + (uri (string-append "http://www.whence.com/minimodem/minimodem-" + version ".tar.gz")) + (sha256 + (base32 "13ipyh39l7p420j1j9kvwyskv2nqnimls1a3z1klsa1zivds9k7q")))) + (build-system gnu-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("alsa-lib" ,alsa-lib) + ("fftwf" ,fftwf) + ("libsndfile" ,libsndfile) + ("pulseaudio" ,pulseaudio))) + (home-page "http://www.whence.com/minimodem/") + (synopsis "Software audio FSK modem") + (description + "Minimodem is a command-line program which decodes (or generates) audio +modem tones at any specified baud rate, using various framing protocols. It +acts a general-purpose software FSK modem, and includes support for various +standard FSK protocols such as Bell103, Bell202, RTTY, TTY/TDD, NOAA SAME, and +Caller-ID.") + (license license:gpl3+))) -- cgit 1.4.1 From 3d704fafbaf5f4796f1c688c412f4b1cb77e916f Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Wed, 26 May 2021 11:48:19 +0200 Subject: gnu: cuirass: Update to 1.0.0-20.524b81d. * gnu/packages/ci.scm (cuirass): Update to 1.0.0-20.524b81d. --- gnu/packages/ci.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm index 1f08fdef15..22c11a8c7a 100644 --- a/gnu/packages/ci.scm +++ b/gnu/packages/ci.scm @@ -73,8 +73,8 @@ (file-name (string-append name "-" version "-checkout"))))))) (define-public cuirass - (let ((commit "e1382f0303d282017aa5d68f0e870863070f28c0") - (revision "19")) + (let ((commit "524b81d9ca6334dc322930a0ccc1d6830a81899b") + (revision "20")) (package (name "cuirass") (version (git-version "1.0.0" revision commit)) @@ -87,7 +87,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0kxackclmcqi44xi1pwnm65c05wkp1z6aid2qzkw7sxc1j24iaw2")))) + "0jq4pdamqv7p85049na9344pr4q3j8zxm5p6k4yl6fq87k096frs")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build utils) -- cgit 1.4.1 From 834f649590db5939e3cd5a18097c7803bd625f82 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 13:09:34 +0200 Subject: gnu: Add r-geneoverlap. * gnu/packages/bioconductor.scm (r-geneoverlap): New variable. --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3359ce16cb..22568353af 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1127,6 +1127,26 @@ annotation, distance to TSS, and overlap of peaks or genes.") genomes and gene ID formats, largely based on the UCSC table browser.") (license license:lgpl2.0+))) +(define-public r-geneoverlap + (package + (name "r-geneoverlap") + (version "1.26.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GeneOverlap" version)) + (sha256 + (base32 + "0bvh00n4fx0h1m83bypib3jvln1ihcv77ywrrn9xm20y73gymhkh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-gplots" ,r-gplots))) + (home-page "https://www.bioconductor.org/packages/GeneOverlap/") + (synopsis "Test and visualize gene overlaps") + (description "This package can be used to test two sets of gene lists +and visualize the results.") + (license license:gpl3))) + (define-public r-pasilla (package (name "r-pasilla") -- cgit 1.4.1 From 99873359edd7882c776afa326eb23d2d89d87ee2 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 13:13:56 +0200 Subject: gnu: Add r-deepsnv. * gnu/packages/bioconductor.scm (r-deepsnv): New variable. --- gnu/packages/bioconductor.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 22568353af..7db99fd5ff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1408,6 +1408,42 @@ data. In addition, provides numerous plotting functions for commonly used visualizations.") (license license:artistic2.0))) +(define-public r-deepsnv + (package + (name "r-deepsnv") + (version "1.36.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "deepSNV" version)) + (sha256 + (base32 + "1lbvx9liql8fkb4y020kwpgp61vzg67cy640dc4kybglcw9dx6j0")))) + (properties `((upstream-name . "deepSNV"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rhtslib" ,r-rhtslib) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation) + ("r-vgam" ,r-vgam))) + (home-page "https://github.com/gerstung-lab/deepSNV/") + (synopsis "Detection of subclonal SNVs in deep sequencing data") + (description + "This package provides quantitative variant callers for detecting +subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. +The deepSNV algorithm is used for a comparative setup with a control experiment +of the same loci and uses a beta-binomial model and a likelihood ratio test to +discriminate sequencing errors and subclonal SNVs. The shearwater algorithm +computes a Bayes classifier based on a beta-binomial model for variant calling +with multiple samples for precisely estimating model parameters - such as local +error rates and dispersion - and prior knowledge, e.g. from variation data +bases such as COSMIC.") + (license license:gpl3))) + (define-public r-delayedarray (package (name "r-delayedarray") -- cgit 1.4.1 From f921981536d6e99f5807f721977e83c13827c091 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 13:31:20 +0200 Subject: gnu: Add r-decipher. * gnu/packages/bioconductor.scm (r-decipher): New variable. --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7db99fd5ff..596e80a9f9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1408,6 +1408,26 @@ data. In addition, provides numerous plotting functions for commonly used visualizations.") (license license:artistic2.0))) +(define-public r-decipher + (package + (name "r-decipher") + (version "2.18.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "DECIPHER" version)) + (sha256 + (base32 + "0jz2lffks9rrk5wzbvnr8yal91kf8rg2xn0fmg9ywk45ql657sm9")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-rsqlite" ,r-rsqlite))) + (home-page "https://www.bioconductor.org/packages/DECIPHER/") + (synopsis "Tools for deciphering and managing biological sequences") + (description "This package provides a toolset for deciphering and managing +biological sequences.") + (license license:gpl3))) + (define-public r-deepsnv (package (name "r-deepsnv") -- cgit 1.4.1 From 1ae67e673594655b5bace7febdf01c66f81a784a Mon Sep 17 00:00:00 2001 From: Lars-Dominik Braun Date: Tue, 18 May 2021 14:05:55 +0200 Subject: gnu: Add r-contfrac. * gnu/packages/cran.scm (r-contfrac): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b8417ec974..14fd834dcd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28733,3 +28733,23 @@ quantile regression and solutions for class imbalanced data. It provides a fast interface using subsampling and confidence regions for variable importance.") (license license:gpl3+))) + +(define-public r-contfrac + (package + (name "r-contfrac") + (version "1.1-12") + (source + (origin + (method url-fetch) + (uri (cran-uri "contfrac" version)) + (sha256 + (base32 + "0sq5c7ny235yrkv2xc4insgxby6rvzc1qsj8h301cd2if3lwbgwm")))) + (properties `((upstream-name . "contfrac"))) + (build-system r-build-system) + (home-page + "https://github.com/RobinHankin/contfrac") + (synopsis "Continued Fractions") + (description + "Various utilities for evaluating continued fractions.") + (license license:gpl2))) -- cgit 1.4.1 From 1af2da50bfed3fb23ef048db10cdb08445e2bc12 Mon Sep 17 00:00:00 2001 From: Lars-Dominik Braun Date: Tue, 18 May 2021 14:07:12 +0200 Subject: gnu: Add r-elliptic. * gnu/packages/cran.scm (r-elliptic): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 14fd834dcd..8108b1b81f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28753,3 +28753,28 @@ importance.") (description "Various utilities for evaluating continued fractions.") (license license:gpl2))) + +(define-public r-elliptic + (package + (name "r-elliptic") + (version "1.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "elliptic" version)) + (sha256 + (base32 + "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn")))) + (properties `((upstream-name . "elliptic"))) + (build-system r-build-system) + (inputs `(("pari-gp" ,pari-gp))) + (propagated-inputs `(("r-mass" ,r-mass))) + (home-page + "https://github.com/RobinHankin/elliptic") + (synopsis + "Weierstrass and Jacobi Elliptic Functions") + (description + "A suite of elliptic and related functions including Weierstrass and +Jacobi forms. Also includes various tools for manipulating and visualizing +complex functions.") + (license license:gpl2))) -- cgit 1.4.1 From fef452b13fc32f63341def0c1aa2ed2df8f77324 Mon Sep 17 00:00:00 2001 From: Lars-Dominik Braun Date: Tue, 18 May 2021 14:07:47 +0200 Subject: gnu: Add r-hypergeo. * gnu/packages/cran.scm (r-hypergeo): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8108b1b81f..d013ffd039 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28778,3 +28778,27 @@ importance.") Jacobi forms. Also includes various tools for manipulating and visualizing complex functions.") (license license:gpl2))) + +(define-public r-hypergeo + (package + (name "r-hypergeo") + (version "1.2-13") + (source + (origin + (method url-fetch) + (uri (cran-uri "hypergeo" version)) + (sha256 + (base32 + "13jdiy216znwhr91iqnh03mvkmyscw439syb3h4i67dd78sphnvd")))) + (properties `((upstream-name . "hypergeo"))) + (build-system r-build-system) + (propagated-inputs + `(("r-contfrac" ,r-contfrac) + ("r-desolve" ,r-desolve) + ("r-elliptic" ,r-elliptic))) + (home-page + "https://cran.r-project.org/web/packages/hypergeo/") + (synopsis "The Gauss Hypergeometric Function") + (description + "The Gaussian hypergeometric function for complex numbers.") + (license license:gpl2))) -- cgit 1.4.1 From 6c7aafbedf656ff7cacf39141c649b82abcd7bf7 Mon Sep 17 00:00:00 2001 From: Lars-Dominik Braun Date: Tue, 18 May 2021 14:09:14 +0200 Subject: gnu: Add r-kknn. * gnu/packages/statistics.scm (r-kknn): New variable. --- gnu/packages/statistics.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 00378db458..27df2091ee 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -6134,3 +6134,24 @@ input, the effect size can be returned as standardized mean difference, Cohen's f, Hedges' g, Pearson's r or Fisher's transformation z, odds ratio or log odds, or eta squared effect size.") (license license:gpl3))) + +(define-public r-kknn + (package + (name "r-kknn") + (version "1.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "kknn" version)) + (sha256 + (base32 + "1nzkg3dxaiqp87p56wm895qx5xn86hv5hjr73qvl1yiaxiq0x112")))) + (properties `((upstream-name . "kknn"))) + (build-system r-build-system) + (propagated-inputs + `(("r-igraph" ,r-igraph) ("r-matrix" ,r-matrix))) + (home-page "https://github.com/KlausVigo/kknn") + (synopsis "Weighted k-Nearest Neighbors") + (description + "Weighted k-Nearest Neighbors for Classification, Regression and Clustering.") + (license license:gpl2+))) -- cgit 1.4.1 From e53ecc60871e97517be27e11a3d88d059ec36777 Mon Sep 17 00:00:00 2001 From: Lars-Dominik Braun Date: Tue, 18 May 2021 14:09:52 +0200 Subject: gnu: Add r-logspline. * gnu/packages/statistics.scm (r-logspline): New variable. --- gnu/packages/statistics.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 27df2091ee..6318efdda1 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -6155,3 +6155,29 @@ or eta squared effect size.") (description "Weighted k-Nearest Neighbors for Classification, Regression and Clustering.") (license license:gpl2+))) + +(define-public r-logspline + (package + (name "r-logspline") + (version "2.1.16") + (source + (origin + (method url-fetch) + (uri (cran-uri "logspline" version)) + (sha256 + (base32 + "12hkdi77vkic05p2vhap025xdcg1n53ywm239v18713pihdlj63l")))) + (properties `((upstream-name . "logspline"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page + "https://cran.r-project.org/web/packages/logspline/") + (synopsis + "Routines for Logspline Density Estimation") + (description + "Contains routines for logspline density estimation. The function +@code{oldlogspline()} uses the same algorithm as the logspline package version +1.0.x; i.e. the Kooperberg and Stone (1992) algorithm (with an improved +interface). The recommended routine @code{logspline()} uses an algorithm from +@url{doi:10.1214/aos/1031594728,Stone et al (1997)}.") + (license license:asl2.0))) -- cgit 1.4.1 From 3ea32f5bcfcf5a3183b5d4ffba899832f9c83e4d Mon Sep 17 00:00:00 2001 From: Lars-Dominik Braun Date: Tue, 18 May 2021 14:10:49 +0200 Subject: gnu: Add r-effects. * gnu/packages/statistics.scm (r-effects): New variable. --- gnu/packages/statistics.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6318efdda1..8b7b25e782 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -6181,3 +6181,36 @@ or eta squared effect size.") interface). The recommended routine @code{logspline()} uses an algorithm from @url{doi:10.1214/aos/1031594728,Stone et al (1997)}.") (license license:asl2.0))) + +(define-public r-effects + (package + (name "r-effects") + (version "4.2-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "effects" version)) + (sha256 + (base32 + "0iks79rd4knrd81x4kvcpgpclr69l0m0v6sfla8k3wzkcnydycv8")))) + (properties `((upstream-name . "effects"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cardata" ,r-cardata) + ("r-colorspace" ,r-colorspace) + ("r-estimability" ,r-estimability) + ("r-insight" ,r-insight) + ("r-lattice" ,r-lattice) + ("r-lme4" ,r-lme4) + ("r-nnet" ,r-nnet) + ("r-survey" ,r-survey))) + (native-inputs + `(("r-knitr" ,r-knitr) + ("r-car", r-car))) + (home-page "https://www.r-project.org") + (synopsis + "Effect Displays for Linear, Generalized Linear, and Other Models") + (description + "Graphical and tabular effect displays, e.g., of interactions, for +various statistical models with linear predictors.") + (license license:gpl2+))) -- cgit 1.4.1 From b085abbeb8edf1fccc1a3aa5b11345e425fdf22f Mon Sep 17 00:00:00 2001 From: Lars-Dominik Braun Date: Tue, 18 May 2021 14:11:14 +0200 Subject: gnu: Add r-bayesfactor. * gnu/packages/statistics.scm (r-bayesfactor): New variable. --- gnu/packages/statistics.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 8b7b25e782..90103ce91a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -6214,3 +6214,38 @@ interface). The recommended routine @code{logspline()} uses an algorithm from "Graphical and tabular effect displays, e.g., of interactions, for various statistical models with linear predictors.") (license license:gpl2+))) + +(define-public r-bayesfactor + (package + (name "r-bayesfactor") + (version "0.9.12-4.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "BayesFactor" version)) + (sha256 + (base32 + "1z083v7is21gm0a458jm5ph3xfdm7mh29a6sg2r1njq82f8x3s3g")))) + (properties `((upstream-name . "BayesFactor"))) + (build-system r-build-system) + (propagated-inputs + `(("r-coda" ,r-coda) + ("r-gtools" ,r-gtools) + ("r-hypergeo" ,r-hypergeo) + ("r-matrix" ,r-matrix) + ("r-matrixmodels" ,r-matrixmodels) + ("r-mvtnorm" ,r-mvtnorm) + ("r-pbapply" ,r-pbapply) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-stringr" ,r-stringr))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://richarddmorey.github.io/BayesFactor/") + (synopsis + "Computation of Bayes Factors for Common Designs") + (description + "This package provides a suite of functions for computing various Bayes +factors for simple designs, including contingency tables, one- and two-sample +designs, one-way designs, general ANOVA designs, and linear regression.") + (license license:gpl2))) -- cgit 1.4.1 From 36a90d0637bb47b113ceda5abb64c50600837436 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 26 May 2021 13:40:59 +0300 Subject: gnu: minimap2: Update to 2.18. * gnu/packages/bioinformatics.scm (minimap2): Update to 2.18. [source]: Remove patch. * gnu/packages/patches/minimap2-aarch64-support.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 5 +-- .../patches/minimap2-aarch64-support.patch | 52 ---------------------- 3 files changed, 2 insertions(+), 56 deletions(-) delete mode 100644 gnu/packages/patches/minimap2-aarch64-support.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index b0df9d582d..8355a208ea 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1424,7 +1424,6 @@ dist_patch_DATA = \ %D%/packages/patches/mingw-w64-6.0.0-gcc.patch \ %D%/packages/patches/mingw-w64-dlltool-temp-prefix.patch \ %D%/packages/patches/mingw-w64-reproducible-gendef.patch \ - %D%/packages/patches/minimap2-aarch64-support.patch \ %D%/packages/patches/minisat-friend-declaration.patch \ %D%/packages/patches/minisat-install.patch \ %D%/packages/patches/mit-krb5-hurd.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 074ff8046f..46092fd589 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12323,7 +12323,7 @@ version does count multisplits.") (define-public minimap2 (package (name "minimap2") - (version "2.17") + (version "2.18") (source (origin (method url-fetch) @@ -12332,8 +12332,7 @@ version does count multisplits.") "minimap2-" version ".tar.bz2")) (sha256 (base32 - "0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn")) - (patches (search-patches "minimap2-aarch64-support.patch")))) + "1d7fvdqcqd6wns875rkyd7f34ii15gc9l1sivd2wbbpcb0fi0mbs")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there are none diff --git a/gnu/packages/patches/minimap2-aarch64-support.patch b/gnu/packages/patches/minimap2-aarch64-support.patch deleted file mode 100644 index 95db8579d6..0000000000 --- a/gnu/packages/patches/minimap2-aarch64-support.patch +++ /dev/null @@ -1,52 +0,0 @@ -This patch should be removed with the next release. There is WIP upstream -support for proper support of more architectures, including aarch64 and powerpc64le. - -diff --git a/Makefile b/Makefile -index ed341f6..94dbd85 100644 ---- a/Makefile -+++ b/Makefile -@@ -6,20 +6,18 @@ PROG= minimap2 - PROG_EXTRA= sdust minimap2-lite - LIBS= -lm -lz -lpthread - --ifeq ($(arm_neon),) # if arm_neon is not defined --ifeq ($(sse2only),) # if sse2only is not defined -- OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o --else # if sse2only is defined -- OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o --endif --else # if arm_neon is defined -+ifneq ($(arm_neon),) # if arm_neon is defined - OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o -- INCLUDES+=-Isse2neon --ifeq ($(aarch64),) #if aarch64 is not defined - CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char --else #if aarch64 is defined -+ INCLUDES+=-Isse2neon -+else ifneq ($(aarch64),) #if aarch64 is defined -+ OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o - CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char --endif -+ INCLUDES+=-Isse2neon -+else ifneq ($(sse2only),) # if sse2only is defined -+ OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o -+else # none of the above -+ OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o - endif - - .PHONY:all extra clean depend -@@ -46,9 +44,12 @@ sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h - - # SSE-specific targets on x86/x86_64 - --ifeq ($(arm_neon),) # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2) -+ifneq ($(arm_neon),) # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2) -+ksw2_ll_sse.o:ksw2_ll_sse.c ksw2.h kalloc.h -+else ifneq ($(aarch64),) - ksw2_ll_sse.o:ksw2_ll_sse.c ksw2.h kalloc.h -- $(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@ -+else -+ $(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@ - endif - - ksw2_extz2_sse41.o:ksw2_extz2_sse.c ksw2.h kalloc.h -- cgit 1.4.1 From c5f7203e3eea9453c773f7e38c4adc50f09b024c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 26 May 2021 13:42:26 +0300 Subject: gnu: minimap2: Install more files. * gnu/packages/bioinformatics.scm (minimap2)[arguments]: Add modules. Adjust custom 'install phase to also install library, headers and a pkg-config file. --- gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++-- 1 file changed, 25 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 46092fd589..af1010f853 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12336,6 +12336,9 @@ version does count multisplits.") (build-system gnu-build-system) (arguments `(#:tests? #f ; there are none + #:modules ((guix build utils) + (guix build gnu-build-system) + (srfi srfi-26)) #:make-flags (list (string-append "CC=" ,(cc-for-target)) (let ((system ,(or (%current-target-system) @@ -12358,10 +12361,30 @@ version does count multisplits.") (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin")) + (lib (string-append out "/lib")) + (inc (string-append out "/include")) (man (string-append out "/share/man/man1"))) (install-file "minimap2" bin) - (mkdir-p man) - (install-file "minimap2.1" man)) + (install-file "libminimap2.a" lib) + (install-file "minimap2.1" man) + (map (cut install-file <> inc) + (find-files "." "\\.h$")) + ;; Not this file. + (delete-file (string-append inc "/emmintrin.h")) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/minimap2.pc") + (lambda _ + (format #t "prefix=~a~@ + exec_prefix=${prefix}~@ + libdir=${exec_prefix}/lib~@ + includedir=${prefix}/include~@ + ~@ + Name: libminimap2~@ + Version: ~a~@ + Description: A versatile pairwise aligner for genomic and spliced nucleotide sequence~@ + Libs: -L${libdir} -lminimap2~@ + Cflags: -I${includedir}~%" + out ,version)))) #t))))) (inputs `(("zlib" ,zlib))) -- cgit 1.4.1 From 93a5505f123766153baf17938c3d4152da2fb698 Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Tue, 25 May 2021 17:03:00 +0200 Subject: gnu: emacs-forge: Update to 0.2.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-forge): Update to 0.2.0. [arguments]<#:phases>: Don’t return #t at the end of phases, this will be redundant once core-updates gets merged. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 86 ++++++++++++++++++++++------------------------ 1 file changed, 42 insertions(+), 44 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 886320cc34..9d5774d66e 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -22969,51 +22969,49 @@ commands (a prefix and a suffix) we prefer to call it just a \"transient\".") (license license:gpl3+))) (define-public emacs-forge - (let ((commit "05ef02913004826165c383bd6d2ff6574542b76c")) - (package - (name "emacs-forge") - (version (git-version "0.1.0" "5" commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/magit/forge") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1vv7xlawj2zmwqk69qlsqflhh0lbyqm5xf4x8l4v2069g0k8mmx1")))) - (build-system emacs-build-system) - (native-inputs - `(("texinfo" ,texinfo))) - (propagated-inputs - `(("emacs-closql" ,emacs-closql) - ("emacs-dash" ,emacs-dash) - ("emacs-emacsql-sqlite" ,emacs-emacsql) - ("emacs-ghub" ,emacs-ghub) - ("emacs-let-alist" ,emacs-let-alist) - ("emacs-magit" ,emacs-magit) - ("emacs-markdown-mode" ,emacs-markdown-mode) - ("emacs-transient" ,emacs-transient))) - (arguments - `(#:tests? #f ;no tests - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'build-info-manual - (lambda _ - (invoke "make" "info") - ;; Move the info file to lisp so that it gets installed by the - ;; emacs-build-system. - (rename-file "docs/forge.info" "lisp/forge.info"))) - (add-after 'build-info-manual 'chdir-lisp - (lambda _ - (chdir "lisp") - #t))))) - (home-page "https://github.com/magit/forge/") - (synopsis "Access Git forges from Magit") - (description "Work with Git forges, such as Github and Gitlab, from the + (package + (name "emacs-forge") + (version "0.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/magit/forge") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "139pndj9l9aifnvv2ak5zwf5gzwhp3m6dfpw1avf4vkh1zywzwa0")))) + (build-system emacs-build-system) + (native-inputs + `(("texinfo" ,texinfo))) + (propagated-inputs + `(("emacs-closql" ,emacs-closql) + ("emacs-dash" ,emacs-dash) + ("emacs-emacsql-sqlite" ,emacs-emacsql) + ("emacs-ghub" ,emacs-ghub) + ("emacs-let-alist" ,emacs-let-alist) + ("emacs-magit" ,emacs-magit) + ("emacs-markdown-mode" ,emacs-markdown-mode) + ("emacs-transient" ,emacs-transient))) + (arguments + `(#:tests? #f ;no tests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'build-info-manual + (lambda _ + (invoke "make" "info") + ;; Move the info file to lisp so that it gets installed by the + ;; emacs-build-system. + (rename-file "docs/forge.info" "lisp/forge.info"))) + (add-after 'build-info-manual 'chdir-lisp + (lambda _ + (chdir "lisp")))))) + (home-page "https://github.com/magit/forge/") + (synopsis "Access Git forges from Magit") + (description "Work with Git forges, such as Github and Gitlab, from the comfort of Magit and the rest of Emacs.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public emacs-matcha (let ((commit "c7df5cf5cdac9ae369e241342389ccda0205eab9")) -- cgit 1.4.1 From a5c9843cfea83346c1f4fa2fafe62792f4b314bb Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Tue, 25 May 2021 13:26:45 +0200 Subject: gnu: emacs-magit: Update to 3.0.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-magit): Update to 3.0.0. [arguments]<#:phases>: Don’t return #t, this will be redundant once the core-updates branch has been merged. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 156 +++++++++++++++++++++------------------------ 1 file changed, 74 insertions(+), 82 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 9d5774d66e..a5d6e2a8a5 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -656,92 +656,84 @@ libgit2 bindings for Emacs, intended to boost the performance of Magit.") (license license:gpl3+)))) (define-public emacs-magit - ;; There hasn't been an official release since 2018-11-16. - (let ((commit "7f486d47fe7042edba8d9a855a4c2c301a30bc6b") - (revision "6")) - (package - (name "emacs-magit") - (version (git-version "2.90.1" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/magit/magit") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "05kyc5y5wa1p3h8j7mbgvfc4zcj998zi26lnnmksj9wnvahzxfms")))) - (build-system emacs-build-system) - (arguments - `(#:emacs ,emacs-no-x ;module support is required - #:tests? #t - #:test-command '("make" "test") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'build-info-manual - (lambda _ - (invoke "make" "info") - ;; Copy info files to the lisp directory, which acts as - ;; the root of the project for the emacs-build-system. - (for-each (lambda (f) - (install-file f "lisp")) - (find-files "Documentation" "\\.info$")) - (chdir "lisp") - #t)) - (add-after 'build-info-manual 'set-magit-version - (lambda _ - (make-file-writable "magit.el") - (emacs-substitute-variables "magit.el" - ("magit-version" ,version)) - #t)) - (add-after 'set-magit-version 'patch-exec-paths - (lambda* (#:key inputs #:allow-other-keys) - (let ((perl (assoc-ref inputs "perl"))) - (make-file-writable "magit-sequence.el") - (emacs-substitute-variables "magit-sequence.el" - ("magit-perl-executable" (string-append perl "/bin/perl"))) - #t))) - (add-before 'check 'configure-git - (lambda _ - ;; Otherwise some tests fail with error "unable to auto-detect - ;; email address". - (setenv "HOME" (getcwd)) - (invoke "git" "config" "--global" "user.name" "toto") - (invoke "git" "config" "--global" "user.email" - "toto@toto.com"))) - (add-after 'configure-git 'disable-tramp-test - (lambda _ - ;; There is an issue causing TRAMP to fail in the build - ;; environment. Setting the tramp-remote-shell parameter of - ;; the sudo-method to the file name of the shell didn't help. - (chdir "..") - (substitute* "t/magit-tests.el" - (("^\\(ert-deftest magit-toplevel:tramp.*" all) - (string-append all " (skip-unless nil)"))) - #t)) - (add-before 'install 'enter-lisp-directory - (lambda _ - (chdir "lisp") - #t))))) - (native-inputs - `(("texinfo" ,texinfo))) - (inputs - `(("git" ,git) - ("perl" ,perl))) - (propagated-inputs - `(("emacs-dash" ,emacs-dash) - ("emacs-libgit" ,emacs-libgit) - ("emacs-transient" ,emacs-transient) - ("emacs-with-editor" ,emacs-with-editor))) - (home-page "https://magit.vc/") - (synopsis "Emacs interface for the Git version control system") - (description - "With Magit, you can inspect and modify your Git repositories + (package + (name "emacs-magit") + (version "3.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/magit/magit") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0dbp3gx43ipxv8zg9m0hfhksz85rnkikaq35rx705qqz6xq6xq9m")))) + (build-system emacs-build-system) + (arguments + `(#:emacs ,emacs-no-x ;module support is required + #:tests? #t + #:test-command '("make" "test") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'build-info-manual + (lambda _ + (invoke "make" "info") + ;; Copy info files to the lisp directory, which acts as + ;; the root of the project for the emacs-build-system. + (for-each (lambda (f) + (install-file f "lisp")) + (find-files "Documentation" "\\.info$")) + (chdir "lisp"))) + (add-after 'build-info-manual 'set-magit-version + (lambda _ + (make-file-writable "magit.el") + (emacs-substitute-variables "magit.el" + ("magit-version" ,version)))) + (add-after 'set-magit-version 'patch-exec-paths + (lambda* (#:key inputs #:allow-other-keys) + (let ((perl (assoc-ref inputs "perl"))) + (make-file-writable "magit-sequence.el") + (emacs-substitute-variables "magit-sequence.el" + ("magit-perl-executable" (string-append perl "/bin/perl")))))) + (add-before 'check 'configure-git + (lambda _ + ;; Otherwise some tests fail with error "unable to auto-detect + ;; email address". + (setenv "HOME" (getcwd)) + (invoke "git" "config" "--global" "user.name" "toto") + (invoke "git" "config" "--global" "user.email" + "toto@toto.com"))) + (add-after 'configure-git 'disable-tramp-test + (lambda _ + ;; There is an issue causing TRAMP to fail in the build + ;; environment. Setting the tramp-remote-shell parameter of + ;; the sudo-method to the file name of the shell didn't help. + (chdir "..") + (substitute* "t/magit-tests.el" + (("^\\(ert-deftest magit-toplevel:tramp.*" all) + (string-append all " (skip-unless nil)"))))) + (add-before 'install 'enter-lisp-directory + (lambda _ + (chdir "lisp")))))) + (native-inputs + `(("texinfo" ,texinfo))) + (inputs + `(("git" ,git) + ("perl" ,perl))) + (propagated-inputs + `(("emacs-dash" ,emacs-dash) + ("emacs-libgit" ,emacs-libgit) + ("emacs-transient" ,emacs-transient) + ("emacs-with-editor" ,emacs-with-editor))) + (home-page "https://magit.vc/") + (synopsis "Emacs interface for the Git version control system") + (description + "With Magit, you can inspect and modify your Git repositories with Emacs. You can review and commit the changes you have made to the tracked files, for example, and you can browse the history of past changes. There is support for cherry picking, reverting, merging, rebasing, and other common Git operations.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public emacs-magit-svn (let ((commit "9e33ceee32f665db59909e1c00a667ccdd04178f")) -- cgit 1.4.1 From bc251bc7e21561fb8636a40df0434dbda188815b Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Tue, 25 May 2021 14:09:27 +0200 Subject: gnu: emacs-transient: Update to 0.3.4. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-transient): Update to 0.3.4. [arguments]<#:phases>: Don’t return #t, this will be redundant once core-updates gets merged. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a5d6e2a8a5..0d7a8d469f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -22921,7 +22921,7 @@ as Emacs Lisp.") (define-public emacs-transient (package (name "emacs-transient") - (version "0.3.2") + (version "0.3.4") (source (origin (method git-fetch) (uri (git-reference @@ -22930,7 +22930,7 @@ as Emacs Lisp.") (file-name (git-file-name name version)) (sha256 (base32 - "1766hdqzg95k62nqhadfv502mpnjlx1l59ppqmc6r0las82dc6a8")))) + "16z0j69sk7k51sd1vri3y2v0xjj0w7wpf5mmwnsxp8y6d3m0yjbv")))) (build-system emacs-build-system) (arguments `(#:tests? #f ;no test suite @@ -22941,12 +22941,10 @@ as Emacs Lisp.") (invoke "make" "info") ;; Move the info file to lisp so that it gets installed by the ;; emacs-build-system. - (rename-file "docs/transient.info" "lisp/transient.info") - #t)) + (rename-file "docs/transient.info" "lisp/transient.info"))) (add-after 'build-info-manual 'enter-lisp-directory (lambda _ - (chdir "lisp") - #t))))) + (chdir "lisp")))))) (native-inputs `(("texinfo" ,texinfo))) (propagated-inputs -- cgit 1.4.1 From a866667f55a72300a98ba004fbabf4f96113f0c1 Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Wed, 26 May 2021 09:36:49 +0200 Subject: gnu: Add emacs-org-inline-pdf. * gnu/packages/emacs-xyz.scm (emacs-org-inline-pdf): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 0d7a8d469f..decd9c0b48 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -4627,6 +4627,36 @@ strike through completed TODO headings, changes Org blocks, changes Org check boxes, and more.") (license license:gpl3+)))) +(define-public emacs-org-inline-pdf + (package + (name "emacs-org-inline-pdf") + (version "0.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/shg/org-inline-pdf.el") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1qc92xvgxmnwjixk8bxwbc1l1jj0qk9dg73jyaip6lk4g0wjk6xf")))) + (build-system emacs-build-system) + (inputs + `(("pdf2svg" ,pdf2svg))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-exec-paths + (lambda* (#:key inputs #:allow-other-keys) + (let ((pdf2svg (assoc-ref inputs "pdf2svg"))) + (substitute* "org-inline-pdf.el" + (("\"pdf2svg\"") (string-append "\"" pdf2svg "/bin/pdf2svg\""))))))))) + (home-page "https://github.com/shg/org-inline-pdf.el") + (synopsis "Inline PDF previewing for Org") + (description "This package provides a minor mode that enables +inline PDF preview in Org buffers by using pdf2svg.") + (license license:gpl3+))) + (define-public emacs-org-rich-yank (package (name "emacs-org-rich-yank") -- cgit 1.4.1 From da08378aa48261a9df24d50606346b47bd2632b9 Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Tue, 25 May 2021 23:48:09 +0200 Subject: gnu: emacs-shell-command+: Use Git repo instead of ELPA URL. * emacs-xyz.scm (emacs-shell-command+)[source]: Use Git repository instead of the unstable ELPA URL. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index decd9c0b48..329ba42062 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -27371,11 +27371,12 @@ Features: (name "emacs-shell-command+") (version "2.2.0") (source (origin - (method url-fetch) - (uri (string-append "https://elpa.gnu.org/packages/" - "shell-command+-" version ".tar")) + (method git-fetch) + (uri (git-reference + (url "https://git.sr.ht/~zge/bang") + (commit version))) (sha256 - (base32 "1ms2xk7xfgd3ngwm90hnmlxwpvyb167bislc2wr3ilfrirbbw476")))) + (base32 "1micvz6smhjma7qbka8h3w0crb3sgrxf9lz2548iqfgww50gb0lj")))) (build-system emacs-build-system) (home-page "http://elpa.gnu.org/packages/shell-command+.html") (synopsis "Extended Emacs @code{shell-command}") -- cgit 1.4.1 From 12bdba70354b234a0d733e180be5455176754a68 Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Wed, 28 Apr 2021 00:12:20 +0800 Subject: gnu: Add rust-ordered-float-2. * gnu/packages/crates-io.scm (rust-ordered-float-2): New variable. (rust-ordered-float-1): Inherit from above. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 25 +++++++++++++++++++++---- 1 file changed, 21 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 318b2c695b..1b4e553559 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -27107,10 +27107,10 @@ system for OpenSSL.") PartialOrd types, like floats.") (license (list license:expat license:asl2.0)))) -(define-public rust-ordered-float-1 +(define-public rust-ordered-float-2 (package (name "rust-ordered-float") - (version "1.0.2") + (version "2.1.1") (source (origin (method url-fetch) @@ -27119,10 +27119,12 @@ PartialOrd types, like floats.") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0625x96987kspdxbikry5mb7hsf5pdc5bbanxd8wjwqlx0ar71hq")))) + "0632g8bacvras6nig1bb1ihgc560476jkrb3is6n542ll86q8vvn")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs + `(#:skip-build? + #t + #:cargo-inputs (("rust-num-traits" ,rust-num-traits-0.2) ("rust-serde" ,rust-serde-1)) #:cargo-development-inputs @@ -27133,6 +27135,21 @@ PartialOrd types, like floats.") "This package provides wrappers for total ordering on floats in Rust.") (license license:expat))) +(define-public rust-ordered-float-1 + (package + (inherit rust-ordered-float-2) + (name "rust-ordered-float") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "ordered-float" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0625x96987kspdxbikry5mb7hsf5pdc5bbanxd8wjwqlx0ar71hq")))))) + (define-public rust-ordermap-0.3 (package (name "rust-ordermap") -- cgit 1.4.1 From 510b9ff26f907ac785dfe18ce15c1e7682593f74 Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Wed, 28 Apr 2021 00:12:21 +0800 Subject: gnu: Add rust-hyphenation-commons-0.8. * gnu/packages/crates-io.scm (rust-hyphenation-commons-0.8): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 1b4e553559..f281f4de6d 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -19132,6 +19132,34 @@ with hyper.") #:cargo-development-inputs (("rust-tokio" ,rust-tokio-0.1)))))) +(define-public rust-hyphenation-commons-0.8 + (package + (name "rust-hyphenation-commons") + (version "0.8.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "hyphenation_commons" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "089jv1pr718aq0yjfcv6x0zljw9f73jm15khdsydzfln3ci7n4hj")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? + #t + #:cargo-inputs + (("rust-fst" ,rust-fst-0.4) + ("rust-serde" ,rust-serde-1)))) + (home-page + "https://github.com/tapeinosyne/hyphenation") + (synopsis + "Proemial code for the @code{hyphenation} library") + (description + "This package provides a proemial code for the @code{hyphenation} library.") + (license (list license:asl2.0 license:expat)))) + (define-public rust-ident-case-1 (package (name "rust-ident-case") -- cgit 1.4.1 From 8de658d54a634a3005d077d192ac43430719be92 Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Wed, 28 Apr 2021 00:12:22 +0800 Subject: gnu: Add rust-hyphenation-0.8. * gnu/packages/crates-io.scm (rust-hyphenation-0.8): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index f281f4de6d..47f5ad2ab9 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -19160,6 +19160,46 @@ with hyper.") "This package provides a proemial code for the @code{hyphenation} library.") (license (list license:asl2.0 license:expat)))) +(define-public rust-hyphenation-0.8 + (package + (name "rust-hyphenation") + (version "0.8.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "hyphenation" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "117h952d2zlpyqmy0kb49wb42rd3l5m5kl3ldfhgygv6lin09b2w")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? + #t + #:cargo-inputs + (("rust-bincode" ,rust-bincode-1) + ("rust-bincode" ,rust-bincode-1) + ("rust-fst" ,rust-fst-0.4) + ("rust-fst" ,rust-fst-0.4) + ("rust-hyphenation-commons" + ,rust-hyphenation-commons-0.8) + ("rust-hyphenation-commons" + ,rust-hyphenation-commons-0.8) + ("rust-pocket-resources" + ,rust-pocket-resources-0.3) + ("rust-serde" ,rust-serde-1) + ("rust-serde" ,rust-serde-1) + ("rust-unicode-normalization" + ,rust-unicode-normalization-0.1)))) + (home-page + "https://github.com/tapeinosyne/hyphenation") + (synopsis + "Knuth-Liang hyphenation for a variety of languages") + (description + "This package provides a Knuth-Liang hyphenation for a variety of languages.") + (license (list license:asl2.0 license:expat)))) + (define-public rust-ident-case-1 (package (name "rust-ident-case") -- cgit 1.4.1 From 754d009a768c31e00c1f085b2e4291f6e2fea088 Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Wed, 28 Apr 2021 00:12:23 +0800 Subject: gnu: Add rust-textwrap-0.12. * gnu/packages/crates-io.scm (rust-textwrap-0.12): New variable. (rust-textwrap-0.11): Inherit from above. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 56 ++++++++++++++++++++++++++++++++-------------- 1 file changed, 39 insertions(+), 17 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 47f5ad2ab9..579a9994f2 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -42421,19 +42421,49 @@ for TLS).") unstable language features.") (license (list license:expat license:asl2.0)))) +(define-public rust-textwrap-0.12 + (package + (name "rust-textwrap") + (version "0.12.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "textwrap" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "12978qmkl5gcp94lxndpvp9qxq8mxp7hm9xbrw3422dgikchhc10")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-hyphenation" ,rust-hyphenation-0.8) + ("rust-terminal-size" ,rust-terminal-size-0.1) + ("rust-unicode-width" ,rust-unicode-width-0.1)))) + (home-page + "https://github.com/mgeisler/textwrap") + (synopsis "Library for word wrapping, indenting, and dedenting strings") + (description + "Textwrap is a small library for word wrapping, indenting, and dedenting +strings. You can use it to format strings (such as help and error messages) +for display in commandline applications. It is designed to be efficient and +handle Unicode characters correctly.") + (license license:expat))) + (define-public rust-textwrap-0.11 (package + (inherit rust-textwrap-0.12) (name "rust-textwrap") (version "0.11.0") (source - (origin - (method url-fetch) - (uri (crate-uri "textwrap" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "0q5hky03ik3y50s9sz25r438bc4nwhqc6dqwynv4wylc807n29nk")))) - (build-system cargo-build-system) + (origin + (method url-fetch) + (uri (crate-uri "textwrap" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0q5hky03ik3y50s9sz25r438bc4nwhqc6dqwynv4wylc807n29nk")))) (arguments `(#:skip-build? #t #:cargo-inputs @@ -42444,15 +42474,7 @@ unstable language features.") (;("rust-lipsum" ,rust-lipsum-0.6) ("rust-rand" ,rust-rand-0.6) ("rust-rand-xorshift" ,rust-rand-xorshift-0.1) - ("rust-version-sync" ,rust-version-sync-0.6)))) - (home-page "https://github.com/mgeisler/textwrap") - (synopsis "Library for word wrapping, indenting, and dedenting strings") - (description - "Textwrap is a small library for word wrapping, indenting, and dedenting -strings. You can use it to format strings (such as help and error messages) -for display in commandline applications. It is designed to be efficient and -handle Unicode characters correctly.") - (license license:expat))) + ("rust-version-sync" ,rust-version-sync-0.6)))))) (define-public rust-thin-slice-0.1 (package -- cgit 1.4.1 From e88170478767458b688595f09e6df0b5f3180b16 Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Wed, 28 Apr 2021 00:12:24 +0800 Subject: gnu: Add rust-os-str-bytes-2. * gnu/packages/crates-io.scm (rust-os-str-bytes-2): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 579a9994f2..7049b91028 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -27278,6 +27278,30 @@ under its new name.") "A cross-platform library for opening OS pipes.") (license license:expat))) +(define-public rust-os-str-bytes-2 + (package + (name "rust-os-str-bytes") + (version "2.4.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "os_str_bytes" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "11agh8n3x2l4sr3sxvx6byc1j3ryb1g6flb1ywn0qhq7xv1y3cmg")))) + (build-system cargo-build-system) + (arguments `(#:skip-build? #t)) + (home-page + "https://github.com/dylni/os_str_bytes") + (synopsis + "Traits for converting between byte sequences and platform-native strings") + (description + "This package provides a traits for converting between byte sequences and +platform-native strings.") + (license (list license:expat license:asl2.0)))) + (define-public rust-output-vt100-0.1 (package (name "rust-output-vt100") -- cgit 1.4.1 From d45b6d9d58dd2d83d66dd3d5d213f687a0a82a5f Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Wed, 28 Apr 2021 00:12:25 +0800 Subject: gnu: Add rust-strsim-0.10. * gnu/packages/crates-io.scm (rust-strsim-0.10): New variable. (rust-strsim-0.9): Inherit from above. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 33 ++++++++++++++++++++++++--------- 1 file changed, 24 insertions(+), 9 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 7049b91028..3bda586f42 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -40413,18 +40413,19 @@ and write it somewhere that does not easily support them, such as a log file.") (license (list license:asl2.0 license:expat)))) -(define-public rust-strsim-0.9 +(define-public rust-strsim-0.10 (package (name "rust-strsim") - (version "0.9.3") + (version "0.10.0") (source - (origin - (method url-fetch) - (uri (crate-uri "strsim" version)) - (file-name (string-append name "-" version ".crate")) - (sha256 - (base32 - "0k497pv882qn3q977ckznm13vxx927g8s1swvcv68j3c1pccwik4")))) + (origin + (method url-fetch) + (uri (crate-uri "strsim" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "08s69r4rcrahwnickvi0kq49z524ci50capybln83mg6b473qivk")))) (build-system cargo-build-system) (home-page "https://github.com/dguo/strsim-rs") (synopsis "Rust implementations of string similarity metrics") @@ -40433,6 +40434,20 @@ metrics. It includes Hamming, Levenshtein, OSA, Damerau-Levenshtein, Jaro, and Jaro-Winkler.") (license license:expat))) +(define-public rust-strsim-0.9 + (package + (inherit rust-strsim-0.10) + (name "rust-strsim") + (version "0.9.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "strsim" version)) + (file-name (string-append name "-" version ".crate")) + (sha256 + (base32 + "0k497pv882qn3q977ckznm13vxx927g8s1swvcv68j3c1pccwik4")))))) + (define-public rust-strsim-0.8 (package (inherit rust-strsim-0.9) -- cgit 1.4.1 From c0371bd0b211903e33e86e7bc81c74592f18345b Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Wed, 28 Apr 2021 00:12:26 +0800 Subject: gnu: Add rust-clap-derive-3. * gnu/packages/crates-io.scm (rust-clap-derive-3): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 3bda586f42..ba60eecd55 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -7088,6 +7088,37 @@ traits.") ("rust-libc" ,rust-libc-0.2) ("rust-libloading" ,rust-libloading-0.3)))))) +(define-public rust-clap-derive-3 + (package + (name "rust-clap-derive") + (version "3.0.0-beta.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "clap_derive" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "18cn82jhcha7m0nkpi1a03jx8k7aaq5kxfcxnsqpaa8ih5dp23rp")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-heck" ,rust-heck-0.3) + ("rust-proc-macro-error" + ,rust-proc-macro-error-1) + ("rust-proc-macro2" ,rust-proc-macro2-1) + ("rust-quote" ,rust-quote-1) + ("rust-syn" ,rust-syn-1)))) + (home-page "https://clap.rs/") + (synopsis + "Parse command line argument by defining a struct, derive crate") + (description + "This package provides a parse command line argument by defining a struct, +derive crate.") + (license (list license:expat license:asl2.0)))) + (define-public rust-clap-2 (package (name "rust-clap") -- cgit 1.4.1 From 0413240e3dc48b7bc28b89c87550728cd154022f Mon Sep 17 00:00:00 2001 From: Zheng Junjie <873216071@qq.com> Date: Wed, 28 Apr 2021 00:12:27 +0800 Subject: gnu: Add rust-clap-3. * gnu/packages/crates-io.scm (rust-clap-3): New variable. (rust-clap-2): Inherit from above. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 61 ++++++++++++++++++++++++++++++++++++---------- 1 file changed, 48 insertions(+), 13 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index ba60eecd55..8b17c35f24 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -7119,19 +7119,59 @@ traits.") derive crate.") (license (list license:expat license:asl2.0)))) +(define-public rust-clap-3 + (package + (name "rust-clap") + (version "3.0.0-beta.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "clap" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0hm1kivw6190rxbfqhdr4hqwlrijvwh90i3d9dyyw0d5k0chdlab")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-atty" ,rust-atty-0.2) + ("rust-bitflags" ,rust-bitflags-1) + ("rust-clap-derive" ,rust-clap-derive-3) + ("rust-indexmap" ,rust-indexmap-1) + ("rust-os-str-bytes" ,rust-os-str-bytes-2) + ("rust-strsim" ,rust-strsim-0.10) + ("rust-termcolor" ,rust-termcolor-1) + ("rust-terminal-size" ,rust-terminal-size-0.1) + ("rust-textwrap" ,rust-textwrap-0.12) + ("rust-unicode-width" ,rust-unicode-width-0.1) + ("rust-vec-map" ,rust-vec-map-0.8) + ("rust-yaml-rust" ,rust-yaml-rust-0.4)) + #:cargo-development-inputs + (("rust-criterion" ,rust-criterion-0.3) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-regex" ,rust-regex-1) + ("rust-version-sync" ,rust-version-sync-0.8)))) + (home-page "https://clap.rs/") + (synopsis "Command Line Argument Parser") + (description + "This package provides a simple to use, efficient, and full-featured +Command Line Argument Parser.") + (license (list license:expat license:asl2.0)))) + (define-public rust-clap-2 (package + (inherit rust-clap-3) (name "rust-clap") (version "2.33.3") (source - (origin - (method url-fetch) - (uri (crate-uri "clap" version)) - (file-name (string-append name "-" version ".crate")) - (sha256 - (base32 - "00i065a58987k1sbzqmlz721rw521zcg08jmsh40gi3khp3qmr9p")))) - (build-system cargo-build-system) + (origin + (method url-fetch) + (uri (crate-uri "clap" version)) + (file-name (string-append name "-" version ".crate")) + (sha256 + (base32 + "00i065a58987k1sbzqmlz721rw521zcg08jmsh40gi3khp3qmr9p")))) (arguments `(#:cargo-inputs (("rust-ansi-term" ,rust-ansi-term-0.11) @@ -7148,11 +7188,6 @@ derive crate.") (("rust-lazy-static" ,rust-lazy-static-1) ("rust-regex" ,rust-regex-1) ("rust-version-sync" ,rust-version-sync-0.8)))) - (home-page "https://clap.rs/") - (synopsis "Command Line Argument Parser") - (description - "This package provides a simple to use, efficient, and full-featured -Command Line Argument Parser.") (license license:expat))) (define-public rust-clicolors-control-1 -- cgit 1.4.1 From a721db8e3bafe3f09257263771ab18cf2f9c95be Mon Sep 17 00:00:00 2001 From: Zheng junjie <873216071@qq.com> Date: Wed, 28 Apr 2021 00:12:28 +0800 Subject: gnu: Add rust-askama-escape-0.10. * gnu/packages/crates-io.scm (rust-askama-escape-0.10): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 8b17c35f24..7424d24190 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -2194,6 +2194,29 @@ ArrayVec and ArrayString.") ("rust-matches" ,rust-matches-0.1) ("rust-serde-test" ,rust-serde-test-1)))))) +(define-public rust-askama-escape-0.10 + (package + (name "rust-askama-escape") + (version "0.10.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "askama_escape" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1ys6wcrkpzygk6r93zd0rhinhy89rraarl0m4afwi023m70hihch")))) + (build-system cargo-build-system) + (arguments `(#:skip-build? #t)) + (home-page "https://github.com/djc/askama") + (synopsis + "Optimized HTML escaping code, extracted from Askama") + (description + "This package provides a optimized HTML escaping code, extracted from +Askama.") + (license (list license:expat license:asl2.0)))) + (define-public rust-as-slice-0.1 (package (name "rust-as-slice") -- cgit 1.4.1 From eb3799e8225809303f70d3cef80ac02c69b875a3 Mon Sep 17 00:00:00 2001 From: Zheng junjie <873216071@qq.com> Date: Wed, 28 Apr 2021 00:12:29 +0800 Subject: gnu: Add rust-askama-shared-0.11. * gnu/packages/crates-io.scm (rust-askama-shared-0.11): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 7424d24190..fe204abb3e 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -2217,6 +2217,42 @@ ArrayVec and ArrayString.") Askama.") (license (list license:expat license:asl2.0)))) +(define-public rust-askama-shared-0.11 + (package + (name "rust-askama-shared") + (version "0.11.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "askama_shared" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1g3ksf5is0qwx9rd5lxn5gbvxfcpby5gl9cahg26wl1w1xzbg0i5")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-askama-escape" ,rust-askama-escape-0.10) + ("rust-humansize" ,rust-humansize-1) + ("rust-nom" ,rust-nom-6) + ("rust-num-traits" ,rust-num-traits-0.2) + ("rust-percent-encoding" + ,rust-percent-encoding-2) + ("rust-proc-macro2" ,rust-proc-macro2-1) + ("rust-quote" ,rust-quote-1) + ("rust-serde" ,rust-serde-1) + ("rust-serde-derive" ,rust-serde-derive-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-serde-yaml" ,rust-serde-yaml-0.8) + ("rust-syn" ,rust-syn-1) + ("rust-toml" ,rust-toml-0.5)))) + (home-page "https://github.com/djc/askama") + (synopsis "Shared code for Askama") + (description "This package provides a shared code for Askama.") + (license (list license:expat license:asl2.0)))) + (define-public rust-as-slice-0.1 (package (name "rust-as-slice") -- cgit 1.4.1 From 296b72db466a42931ea6beb9824f29c0b07e84ad Mon Sep 17 00:00:00 2001 From: Zheng junjie <873216071@qq.com> Date: Wed, 28 Apr 2021 00:12:30 +0800 Subject: gnu: Add rust-askama-derive-0.10. * gnu/packages/crates-io.scm (rust-askama-derive-0.10): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index fe204abb3e..e3c02ebf9b 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -2253,6 +2253,32 @@ Askama.") (description "This package provides a shared code for Askama.") (license (list license:expat license:asl2.0)))) +(define-public rust-askama-derive-0.10 + (package + (name "rust-askama-derive") + (version "0.10.5") + (source + (origin + (method url-fetch) + (uri (crate-uri "askama_derive" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "08jmqb4lq5cvfjjcq7kjk5q4589zlsvc3ld35yfjyf4hqb22aafa")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-askama-shared" ,rust-askama-shared-0.11) + ("rust-proc-macro2" ,rust-proc-macro2-1) + ("rust-syn" ,rust-syn-1)))) + (home-page "https://github.com/djc/askama") + (synopsis "Procedural macro package for Askama") + (description + "This package provide procedural macro package for Askama.") + (license (list license:expat license:asl2.0)))) + (define-public rust-as-slice-0.1 (package (name "rust-as-slice") -- cgit 1.4.1 From 8bdc62757d77d607f6a728f0a2fc740791bfcd20 Mon Sep 17 00:00:00 2001 From: Zheng junjie <873216071@qq.com> Date: Wed, 28 Apr 2021 00:12:31 +0800 Subject: gnu: Add rust-askama-0.10. * gnu/packages/crates-io.scm (rust-askama-0.10): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index e3c02ebf9b..6dbdf736ce 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -2279,6 +2279,35 @@ Askama.") "This package provide procedural macro package for Askama.") (license (list license:expat license:asl2.0)))) +(define-public rust-askama-0.10 + (package + (name "rust-askama") + (version "0.10.5") + (source + (origin + (method url-fetch) + (uri (crate-uri "askama" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0d1iwywdgw3nba2iphayw8sfm3s8m9izwnhfar707qa7ds5p766j")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-askama-derive" ,rust-askama-derive-0.10) + ("rust-askama-escape" ,rust-askama-escape-0.10) + ("rust-askama-shared" ,rust-askama-shared-0.11) + ("rust-mime" ,rust-mime-0.3) + ("rust-mime-guess" ,rust-mime-guess-2)))) + (home-page "https://github.com/djc/askama") + (synopsis + "Type-safe, compiled Jinja-like templates for Rust") + (description + "This package provides a type-safe, compiled Jinja-like templates for Rust.") + (license (list license:expat license:asl2.0)))) + (define-public rust-as-slice-0.1 (package (name "rust-as-slice") -- cgit 1.4.1 From cba634e56cc8acb7d48aec7ea65cd6244099f9db Mon Sep 17 00:00:00 2001 From: Zheng junjie <873216071@qq.com> Date: Wed, 28 Apr 2021 00:12:32 +0800 Subject: gnu: Add rust-seq-macro-0.2. * gnu/packages/crates-io.scm (rust-seq-macro-0.2): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 6dbdf736ce..58ff4ca431 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -36963,6 +36963,33 @@ also have to make sure that the wrapper is dropped from within the original thread. If any of these constraints is violated, a panic occurs.") (license (list license:expat license:asl2.0)))) +(define-public rust-seq-macro-0.2 + (package + (name "rust-seq-macro") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "seq-macro" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "168y8k344gssy1q0q6napy8cswgl4hyh2kcim9pk3b9wxbx4g7ss")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-development-inputs + (("rust-rustversion" ,rust-rustversion-1) + ("rust-trybuild" ,rust-trybuild-1)))) + (home-page + "https://github.com/dtolnay/seq-macro") + (synopsis + "Macro to repeat sequentially indexed copies of a fragment of code") + (description + "This package provides a macro to repeat sequentially indexed copies of a +fragment of code.") + (license (list license:expat license:asl2.0)))) + (define-public rust-sequoia-openpgp-0.9 (package (name "rust-sequoia-openpgp") -- cgit 1.4.1 From efff3fd87921b27d536c622410fab2255e5b5457 Mon Sep 17 00:00:00 2001 From: Zheng junjie <873216071@qq.com> Date: Wed, 28 Apr 2021 00:12:33 +0800 Subject: gnu: Add zoxide. * gnu/packages/rust-apps.scm (zoxide): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/rust-apps.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm index d31f95ca05..c75d431c04 100644 --- a/gnu/packages/rust-apps.scm +++ b/gnu/packages/rust-apps.scm @@ -802,3 +802,40 @@ the details of how it was triggered. library and a dynamic library, and a C header to be used by any C (and C-compatible) software.") (license license:expat))) + +(define-public zoxide + (package + (name "zoxide") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "zoxide" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1ih01l3xp8plicxhmyxjkq12ncpdb8954jcj3dh3lwvkhvw29nkk")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-anyhow" ,rust-anyhow-1) + ("rust-askama" ,rust-askama-0.10) + ("rust-bincode" ,rust-bincode-1) + ("rust-clap" ,rust-clap-3) + ("rust-dirs-next" ,rust-dirs-next-2) + ("rust-dunce" ,rust-dunce-1) + ("rust-glob" ,rust-glob-0.3) + ("rust-once-cell" ,rust-once-cell-1) + ("rust-ordered-float" ,rust-ordered-float-2) + ("rust-rand" ,rust-rand-0.7) + ("rust-serde" ,rust-serde-1) + ("rust-tempfile" ,rust-tempfile-3)) + #:cargo-development-inputs + (("rust-assert-cmd" ,rust-assert-cmd-1) + ("rust-seq-macro" ,rust-seq-macro-0.2)))) + (home-page "https://github.com/ajeetdsouza/zoxide/") + (synopsis "Fast way to navigate your filesystem") + (description + "Zoxide is a fast replacement for your @command{cd} command. It keeps +track of the directories you use most frequently, and uses a ranking algorithm +to navigate to the best match.") + (license license:expat))) -- cgit 1.4.1 From d3dcb8c73689b4cf47d1f1707c92b83db145f0e7 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Wed, 26 May 2021 15:36:20 +0200 Subject: gnu: Add lightspark. * gnu/packages/animation.scm (lightspark): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/animation.scm | 78 +++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 77 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/animation.scm b/gnu/packages/animation.scm index 3a915c7fda..bf139ac88e 100644 --- a/gnu/packages/animation.scm +++ b/gnu/packages/animation.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2015, 2017 Ricardo Wurmus ;;; Copyright © 2018–2021 Tobias Geerinckx-Rice ;;; Copyright © 2019 Pkill -9 -;;; Copyright © 2020 Vinicius Monego +;;; Copyright © 2020, 2021 Vinicius Monego ;;; ;;; This file is part of GNU Guix. ;;; @@ -25,10 +25,12 @@ #:use-module (guix git-download) #:use-module (guix utils) #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix build-system meson) #:use-module (gnu packages) #:use-module (gnu packages algebra) + #:use-module (gnu packages assembly) #:use-module (gnu packages autotools) #:use-module (gnu packages boost) #:use-module (gnu packages check) @@ -45,6 +47,8 @@ #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages jemalloc) + #:use-module (gnu packages networking) + #:use-module (gnu packages pcre) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) @@ -320,6 +324,78 @@ audio or video backends, ensuring good performance.") (home-page "https://www.gnu.org/software/gnash/") (license license:gpl3+)))) +;; This package provides a standalone (no browser plugin) version of +;; Lightspark. +(define-public lightspark + (package + (name "lightspark") + (version "0.8.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/lightspark/lightspark") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1mkvjmrjdqx4rsvavd619m144pdfkgs3jb6z7i9fmzyvh4i0jp37")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f ;requires Adobe Flex SDK, see README.tests + ;; Disable browser plugins because neither NPAPI nor PPAPI is + ;; supported in the browsers we have. + #:configure-flags + '("-DCOMPILE_NPAPI_PLUGIN=FALSE" + "-DCOMPILE_PPAPI_PLUGIN=FALSE") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'prepare-build-environment + (lambda _ + ;; Use relative etc path. + (substitute* "CMakeLists.txt" (("\\/etc") "etc")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "./tests"))))))) + (native-inputs + `(("gettext" ,gettext-minimal) + ("glib:bin" ,glib "bin") + ("nasm" ,nasm) + ("perl" ,perl) + ("pkg-config" ,pkg-config) + ("python" ,python-wrapper))) + (inputs + `(("cairo" ,cairo) + ("curl" ,curl) + ("ffmpeg" ,ffmpeg) + ("freeglut" ,freeglut) + ("glew" ,glew) + ("glibmm" ,glibmm) + ("gnash" ,gnash) + ("gnutls" ,gnutls) + ("libjpeg" ,libjpeg-turbo) + ("openssl" ,openssl) + ("pango" ,pango) + ("pcre2" ,pcre2) + ("rtmpdump" ,rtmpdump) + ("sdl2" ,sdl2) + ("sdl2-mixer" ,sdl2-mixer) + ("zlib" ,zlib))) + (home-page "https://lightspark.github.io/") + (synopsis "Flash player implementation") + (description + "Lightspark is a Flash player implementation for playing files in the SWF +format. It supports SWF files written on all versions of the ActionScript +language.") + ;; NOTE: The bundled pugixml is a fork specific to Lightspark and + ;; incompatible with the one we have. + ;; FIXME: we also have jxrlib, but the build fails to find JXRMeta.h so we + ;; use the bundled one for now. + (license (list license:lgpl3+ ;lightspark + license:mpl2.0 ;avmplus + license:bsd-2 ;jxrlib + license:expat)))) ;pugixml, PerlinNoise + (define-public papagayo (let ((commit "e143684b30e59fe4a554f965cb655d23cbe93ee7") (revision "1")) -- cgit 1.4.1 From f5282a17381a0ea2f0aee4702e95bcd24509a256 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 15:37:43 +0200 Subject: gnu: Add r-rcppnumerical. * gnu/packages/cran.scm (r-rcppnumerical): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d013ffd039..4278ef2af2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2989,6 +2989,27 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see safely be interrupted from R.") (license license:expat))) +(define-public r-rcppnumerical + (package + (name "r-rcppnumerical") + (version "0.4-0") + (source (origin + (method url-fetch) + (uri (cran-uri "RcppNumerical" version)) + (sha256 + (base32 + "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen))) + (home-page "https://github.com/yixuan/RcppNumerical") + (synopsis"Numerical computing libraries integration with @code{Rcpp}") + (description "This package provides a collection of libraries for numerical +computing (numerical integration, optimization, etc.) and their integration +with @code{Rcpp}.") + (license license:gpl2+))) + (define-public r-bindr (package (name "r-bindr") -- cgit 1.4.1 From aabea838748bd88008988062f8a9751c33d954e4 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Mon, 26 Apr 2021 23:50:31 +0000 Subject: gnu: muse-sequencer: Update to 4.0.0. * gnu/packages/music.scm (muse-sequencer): Update to 4.0.0. Signed-off-by: Nicolas Goaziou --- gnu/packages/music.scm | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index aed10632cb..b38566450a 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -4770,19 +4770,16 @@ sample library.") (define-public muse-sequencer (package (name "muse-sequencer") - (version "3.1.1") + (version "4.0.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/muse-sequencer/muse") - (commit (string-append "muse_" - (string-map (lambda (c) - (if (char=? c #\.) - #\_ c)) version))))) + (commit version))) (file-name (git-file-name name version)) (sha256 (base32 - "1rasp2v1ds2aw296lbf27rzw0l9fjl0cvbvw85d5ycvh6wkm301p")))) + "1gamr9ln10l26wwyin1a4grrqy6h05qzcgp28wsp85yczkpsh02c")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; there is no test target @@ -4800,7 +4797,7 @@ sample library.") #:phases (modify-phases %standard-phases (add-after 'unpack 'chdir - (lambda _ (chdir "muse3") #t)) + (lambda _ (chdir "src") #t)) (add-after 'chdir 'fix-include (lambda _ (substitute* "muse/driver/rtaudio.h" -- cgit 1.4.1 From 62d6da68d0fc238a949650d6fffaec5895495695 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Mon, 26 Apr 2021 23:53:11 +0000 Subject: gnu: muse-sequencer: Add optional dependencies. * gnu/packages/music.scm (muse-sequencer)[native-inputs]: Add perl, python. [inputs]: Add glib, libinstpatch. Sort alphabetically. [arguments]: Remove "-DENABLE_INSTPATCH=OFF" from #:configure-flags. Signed-off-by: Nicolas Goaziou --- gnu/packages/music.scm | 27 +++++++++++++++------------ 1 file changed, 15 insertions(+), 12 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index b38566450a..6aa368fa82 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -4784,8 +4784,7 @@ sample library.") (arguments `(#:tests? #f ; there is no test target #:configure-flags - (list "-DENABLE_INSTPATCH=OFF" ; FIXME: not packaged - "-DENABLE_VST_NATIVE=OFF" + (list "-DENABLE_VST_NATIVE=OFF" (string-append "-DCMAKE_EXE_LINKER_FLAGS=" "-Wl,-rpath=" (assoc-ref %outputs "out") "/lib/muse-" @@ -4805,26 +4804,30 @@ sample library.") #t))))) (inputs `(("alsa-lib" ,alsa-lib) - ("lash" ,lash) - ("jack" ,jack-1) - ("liblo" ,liblo) ("dssi" ,dssi) + ("fluidsynth" ,fluidsynth) + ("glib" ,glib) + ("jack" ,jack-1) ("ladspa" ,ladspa) - ("lv2" ,lv2) - ("lilv" ,lilv) - ("sord" ,sord) - ("libsndfile" ,libsndfile) + ("lash" ,lash) + ("libinstpatch" ,libinstpatch) + ("liblo" ,liblo) ("libsamplerate" ,libsamplerate) + ("libsndfile" ,libsndfile) + ("lilv" ,lilv) ("lrdf" ,lrdf) - ("fluidsynth" ,fluidsynth) + ("lv2" ,lv2) ("pcre" ,pcre) ("pulseaudio" ,pulseaudio) ; required by rtaudio ("qtbase" ,qtbase) ("qtsvg" ,qtsvg) ("rtaudio" ,rtaudio) - ("rubberband" ,rubberband))) + ("rubberband" ,rubberband) + ("sord" ,sord))) (native-inputs - `(("pkg-config" ,pkg-config) + `(("perl" ,perl) + ("pkg-config" ,pkg-config) + ("python" ,python-wrapper) ("qttools" ,qttools))) (home-page "https://muse-sequencer.github.io/") (synopsis "MIDI/Audio sequencer") -- cgit 1.4.1 From 001bb08cab24f5b1d939e385b0197898c0719ebb Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Mon, 26 Apr 2021 23:53:12 +0000 Subject: gnu: muse-sequencer: Use qt-build-system. * gnu/packages/music.scm (muse-sequencer)[build-system]: Use qt-build-system. Signed-off-by: Nicolas Goaziou --- gnu/packages/music.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 6aa368fa82..fb15a6ea84 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -71,6 +71,7 @@ #:use-module (guix build-system waf) #:use-module (guix build-system trivial) #:use-module (guix build-system go) + #:use-module (guix build-system qt) #:use-module (gnu packages) #:use-module (gnu packages admin) #:use-module (gnu packages algebra) @@ -4780,7 +4781,7 @@ sample library.") (sha256 (base32 "1gamr9ln10l26wwyin1a4grrqy6h05qzcgp28wsp85yczkpsh02c")))) - (build-system cmake-build-system) + (build-system qt-build-system) (arguments `(#:tests? #f ; there is no test target #:configure-flags -- cgit 1.4.1 From 2aa622ca7d82f9093e3dd3b766bbebffa96e904a Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 26 May 2021 15:48:45 +0200 Subject: gnu: zoxide: Add missing space in description. * gnu/packages/rust-apps.scm (zoxide)[description]: Add missing space. --- gnu/packages/rust-apps.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm index c75d431c04..da61b8a582 100644 --- a/gnu/packages/rust-apps.scm +++ b/gnu/packages/rust-apps.scm @@ -835,7 +835,7 @@ C-compatible) software.") (home-page "https://github.com/ajeetdsouza/zoxide/") (synopsis "Fast way to navigate your filesystem") (description - "Zoxide is a fast replacement for your @command{cd} command. It keeps + "Zoxide is a fast replacement for your @command{cd} command. It keeps track of the directories you use most frequently, and uses a ranking algorithm to navigate to the best match.") (license license:expat))) -- cgit 1.4.1 From 4e9bb49688f30724e0459df0457bcdfd783b9b64 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 16:07:17 +0200 Subject: gnu: Add r-structuralvariantannotation. * gnu/packages/bioconductor.scm (r-structuralvariantannotation): New variable. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 596e80a9f9..8ec7a6d90d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2600,6 +2600,36 @@ purposes. The package also contains legacy support for early single-end, ungapped alignment formats.") (license license:artistic2.0))) +(define-public r-structuralvariantannotation + (package + (name "r-structuralvariantannotation") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "StructuralVariantAnnotation" version)) + (sha256 + (base32 + "0ff40703iyf5wk77hbqhphfxnzc2wcshnjhvh66c5l0jvj9z8xvc")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-dplyr" ,r-dplyr) + ("r-genomicranges" ,r-genomicranges) + ("r-rtracklayer" ,r-rtracklayer) + ("r-stringr" ,r-stringr) + ("r-assertthat" ,r-assertthat) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/") + (synopsis "R package designed to simplify structural variant analysis") + (description + "This package contains useful helper functions for dealing with structural +variants in VCF format. The packages contains functions for parsing VCFs from +a number of popular callers as well as functions for dealing with breakpoints +involving two separate genomic loci encoded as GRanges objects.") + (license license:gpl3))) + (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") -- cgit 1.4.1 From cd5d1df15292a1aa59caf4c9ee5efb6e1c3bebc8 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 16:17:06 +0200 Subject: gnu: Add r-hiddenmarkov. * gnu/packages/cran.scm (r-hiddenmarkov): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4278ef2af2..9f89d2f38f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1234,6 +1234,28 @@ and make inference with discrete time and discrete space hidden Markov models.") (license license:gpl2+))) +(define-public r-hiddenmarkov + (package + (name "r-hiddenmarkov") + (version "1.8-13") + (source (origin + (method url-fetch) + (uri (cran-uri "HiddenMarkov" version)) + (sha256 + (base32 + "05dm3nl0ffsz2ziw3bz5bivyxk7r5bxs8xhky3hz660qaqzd51ki")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/HiddenMarkov/") + (synopsis "Hidden markov models for R") + (description "This package contains functions for the analysis of Discrete +Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated +Poisson Process. It includes functions for simulation, parameter estimation, +and the Viterbi algorithm. The algorithms are based of those of Walter +Zucchini.") + (license license:gpl2+))) + (define-public r-httpuv (package (name "r-httpuv") -- cgit 1.4.1 From c66248528707d1b8f9b81236b1220db98fb3b7e7 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 16:21:13 +0200 Subject: gnu: Add r-depmixs4. * gnu/packages/cran.scm (r-depmixs4): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9f89d2f38f..bf793d286a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1130,6 +1130,29 @@ without affecting the current R process at all. This package does exactly that.") (license license:expat))) +(define-public r-depmixs4 + (package + (name "r-depmixs4") + (version "1.5-0") + (source (origin + (method url-fetch) + (uri (cran-uri "depmixS4" version)) + (sha256 + (base32 + "1pacvhw5m4fsk3ysbal50fdqbvlaz8ywyqp6bn1wh42wipqbb2i8")))) + (propagated-inputs + `(("r-nnet" ,r-nnet) + ("r-nlme" ,r-nlme) + ("r-mass" ,r-mass) + ("r-rsolnp" ,r-rsolnp))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/depmixS4/") + (synopsis "Dependent Mixture Models") + (description "This package fits latent (hidden) Markov models on mixed +categorical and continuous (time series) data, otherwise known as dependent +mixture models.") + (license license:gpl2+))) + (define-public r-readxl (package (name "r-readxl") -- cgit 1.4.1 From d80cb98b86d1e060f325b364fc0d375eb9ad55fa Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 16:25:06 +0200 Subject: gnu: Add r-rnmf. * gnu/packages/cran.scm (r-rnmf): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index bf793d286a..4005bacc7b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19761,6 +19761,31 @@ introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.") (license license:bsd-3))) +(define-public r-rnmf + (package + (name "r-rnmf") + (version "0.5.0") + (source (origin + (method url-fetch) + (uri (cran-uri "rNMF" version)) + (sha256 + (base32 + "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597")))) + (build-system r-build-system) + (propagated-inputs + `(("r-knitr" ,r-knitr) + ("r-nnls" ,r-nnls))) + (home-page "https://cran.r-project.org/web/packages/rNMF/") + (synopsis "Robust nonnegative matrix factorization") + (description + "This package provides an implementation of robust nonnegative matrix +factorization (rNMF). The rNMF algorithm decomposes a nonnegative high +dimension data matrix into the product of two low rank nonnegative matrices, +while detecting and trimming outliers. The main function is @code{rnmf()}. +The package also includes a visualization tool, @code{see()}, that arranges +and prints vectorized images.") + (license license:gpl2+))) + (define-public r-randtoolbox (package (name "r-randtoolbox") -- cgit 1.4.1 From 64eda9c881b9d7008ae562dbcd5718ae8cb1a797 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 16:32:25 +0200 Subject: gnu: Add r-tree. * gnu/packages/cran.scm (r-tree): New variable. --- gnu/packages/cran.scm | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4005bacc7b..6405a2d5f9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20494,6 +20494,23 @@ modeling often used in @dfn{analytical customer relationship management} (aCRM).") (license license:gpl2+))) +(define-public r-tree + (package + (name "r-tree") + (version "1.0-40") + (source (origin + (method url-fetch) + (uri (cran-uri "tree" version)) + (sha256 + (base32 + "1rr6ws62j9h36f3nl713f8h3ndkh95mv46l055jvgmby5lw1dazz")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/tree/") + (synopsis "Classification and regression trees") + (description "This package provides procedures to work with classification +and regression trees.") + (license license:gpl2+))) + (define-public r-treeclust (package (name "r-treeclust") -- cgit 1.4.1 From 315472eddd8281a5678c9e5f6fc3ae8afeb97739 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 16:35:25 +0200 Subject: gnu: Add r-heatmap3. * gnu/packages/cran.scm (r-heatmap3): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6405a2d5f9..db7f7f01e3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6396,6 +6396,30 @@ fixed values. Other functions include a custom @code{geom}, and helper functions to enforce symmetric scales or add tags to facetted plots.") (license license:gpl3))) +(define-public r-heatmap3 + (package + (name "r-heatmap3") + (version "1.1.9") + (source + (origin + (method url-fetch) + (uri (cran-uri "heatmap3" version)) + (sha256 + (base32 + "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r")))) + (build-system r-build-system) + (propagated-inputs + `(("r-fastcluster" ,r-fastcluster))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/heatmap3/") + (synopsis "Improved heatmap package") + (description + "This package provides an improved heatmap package. It is completely +compatible with the original R function @code{heatmap}, and provides more +powerful and convenient features.") + (license license:gpl2+))) + (define-public r-heatmaply (package (name "r-heatmaply") -- cgit 1.4.1 From 4fa12759f5589af84da81e3547684053954313ed Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 16:59:17 +0200 Subject: gnu: Add r-visdat. * gnu/packages/cran.scm (r-visdat): New variable. --- gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index db7f7f01e3..5497950313 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25594,6 +25594,35 @@ so that natural sort function arranges a character vector by their numbers, not digit characters.") (license license:bsd-3))) +(define-public r-visdat + (package + (name "r-visdat") + (version "0.5.3") + (source (origin + (method url-fetch) + (uri (cran-uri "visdat" version)) + (sha256 + (base32 + "1ikqp29nncbw1xlwyb9dqqgcdk9q0bs3wxhnhnjpb11vcjv7cz2j")))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-glue" ,r-glue) + ("r-magrittr" ,r-magrittr) + ("r-purrr" ,r-purrr) + ("r-readr" ,r-readr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://visdat.njtierney.com/") + (synopsis "Preliminary Visualisation of Data") + (description "This package provides procedures to create preliminary exploratory +data visualisations of an entire dataset to identify problems or unexpected features +using @code{ggplot2}.") + (license license:expat))) + (define-public r-muhaz (package (name "r-muhaz") -- cgit 1.4.1 From eba5b5cd79c02f487a2b243888d52648e081a468 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Thu, 13 May 2021 20:05:35 -0400 Subject: gnu: gwenhywfar: Update to 5.6.0. * gnu/packages/gnucash.scm (gwenhywfar): Update to 5.6.0. --- gnu/packages/gnucash.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gnucash.scm b/gnu/packages/gnucash.scm index f71e8209fa..6675346f10 100644 --- a/gnu/packages/gnucash.scm +++ b/gnu/packages/gnucash.scm @@ -256,14 +256,14 @@ to be read using the GNOME Yelp program.") (define-public gwenhywfar (package (name "gwenhywfar") - (version "4.99.25rc9") + (version "5.6.0") (source (origin (method url-fetch) (uri (string-append "https://www.aquamaniac.de/rdm/attachments/" - "download/223/gwenhywfar-" version ".tar.gz")) + "download/364/gwenhywfar-" version ".tar.gz")) (sha256 - (base32 "14ws780zfyv9qg41z42hlk8sh31w80w3v8n5riaslqhvvxqbfgkq")))) + (base32 "1isbj4a7vdgagp3kkvx2pjcjy8lba6kzjr11fmr06aci1694dbsp")))) (build-system gnu-build-system) (arguments `(#:configure-flags -- cgit 1.4.1 From 88c442b4afd7a714397561fa98dd0b49ce18f8d5 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Thu, 13 May 2021 19:12:49 -0400 Subject: gnu: aqbanking: Update to 6.3.0. * gnu/packages/gnucash.scm (aqbanking): Update to 6.3.0. --- gnu/packages/gnucash.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gnucash.scm b/gnu/packages/gnucash.scm index 6675346f10..f28c034f55 100644 --- a/gnu/packages/gnucash.scm +++ b/gnu/packages/gnucash.scm @@ -293,14 +293,14 @@ applications and libraries. It is used by AqBanking.") (define-public aqbanking (package (name "aqbanking") - (version "5.99.44beta") + (version "6.3.0") (source (origin (method url-fetch) (uri (string-append "https://www.aquamaniac.de/rdm/attachments/" - "download/224/aqbanking-" version ".tar.gz")) + "download/372/aqbanking-" version ".tar.gz")) (sha256 - (base32 "1cgj8g3wy53galp9pk50a85w0kmwfx3dwl93cbvq6sqb9izxmwdb")))) + (base32 "1k2mhdnk0jc0inq1hmp74m3y7azxrjm8r07x5k1pp4ic0yi5vs50")))) (build-system gnu-build-system) (arguments `(;; Parallel building fails because aqhbci is required before it's -- cgit 1.4.1 From 2a8417d3b2c0256ba0bbb83b4fdfe3cac2f5dbe2 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Mon, 10 May 2021 19:54:12 -0400 Subject: gnu: warzone2100: Update to 4.0.1. * gnu/packages/games.scm (warzone2100): Update to 4.0.1. [arguments]: Disable vulkan backend with "-DWZ_ENABLE_BACKEND_VULKAN=off" configure flag. [inputs]: Add sqlite. --- gnu/packages/games.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index c7e6097bd4..9753f5af47 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -5127,7 +5127,7 @@ in-window at 640x480 resolution or fullscreen.") (define-public warzone2100 (package (name "warzone2100") - (version "3.4.1") + (version "4.0.1") (source (origin (method url-fetch) @@ -5135,7 +5135,7 @@ in-window at 640x480 resolution or fullscreen.") version "/warzone2100_src.tar.xz")) (sha256 - (base32 "0savalmw1kp1sf8vg5aqrl5hc77p4jacxy5y9qj8k2hi2vqdfb7a")) + (base32 "1f8a4kflslsjl8jrryhwg034h1yc9y3y1zmllgww3fqkz3aj4xik")) (modules '((guix build utils))) (snippet '(begin @@ -5149,6 +5149,7 @@ in-window at 640x480 resolution or fullscreen.") (build-system cmake-build-system) (arguments `(#:configure-flags '("-DWZ_DISTRIBUTOR=Guix" + "-DWZ_ENABLE_BACKEND_VULKAN=off" "-DENABLE_DISCORD=off") #:tests? #f ; TODO: Tests seem to be broken, configure.ac is missing. #:phases @@ -5194,6 +5195,7 @@ in-window at 640x480 resolution or fullscreen.") ("qtscript" ,qtscript) ("openssl" ,openssl) ("sdl2" ,sdl2) + ("sqlite" ,sqlite) ("utfcpp" ,utfcpp))) (home-page "https://wz2100.net") (synopsis "3D Real-time strategy and real-time tactics game") -- cgit 1.4.1 From b7664dfb780336114c229683b87d3564e9a72268 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 21:54:13 +0200 Subject: gnu: Add r-rnexml. * gnu/packages/cran.scm (r-rnexml): New variable. --- gnu/packages/cran.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5497950313..19aa2b407b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12525,6 +12525,40 @@ Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007).") (license license:gpl2))) +(define-public r-rnexml + (package + (name "r-rnexml") + (version "2.4.5") + (source (origin + (method url-fetch) + (uri (cran-uri "RNeXML" version)) + (sha256 + (base32 + "1wsl4xq9w5bp3wk69dw57bg0qcw1vs6ajwya4p0w1r00ck5pwrib")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-dplyr" ,r-dplyr) + ("r-httr" ,r-httr) + ("r-lazyeval" ,r-lazyeval) + ("r-plyr" ,r-plyr) + ("r-reshape2" ,r-reshape2) + ("r-stringi" ,r-stringi) + ("r-stringr" ,r-stringr) + ("r-tidyr" ,r-tidyr) + ("r-uuid" ,r-uuid) + ("r-xml" ,r-xml) + ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://docs.ropensci.org/RNeXML/") + (synopsis "Semantically rich I/O for the NeXML Format") + (description "This package provides access to phyloinformatic data in +NeXML format. The package should add new functionality to R such as the +possibility to manipulate NeXML objects in more various and refined way +and compatibility with @code{ape} objects.") + (license license:bsd-3))) + (define-public r-rnifti (package (name "r-rnifti") -- cgit 1.4.1 From 84d551d45ecf360fd0399395330d1eac03cd80e9 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 22:46:06 +0200 Subject: gnu: Add r-howmany. * gnu/packages/cran.scm (r-howmany): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 19aa2b407b..e59431ac5f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1382,6 +1382,29 @@ documents that can be converted to HTML files (e.g., R Markdown) under a given directory.") (license license:expat))) +(define-public r-howmany + (package + (name "r-howmany") + (version "0.3-1") + (source (origin + (method url-fetch) + (uri (cran-uri "howmany" version)) + (sha256 + (base32 + "045ck8qahfg2swbgyf7dpl32ryq1m4sbalhr7m5qdgpm62vz8h7f")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/howmany/") + (synopsis "Lower bound for the number of correct rejections") + (description "When testing multiple hypotheses simultaneously, this package +provides functionality to calculate a lower bound for the number of correct +rejections (as a function of the number of rejected hypotheses), which holds +simultaneously -with high probability- for all possible number of rejections. +As a special case, a lower bound for the total number of false null hypotheses +can be inferred. Dependent test statistics can be handled for multiple tests +of associations. For independent test statistics, it is sufficient to provide +a list of p-values.") + (license license:gpl2+))) + (define-public r-htmltools (package (name "r-htmltools") -- cgit 1.4.1 From 416eaacbb13361e0fa7f1ff573543445269f5e59 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 22:49:45 +0200 Subject: gnu: Add r-locfdr. * gnu/packages/cran.scm (r-locfdr): New variable. --- gnu/packages/cran.scm | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e59431ac5f..266f509732 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13701,6 +13701,23 @@ Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty, Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)") (license license:gpl2+))) +(define-public r-locfdr + (package + (name "r-locfdr") + (version "1.1-8") + (source (origin + (method url-fetch) + (uri (cran-uri "locfdr" version)) + (sha256 + (base32 + "1falkbp2xz07am8jlhwlvyqvxnli4nwl188kd0g58vdfjcjy3mj2")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/locfdr/") + (synopsis "Computes local false discovery rates") + (description "This package can be used to compute local false +discovery rates.") + (license license:gpl2))) + (define-public r-longitudinal (package (name "r-longitudinal") -- cgit 1.4.1 From 22950d66152e1bbd9ab445fc596e1cde85b15807 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 22:58:18 +0200 Subject: gnu: Add r-rncl. * gnu/packages/cran.scm (r-rncl): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 266f509732..efba6e217b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12548,6 +12548,30 @@ Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007).") (license license:gpl2))) +(define-public r-rncl + (package + (name "r-rncl") + (version "0.8.4") + (source (origin + (method url-fetch) + (uri (cran-uri "rncl" version)) + (sha256 + (base32 + "0ss9jqrvv7bhvl5j74cjrp8r866d9dlavrbbfscwz3mhkgfx06bb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-progress" ,r-progress) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/fmichonneau/rncl") + (synopsis "Interface to the Nexus class library") + (description "This package provides an interface to the Nexus class +library which allows parsing of NEXUS, Newick and other phylogenetic tree + file formats. It provides elements of the file that can be used to build + phylogenetic objects such as @code{ape}'s @code{phylo} or @code{phylobase}'s +@code{phylo4(d)}. This functionality is demonstrated with +@code{read_newick_phylo()} and @code{read_nexus_phylo()}.") + (license license:bsd-2))) + (define-public r-rnexml (package (name "r-rnexml") -- cgit 1.4.1 From 9f27579fb9ce4c8f464653e24c507e3e39748f24 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 23:04:12 +0200 Subject: gnu: Add r-phylobase. * gnu/packages/cran.scm (r-phylobase): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index efba6e217b..b40298527c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12572,6 +12572,31 @@ library which allows parsing of NEXUS, Newick and other phylogenetic tree @code{read_newick_phylo()} and @code{read_nexus_phylo()}.") (license license:bsd-2))) +(define-public r-phylobase + (package + (name "r-phylobase") + (version "0.8.10") + (source (origin + (method url-fetch) + (uri (cran-uri "phylobase" version)) + (sha256 + (base32 + "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ade4" ,r-ade4) + ("r-ape" ,r-ape) + ("r-rcpp" ,r-rcpp) + ("r-rncl" ,r-rncl) + ("r-rnexml" ,r-rnexml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/fmichonneau/phylobase") + (synopsis "Base package for phylogenetic structures and comparative data") + (description "This package provides a base @code{S4} class for comparative +methods, incorporating one or more trees and trait data.") + (license license:gpl2+))) + (define-public r-rnexml (package (name "r-rnexml") -- cgit 1.4.1 From 1edec0e8999cf4900fa0eddb4e11a790021a002c Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 23:09:06 +0200 Subject: gnu: Add r-zinbwave. * gnu/packages/bioconductor.scm (r-zinbwave): New variable. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8ec7a6d90d..23a87c3dde 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6629,6 +6629,39 @@ deployed as a centralized bioinformatics resource for use by many users. Currently only Affymetrix oligonucleotide analysis is supported.") (license license:gpl2+))) +(define-public r-zinbwave + (package + (name "r-zinbwave") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "zinbwave" version)) + (sha256 + (base32 + "0m5f0wrk6kg88m41cchjwi4ssi7kr3196m8h9hrhygak964nsd4q")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-edger" ,r-edger) + ("r-genefilter" ,r-genefilter) + ("r-matrix" ,r-matrix) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-softimpute" ,r-softimpute) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/zinbwave") + (synopsis "Zero-inflated negative binomial model for RNA-seq data") + (description "This package implements a general and flexible zero-inflated +negative binomial model that can be used to provide a low-dimensional +representations of single-cell RNA-seq data. The model accounts for zero +inflation (dropouts), over-dispersion, and the count nature of the data. +The model also accounts for the difference in library sizes and optionally +for batch effects and/or other covariates, avoiding the need for pre-normalize +the data.") + (license license:artistic2.0))) + (define-public r-zfpkm (package (name "r-zfpkm") -- cgit 1.4.1 From 2f91ab762827d117fcb9e59e9a4957064ca778c7 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 23:46:32 +0200 Subject: gnu: Add r-benchmarkmedata. * gnu/packages/cran.scm (r-benchmarkmedata): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b40298527c..aba92fdb93 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -351,6 +351,26 @@ easier.") for authoring journal articles and conference submissions.") (license license:gpl3))) +(define-public r-benchmarkmedata + (package + (name "r-benchmarkmedata") + (version "1.0.4") + (source (origin + (method url-fetch) + (uri (cran-uri "benchmarkmeData" version)) + (sha256 + (base32 + "1n4vjkagqlm6kw2hilf4gjfcdjad0bcg652j9nl2ygbq3kdnh1vf")))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/csgillespie/benchmarkme-data") + (synopsis "Data set for the @code{benchmarkme} package") + (description "This pacakge contains the data set for the crowd sourced +benchmarks from running the @code{benchmarkme} package.") + (license license:gpl2+))) + (define-public r-bezier (package (name "r-bezier") -- cgit 1.4.1 From ad827f5bc169e1c87a8fe5538014b5ead94ec850 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 23:47:04 +0200 Subject: gnu: Add r-benchmarkme. * gnu/packages/cran.scm (r-benchmarkme): New variable. --- gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index aba92fdb93..e0b26e870f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -371,6 +371,34 @@ for authoring journal articles and conference submissions.") benchmarks from running the @code{benchmarkme} package.") (license license:gpl2+))) +(define-public r-benchmarkme + (package + (name "r-benchmarkme") + (version "1.0.7") + (source (origin + (method url-fetch) + (uri (cran-uri "benchmarkme" version)) + (sha256 + (base32 + "0ymgsxzrvnpyvs0cff09d3lrkl12qyqx5bwammsc4vgl5ng9p69p")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (propagated-inputs + `(("r-benchmarkmedata" ,r-benchmarkmedata) + ("r-doparallel" ,r-doparallel) + ("r-dplyr" ,r-dplyr) + ("r-foreach" ,r-foreach) + ("r-httr" ,r-httr) + ("r-matrix" ,r-matrix) + ("r-tibble" ,r-tibble))) + (home-page "https://csgillespie.github.io/benchmarkme/") + (synopsis "Crowd-sourced system benchmarks") + (description "This package provides functionality to benchmark your CPU +and compare against other CPUs. Also provides functions for obtaining system +specifications, such as RAM, CPU type, and R version.") + (license license:gpl2+))) + (define-public r-bezier (package (name "r-bezier") -- cgit 1.4.1 From 700b10f1810a90c49c0403cfec40ad3223cbe805 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 23:49:28 +0200 Subject: gnu: Add r-mbkmeans. * gnu/packages/bioconductor.scm (r-mbkmeans): New variable. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 23a87c3dde..39f2a81794 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3075,6 +3075,38 @@ package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.") (license license:gpl2))) +(define-public r-mbkmeans + (package + (name "r-mbkmeans") + (version "1.6.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "mbkmeans" version)) + (sha256 + (base32 + "0rc83mh9xzwczfn88j0xah86ldzi1kdfqgd938nj57ifx3zci4xh")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (propagated-inputs + `(("r-delayedarray" ,r-delayedarray) + ("r-rcpp" ,r-rcpp) + ("r-s4vectors" ,r-s4vectors) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-clusterr" ,r-clusterr) + ("r-benchmarkme" ,r-benchmarkme) + ("r-matrix" ,r-matrix) + ("r-bluster" ,r-bluster) + ("r-beachmat" ,r-beachmat) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-biocparallel" ,r-biocparallel))) + (home-page "https://bioconductor.org/packages/mbkmeans") + (synopsis "Mini-batch k-means clustering for single-cell RNA-seq") + (description "This package implements the mini-batch k-means algorithm for +large datasets, including support for on-disk data representation.") + (license license:expat))) + (define-public r-multtest (package (name "r-multtest") -- cgit 1.4.1 From 2fc74f3176f0aae1269ba9eb754f8d9eb7c3a848 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 23:54:14 +0200 Subject: gnu: Add r-clusterexperiment. * gnu/packages/bioconductor.scm (r-clusterexperiment): New variable. --- gnu/packages/bioconductor.scm | 46 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 39f2a81794..025faadf76 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5293,6 +5293,52 @@ All the visualization methods are developed based on ggplot2 graphics.") profiles (GO and KEGG) of gene and gene clusters.") (license license:artistic2.0))) +(define-public r-clusterexperiment + (package + (name "r-clusterexperiment") + (version "2.10.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "clusterExperiment" version)) + (sha256 + (base32 + "04n3lcm7dh07sjkzyv83m55mx3lz0lkcy8yq9hi0zywqyrhyzz7z")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-biocgenerics" ,r-biocgenerics) + ("r-cluster" ,r-cluster) + ("r-delayedarray" ,r-delayedarray) + ("r-edger" ,r-edger) + ("r-hdf5array" ,r-hdf5array) + ("r-howmany" ,r-howmany) + ("r-kernlab" ,r-kernlab) + ("r-limma" ,r-limma) + ("r-locfdr" ,r-locfdr) + ("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) + ("r-mbkmeans" ,r-mbkmeans) + ("r-nmf" ,r-nmf) + ("r-phylobase" ,r-phylobase) + ("r-pracma" ,r-pracma) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rspectra" ,r-rspectra) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-zinbwave" ,r-zinbwave))) + (home-page "https://bioconductor.org/packages/clusterExperiment/") + (synopsis "Compare clusterings for single-cell sequencing") + (description "This package provides functionality for running and comparing +many different clusterings of single-cell sequencing data or other large mRNA +expression data sets.") + (license license:artistic2.0))) + (define-public r-mlinterfaces (package (name "r-mlinterfaces") -- cgit 1.4.1 From 832f7c3dd2ea7d1ca05781edbf60bb7c80382e40 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Wed, 26 May 2021 22:01:06 +0100 Subject: gnu: guix-build-coordinator: Update to 0-28.675c52d. * gnu/packages/package-management.scm (guix-build-coordinator): Update to 0-28.675c52d. --- gnu/packages/package-management.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 1cea8ed83d..1ff9f4908c 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -1061,8 +1061,8 @@ environments.") (license (list license:gpl3+ license:agpl3+ license:silofl1.1)))) (define-public guix-build-coordinator - (let ((commit "1305724c7ea3c2bb3e557918d5a1b17d572aa110") - (revision "27")) + (let ((commit "675c52d732f504232c0764ba1f03c5c54fd47763") + (revision "28")) (package (name "guix-build-coordinator") (version (git-version "0" revision commit)) @@ -1073,7 +1073,7 @@ environments.") (commit commit))) (sha256 (base32 - "179n33mkhl6f2fv0gyn7sdm3k4hhm1hvca6dgc923d0w7zv4p577")) + "1mbhpvrws4vf2ln3kj0a1j2p9zqvgn3nw3a85zff376s02937yqn")) (file-name (string-append name "-" version "-checkout")))) (build-system gnu-build-system) (arguments -- cgit 1.4.1 From 829610986d7ae1dccbfd9da0be3519b94b09bf61 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 26 May 2021 14:06:18 -0400 Subject: gnu: linux-libre: Update to 5.12.7. * gnu/packages/linux.scm (linux-libre-5.12-version): Update to 5.12.7. (linux-libre-5.12-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index affc3066c0..4124e0746f 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -356,7 +356,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernels. That is, the most recently released major ;; versions that are still supported upstream. -(define-public linux-libre-5.12-version "5.12.6") +(define-public linux-libre-5.12-version "5.12.7") (define deblob-scripts-5.12 (linux-libre-deblob-scripts linux-libre-5.12-version @@ -364,7 +364,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1qp25fd4wgjyk7dzdq9yirm1z5w68sd1p3wv8lch8259i51gwjnf"))) (define-public linux-libre-5.12-pristine-source (let ((version linux-libre-5.12-version) - (hash (base32 "1cdxda5mgdi5dky6hvrq2727rrlw9lnzf30kf3lbiikjybvlqw2b"))) + (hash (base32 "0ircrclggrbmm80vz7irhg73qvhjddsmf7zclw5cqnnmm3qfj8jk"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.12))) -- cgit 1.4.1 From 92d459dff85232527695a96cc0980f54b90215d7 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 26 May 2021 14:06:57 -0400 Subject: gnu: linux-libre 5.10: Update to 5.10.40. * gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.40. (linux-libre-5.10-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 4124e0746f..56edbf28e2 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -372,7 +372,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; -(define-public linux-libre-5.10-version "5.10.39") +(define-public linux-libre-5.10-version "5.10.40") (define deblob-scripts-5.10 (linux-libre-deblob-scripts linux-libre-5.10-version @@ -380,7 +380,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0hh27ccqimagr3aij7ygwikxw66y63sqwd0xlf49bhpjd090r9a7"))) (define-public linux-libre-5.10-pristine-source (let ((version linux-libre-5.10-version) - (hash (base32 "057nnfkbm69ji80rx9lqgmvqsv74x9lcaq3kfs0k91cpr8asaf2p"))) + (hash (base32 "091g9g29m4vh66bxihiylyprb3cxr8cy4m494klb2lkirlx8103l"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.10))) -- cgit 1.4.1 From f9677bf3ea187fc88b8b99ef4f6728a668072372 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 26 May 2021 14:07:15 -0400 Subject: gnu: linux-libre 5.4: Update to 5.4.122. * gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.122. (linux-libre-5.4-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 56edbf28e2..81ec4fc7e5 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -385,7 +385,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.10))) -(define-public linux-libre-5.4-version "5.4.121") +(define-public linux-libre-5.4-version "5.4.122") (define deblob-scripts-5.4 (linux-libre-deblob-scripts linux-libre-5.4-version @@ -393,7 +393,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1xghbbnaisjd0k1klbyn1p7r6r4x5a1bpmkm56a3gh2zvw4s7mj8"))) (define-public linux-libre-5.4-pristine-source (let ((version linux-libre-5.4-version) - (hash (base32 "0prparsdyi8n3cfq3vbhn5var2xcw5dglscxqny19qcplgy2g4wx"))) + (hash (base32 "00g6s3ymriwddshy5sd458b1wfvw2ynxv6dr63ziykwfq50jlr9p"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.4))) -- cgit 1.4.1 From 72538adf6561857749fe8e91a0e2905023524568 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 26 May 2021 14:07:35 -0400 Subject: gnu: linux-libre 4.19: Update to 4.19.192. * gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.192. (linux-libre-4.19-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 81ec4fc7e5..b81c196763 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -398,7 +398,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.4))) -(define-public linux-libre-4.19-version "4.19.191") +(define-public linux-libre-4.19-version "4.19.192") (define deblob-scripts-4.19 (linux-libre-deblob-scripts linux-libre-4.19-version @@ -406,7 +406,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1jiaw0as1ippkrjdpd52657w5mz9qczg3y2hlra7m9k0xawwiqlf"))) (define-public linux-libre-4.19-pristine-source (let ((version linux-libre-4.19-version) - (hash (base32 "1jd97rzv900mnyzps4xmf6k166zrg391vcrbmr5zvcway5qbn9mm"))) + (hash (base32 "1680dz4wjg721a8lqwh6ijd90zcr2f3wzcvhwgn3shbwgjkwsk87"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.19))) -- cgit 1.4.1 From 2239d98578835f4aaa61a3101356ffe51706db51 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 26 May 2021 14:07:56 -0400 Subject: gnu: linux-libre 4.14: Update to 4.14.234. * gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.234. (linux-libre-4.14-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index b81c196763..84f290f4d6 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -411,7 +411,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.19))) -(define-public linux-libre-4.14-version "4.14.233") +(define-public linux-libre-4.14-version "4.14.234") (define deblob-scripts-4.14 (linux-libre-deblob-scripts linux-libre-4.14-version @@ -419,7 +419,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1qij18inijj6c3ma8hv98yjagnzxdxyn134da9fd23ky8q6hbvky"))) (define-public linux-libre-4.14-pristine-source (let ((version linux-libre-4.14-version) - (hash (base32 "0sqikz8cvrjfs46mcqx9gbdfkpdims0m5xxxzwr5vcfph5rdvj26"))) + (hash (base32 "1mwqb9sq6qd9angl3xysdsrfpgppf46g3kiwg1svqgpgrx7cqn1b"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.14))) -- cgit 1.4.1 From aa024b7ccc22337a5c9a2074c2921d8d57673294 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 26 May 2021 14:08:16 -0400 Subject: gnu: linux-libre 4.9: Update to 4.9.270. * gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.270. (linux-libre-4.9-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 84f290f4d6..13c31a8525 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -424,7 +424,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.14))) -(define-public linux-libre-4.9-version "4.9.269") +(define-public linux-libre-4.9-version "4.9.270") (define deblob-scripts-4.9 (linux-libre-deblob-scripts linux-libre-4.9-version @@ -432,7 +432,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0fxajshb75siq39lj5h8xvhdj8lcmddkslwlyj65rhlwk6g2r4b2"))) (define-public linux-libre-4.9-pristine-source (let ((version linux-libre-4.9-version) - (hash (base32 "1pnggwc9i6hka21vvl4yd9pd38hpnym9z56m4mhl970ijl4zywbr"))) + (hash (base32 "0ck5abzpla291gcxrxjindj5szgcvmb2fwfilvdnzc6pnqk00ay3"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.9))) -- cgit 1.4.1 From e7d5ea9275a580d1653b0a21efca93ce07d57de7 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 26 May 2021 14:08:37 -0400 Subject: gnu: linux-libre 4.4: Update to 4.4.270. * gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.270. (linux-libre-4.4-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 13c31a8525..e2c938beab 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -437,7 +437,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.9))) -(define-public linux-libre-4.4-version "4.4.269") +(define-public linux-libre-4.4-version "4.4.270") (define deblob-scripts-4.4 (linux-libre-deblob-scripts linux-libre-4.4-version @@ -445,7 +445,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0hhin1jpfkd6nwrb6xqxjzl3hdxy4pn8a15hy2d3d83yw6pflbsf"))) (define-public linux-libre-4.4-pristine-source (let ((version linux-libre-4.4-version) - (hash (base32 "0qx5zwi2ijwv9jwhs4cz91z7yxy6nd0g8ryzrlg1ar2xyk8w4yh4"))) + (hash (base32 "1lz48gv1v3wvw9xvd3y9q4py7ii1g9fj4dwyvvjdzbipyw7s21pq"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.4))) -- cgit 1.4.1 From 1ab3aab59af43f42113408020cf052389cb6e303 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Wed, 26 May 2021 23:02:50 +0100 Subject: gnu: Add cl-for. * gnu/packages/lisp-xyz.scm: (sbcl-for, ecl-for, cl-for): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index eb431cab11..14e1050316 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -17105,3 +17105,38 @@ Django with a syntax similar to Python Jinja2.") (define-public cl-djula (sbcl-package->cl-source-package sbcl-djula)) + +(define-public sbcl-for + (let ((commit "2e4fcfa0f9c1d2f4559c58cef20ccefa50ba180d") + (revision "1")) + (package + (name "sbcl-for") + (version (git-version "1.1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Shinmera/for") + (commit commit))) + (file-name (git-file-name "for" version)) + (sha256 + (base32 "1akz9ggh33x2cq3h0f1cd0p632v1mbagv3dzsb0r10bwg9lh3nmv")))) + (build-system asdf-build-system/sbcl) + (inputs + `(("documentation-utils" ,sbcl-documentation-utils) + ("form-fiddle" ,sbcl-form-fiddle) + ("lambda-fiddle" ,sbcl-lambda-fiddle))) + (home-page "https://shinmera.github.io/for/") + (synopsis "Extensible iteration macro library") + (description + "For is a library for an extensible iteration macro. It allows you to write +concise looping constructs similar to @code{loop} and @code{iterate}. Unlike +loop however it is extensible and sensible, and unlike iterate it does not +require code-walking and is easier to extend.") + (license license:zlib)))) + +(define-public ecl-for + (sbcl-package->ecl-package sbcl-for)) + +(define-public cl-for + (sbcl-package->cl-source-package sbcl-for)) -- cgit 1.4.1 From 23ab7067f32495a8a02710c08b7cfe0e21be7f3f Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Wed, 26 May 2021 23:05:00 +0100 Subject: gnu: Add cl-flare. * gnu/packages/lisp-xyz.scm: (sbcl-flare, ecl-flare, cl-flare): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 14e1050316..3bf1552d66 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -17140,3 +17140,41 @@ require code-walking and is easier to extend.") (define-public cl-for (sbcl-package->cl-source-package sbcl-for)) + +(define-public sbcl-flare + (let ((commit "4f9f17a4fc5b368c2a1988b9a20288695b8d8c48") + (revision "1")) + (package + (name "sbcl-flare") + (version (git-version "1.1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Shinmera/flare") + (commit commit))) + (file-name (git-file-name "flare" version)) + (sha256 + (base32 "00nm3sjngbflj2gd5q0xs2m136w4kix6krww23nk64pkkyq2fs86")))) + (build-system asdf-build-system/sbcl) + (inputs + `(("3d-vectors" ,sbcl-3d-vectors) + ("array-utils" ,sbcl-array-utils) + ("documentation-utils" ,sbcl-documentation-utils) + ("for" ,sbcl-for) + ("lambda-fiddle" ,sbcl-lambda-fiddle) + ("trivial-garbage" ,sbcl-trivial-garbage))) + (home-page "https://shinmera.github.io/flare/") + (synopsis "Easy particle systems with fine grained control") + (description + "FLARE is a library designed to allow quick and precise particle effect +creations. It does not concern itself with displaying and only with the +management and movement of particles. As such, it can easily be integrated into +any existing or future application.") + (license license:zlib)))) + +(define-public ecl-flare + (sbcl-package->ecl-package sbcl-flare)) + +(define-public cl-flare + (sbcl-package->cl-source-package sbcl-flare)) -- cgit 1.4.1 From c555f54af5faefdfeb9f00abd50c9b82aefe572f Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 27 May 2021 11:24:44 +0200 Subject: gnu: Add perl-bsd-resource. * gnu/packages/perl.scm (perl-bsd-resource): New variable. --- gnu/packages/perl.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 7d3a5f7010..d449abc78c 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -667,6 +667,25 @@ presence, and the first one found is executed. With an optional parameter, all known commands are checked.") (license (package-license perl)))) +(define-public perl-bsd-resource + (package + (name "perl-bsd-resource") + (version "1.2911") + (source + (origin + (method url-fetch) + (uri (string-append + "https://cpan.metacpan.org/authors/id/J/JH/JHI/BSD-Resource-" + version ".tar.gz")) + (sha256 + (base32 "0g8c7825ng2m0yz5sy6838rvfdl8j3vm29524wjgf66ccfhgn74x")))) + (build-system perl-build-system) + (home-page "https://metacpan.org/release/BSD-Resource") + (synopsis "BSD process resource limit and priority functions") + (description "This package provides procedures to get and set resource +limits like @code{getrlimit} and @code{setpriority}.") + (license license:artistic2.0))) + (define-public perl-b-hooks-endofscope (package (name "perl-b-hooks-endofscope") -- cgit 1.4.1 From 12392cff5063c01b8de870ceae99e6e8fbec546f Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 27 May 2021 13:30:48 +0200 Subject: gnu: Add r-princurve. * gnu/packages/cran.scm (r-princurve): New variable. --- gnu/packages/cran.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e0b26e870f..894f2bc4d7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3475,6 +3475,25 @@ statistical functions and other utilities to ease their usage.") quantities.") (license license:expat))) +(define-public r-princurve + (package + (name "r-princurve") + (version "2.1.6") + (source (origin + (method url-fetch) + (uri (cran-uri "princurve" version)) + (sha256 + (base32 + "0wzk329bxljkzz57y220lsfckpsn45w348m6dcxh29zbj0ik65h2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/rcannood/princurve") + (synopsis "Fit a principal curve in arbitrary dimension") + (description "This package provides procedures for fitting a principal +curve to a data matrix in arbitrary dimensions.") + (license license:gpl2))) + (define-public r-reshape (package (name "r-reshape") -- cgit 1.4.1 From 5abf8a56ee90ccb8616bd90082b5655a91bef63e Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 27 May 2021 13:31:29 +0200 Subject: gnu: Add r-slingshot. * gnu/packages/bioconductor.scm (r-slingshot): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 025faadf76..8ca0521578 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2600,6 +2600,37 @@ purposes. The package also contains legacy support for early single-end, ungapped alignment formats.") (license license:artistic2.0))) +(define-public r-slingshot + (package + (name "r-slingshot") + (version "1.8.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "slingshot" version)) + (sha256 + (base32 + "0sz4frlk7c1g8adyfcgi1mf1xsf9n5zib4bw7j9kl711dbhvkqwl")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-igraph" ,r-igraph) + ("r-matrixstats" ,r-matrixstats) + ("r-princurve" ,r-princurve) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/slingshot") + (synopsis "Tools for ordering single-cell sequencing") + (description "This package provides functions for inferring continuous, +branching lineage structures in low-dimensional data. Slingshot was designed +to model developmental trajectories in single-cell RNA sequencing data and +serve as a component in an analysis pipeline after dimensionality reduction +and clustering. It is flexible enough to handle arbitrarily many branching +events and allows for the incorporation of prior knowledge through supervised +graph construction.") + (license license:artistic2.0))) + (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") -- cgit 1.4.1 From cf9ddbd4bcd0f5c76234e03d7986f8639d11bd83 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 27 May 2021 13:40:10 +0200 Subject: gnu: Add r-tradeseq. * gnu/packages/bioconductor.scm (r-tradeseq): New variable. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8ca0521578..b58c5bc11f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5013,6 +5013,51 @@ Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results; and a routine for graphical display.") (license license:gpl2))) +(define-public r-tradeseq + (package + (name "r-tradeseq") + (version "1.4.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tradeSeq" version)) + (sha256 + (base32 + "1ncmvn9kaksismvsjs042xsp8bfq1xnm0ds87dwpk95bnpj96a89")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocparallel" ,r-biocparallel) + ("r-clusterexperiment" ,r-clusterexperiment) + ("r-dplyr" ,r-dplyr) + ("r-edger" ,r-edger) + ("r-ggplot2" ,r-ggplot2) + ("r-igraph" ,r-igraph) + ("r-magrittr" ,r-magrittr) + ("r-mgcv" ,r-mgcv) + ("r-monocle" ,r-monocle) + ("r-pbapply" ,r-pbapply) + ("r-princurve" ,r-princurve) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-s4vectors" ,r-s4vectors) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-slingshot" ,r-slingshot) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tibble" ,r-tibble))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://statomics.github.io/tradeSeq/index.html") + (synopsis "Trajectory-based differential expression analysis") + (description + "This package provides a flexible method for fitting regression models that +can be used to find genes that are differentially expressed along one or +multiple lineages in a trajectory. Based on the fitted models, it uses a +variety of tests suited to answer different questions of interest, e.g. the +discovery of genes for which expression is associated with pseudotime, or which +are differentially expressed (in a specific region) along the trajectory. It +fits a negative binomial generalized additive model (GAM) for each gene, and +performs inference on the parameters of the GAM.") + (license license:expat))) + (define-public r-triform (package (name "r-triform") -- cgit 1.4.1 From 89fd577ec2c0a431d0522617227ee99447b3db6c Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 27 May 2021 13:55:33 +0200 Subject: gnu: Add r-rffc. * gnu/packages/cran.scm (r-rffc): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 894f2bc4d7..56e74da32d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25658,6 +25658,30 @@ maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions.") (license license:gpl2+))) +(define-public r-rffc + (package + (name "r-rffc") + (version "1.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://download.r-forge.r-project.org/src/contrib/" + "rfFC_" version ".tar.gz")) + (sha256 + (base32 + "05x9wgzsmx4vb12lmcspymgmpb2xw8bwryb8ysg7vzg2nkh0ma3g")))) + (build-system r-build-system) + (propagated-inputs + `(("r-randomforest",r-randomforest))) + (home-page "https://r-forge.r-project.org/projects/rffc/") + (synopsis "Random Forest Feature Contributions") + (description "This package provides functions for extracting feature +contributions from a random forest model from package @code{randomForest}. +Feature contributions provide detailed information about the relationship +between data variables and the predicted value returned by random forest +model.") + (license license:gpl2))) + (define-public r-clusterr (package (name "r-clusterr") -- cgit 1.4.1 From e7698cb20a58ec1fc8382ea6ff25f3f9ddaee2b0 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 27 May 2021 14:11:39 +0200 Subject: gnu: Add r-pacman. * gnu/packages/cran.scm (r-pacman): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 56e74da32d..a1c7d4c29b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -719,6 +719,28 @@ provides methods for automatically determining breaks and labels for axes and legends.") (license license:expat))) +(define-public r-pacman + (package + (name "r-pacman") + (version "0.5.1") + (source (origin + (method url-fetch) + (uri (cran-uri "pacman" version)) + (sha256 + (base32 + "0z7gngd6h83cpjhq1vg75wvzhdjbgjh7gj5d4zvvi9gd2lmagjcy")))) + (build-system r-build-system) + (propagated-inputs + `(("r-remotes" ,r-remotes))) + (home-page "https://github.com/trinker/pacman") + (synopsis "Package Management Tool") + (description "This package provides tools to more conveniently perform +tasks associated with add-on packages. @code{pacman} conveniently wraps +library and package related functions and names them in an intuitive and +consistent fashion. It seeks to combine functionality from lower level +functions which can speed up workflow.") + (license license:gpl2))) + (define-public r-pheatmap (package (name "r-pheatmap") -- cgit 1.4.1 From 9bffc2ba4581c2fd975ba7d7cfb170badef56ec3 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 27 May 2021 14:15:59 +0200 Subject: gnu: Add r-memuse. * gnu/packages/cran.scm (r-memuse): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a1c7d4c29b..e99f45ad18 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25274,6 +25274,26 @@ theory; see @url{Strumbel and Kononenko (2014), doi.org/10.1007/s10115-013-0679-x} for details.") (license license:gpl2+))) +(define-public r-memuse + (package + (name "r-memuse") + (version "4.1-0") + (source (origin + (method url-fetch) + (uri (cran-uri "memuse" version)) + (sha256 + (base32 + "1bbjp8y0ji71956fbaxiil7ynq2nkmmgz7i9xps83m3bbp5d3mjq")))) + (properties `((upstream-name . "memuse"))) + (build-system r-build-system) + (home-page "https://github.com/shinra-dev/memuse") + (synopsis "Memory Estimation Utilities") + (description + "This package provides procedures to answer the following questions: +How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is +your current R session using? How much ram do you even have?") + (license license:bsd-2))) + (define-public r-metrics (package (name "r-metrics") -- cgit 1.4.1 From 32cce4215412fc141fdf10eb07ebae51613939a4 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 27 May 2021 14:21:12 +0200 Subject: gnu: Add r-pinfsc50. * gnu/packages/cran.scm (r-pinfsc50): New variable. --- gnu/packages/cran.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e99f45ad18..00ea096bbd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5763,6 +5763,25 @@ columns of data using the full range of colours provided by modern terminals.") (license license:gpl3))) +(define-public r-pinfsc50 + (package + (name "r-pinfsc50") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (cran-uri "pinfsc50" version)) + (sha256 + (base32 + "1547xyxmfb7zi8h9bsm6k67dcw4hpp129xzvmgwfw7r6p4af47zd")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/pinfsc50/") + (synopsis "Genomic data for the plant pathogen Phytophthora infestans") + (description "This package contains genomic data for the plant pathogen +Phytophthora infestans. It includes a variant file, a sequence file and an +annotation file. This package is intended to be used as example data for +packages that work with genomic data.") + (license license:gpl2+))) + (define-public r-uuid (package (name "r-uuid") -- cgit 1.4.1 From c8286c8d4a1a720362b3f87fa19b4d6770c38584 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 27 May 2021 14:26:41 +0200 Subject: gnu: Add r-vcfr. * gnu/packages/cran.scm (r-vcfr): New variable. --- gnu/packages/cran.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 00ea096bbd..94966e8d41 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5286,6 +5286,44 @@ Friendly and is now the main support package for a new book, \"Discrete Data Analysis with R\" by Michael Friendly and David Meyer (2015).") (license license:gpl2))) +(define-public r-vcfr + (package + (name "r-vcfr") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (cran-uri "vcfR" version)) + (sha256 + (base32 + "0lhxb3ac4fafwik9q3cds46svzf0hyca8k54chw3dpk50c0zz1yx")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-dplyr" ,r-dplyr) + ("r-magrittr" ,r-magrittr) + ("r-memuse" ,r-memuse) + ("r-pinfsc50" ,r-pinfsc50) + ("r-rcpp" ,r-rcpp) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-vegan" ,r-vegan) + ("r-viridislite" ,r-viridislite))) + (home-page "https://github.com/knausb/vcfR") + (synopsis "Manipulate and visualize VCF data") + (description "This package facilitates easy manipulation of variant call +format (VCF) data. Functions are provided to rapidly read from and write to +VCF files. Once VCF data is read into R, a parser function extracts matrices +of data. This information can then be used for quality control or other +purposes. Additional functions provide visualization of genomic data. Once +processing is complete data may be written to a VCF file. It also may be +converted into other popular R objects. This package provides a link between +VCF data and familiar R software.") + (license license:gpl3))) + (define-public r-ica (package (name "r-ica") -- cgit 1.4.1 From c7e5007de435af5822ab103f097970d2886d3002 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 27 May 2021 15:05:29 +0200 Subject: gnu: emacs-modus-themes: Update to 1.4.0. * gnu/packages/emacs-xyz.scm (emacs-modus-themes): Update to 1.4.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 329ba42062..5ddeb09230 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -25207,7 +25207,7 @@ Emacs that integrate with major modes like Org-mode.") (define-public emacs-modus-themes (package (name "emacs-modus-themes") - (version "1.3.0") + (version "1.4.0") (source (origin (method git-fetch) @@ -25216,7 +25216,7 @@ Emacs that integrate with major modes like Org-mode.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0dw33kvs6k1a933d64fnrckzhs12d8m03a31cwblm39vmirgmf6y")))) + (base32 "1lw3spg7r7ga8sl2pnr1snviqgbvhxayl1mm7dny720a8mgv49f0")))) (build-system emacs-build-system) (home-page "https://protesilaos.com/modus-themes/") (synopsis "Accessible themes (WCAG AAA)") -- cgit 1.4.1 From 35311e3b25c161175f983be888606b3b371acad0 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 27 May 2021 15:12:52 +0300 Subject: gnu: Add python-simpervisor. * gnu/packages/python-xyz.scm (python-simpervisor): New variable. --- gnu/packages/python-xyz.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 770beb0336..b10b55357f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -24900,6 +24900,41 @@ module patches @code{asyncio} to allow nested use of @code{asyncio.run} and @code{loop.run_until_complete}.") (license license:bsd-3))) +(define-public python-simpervisor + (package + (name "python-simpervisor") + (version "0.4") + (source + (origin + ;; Tests not included in release. + (method git-fetch) + (uri (git-reference + (url "https://github.com/yuvipanda/simpervisor") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1brsisx7saf4ic0dih1n5y7rbdbwn1ywv9pl32bch3061r46prvv")))) + (build-system python-build-system) + (arguments + `(#:tests? #f ; Test suite can't find aiohttp. + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "pytest" "--maxfail" "3" "--verbose")) + #t))))) + (native-inputs + `(("python-aiohttp" ,python-aiohttp) + ("python-pytest" ,python-pytest) + ("python-pytest-asyncio" ,python-pytest-asyncio))) + (home-page "https://github.com/yuvipanda/simpervisor") + (synopsis "Simple async process supervisor") + (description + "This package provides a simple async process supervisor in Python.") + (license license:bsd-3))) + (define-public python-parallel (package (name "python-parallel") -- cgit 1.4.1 From 34ab622dc355e425ae45414cc36cff93ccd5717a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 27 May 2021 15:16:17 +0300 Subject: gnu: Add julia-versionparsing. * gnu/packages/julia-xyz.scm (julia-versionparsing): New variable. --- gnu/packages/julia-xyz.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 38a82c7de2..448197ca06 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1789,6 +1789,31 @@ working with @acronym{URIs,Uniform Resource Identifiers}, as defined in RFC system.") (license license:expat))) +(define-public julia-versionparsing + (package + (name "julia-versionparsing") + (version "1.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaInterop/VersionParsing.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "060s72dsnpavgilf7f7315lw2sn4npk8lkndmj6bg7i23hppiwva")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaInterop/VersionParsing.jl") + (synopsis "Flexible VersionNumber parsing in Julia") + (description "The @code{VersionParsing} package implements flexible parsing +of version-number strings into Julia's built-in @code{VersionNumber} type, via +the @code{vparse(string)} function. Unlike the @code{VersionNumber(string)} +constructor, @code{vparse(string)} can handle version-number strings in a much +wider range of formats than are encompassed by the semver standard. This is +useful in order to support @code{VersionNumber} comparisons applied to +\"foreign\" version numbers from external packages.") + (license license:expat))) + (define-public julia-zipfile (package (name "julia-zipfile") -- cgit 1.4.1 From 114db2b9c40181f6c4c0f7121197b26060b50909 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 27 May 2021 15:52:10 +0300 Subject: gnu: Add julia-invertedindices. * gnu/packages/julia-xyz.scm (julia-invertedindices): New variable. --- gnu/packages/julia-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 448197ca06..c18be17be7 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -919,6 +919,29 @@ conditional ifelse. It is similar to @code{Core.ifelse} but it is extendable.") interfaces with @file{.ini} files.") (license license:expat))) +(define-public julia-invertedindices + (package + (name "julia-invertedindices") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mbauman/InvertedIndices.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1179z20yxnkyziip7gn26wr1g3k3ssl1ci7pig3khc900f62di46")))) + (build-system julia-build-system) + (native-inputs + `(("julia-offsetarrays" ,julia-offsetarrays))) + (home-page "https://github.com/mbauman/InvertedIndices.jl") + (synopsis "Index type that allows for inverted selections") + (description "This package just exports one type: the @code{InvertedIndex}, +or @code{Not} for short. It can wrap any supported index type and may be used +as an index into any @code{AbstractArray} subtype, including OffsetArrays.") + (license license:expat))) + (define-public julia-iocapture (package (name "julia-iocapture") -- cgit 1.4.1 From ced47448b0c6619e8d7cd83823f0fd327dca9f10 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 27 May 2021 15:57:38 +0300 Subject: gnu: Add julia-fuzzycompletions. * gnu/packages/julia-xyz.scm (julia-fuzzycompletions): New variable. --- gnu/packages/julia-xyz.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index c18be17be7..52b94a2932 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -716,6 +716,26 @@ functions (or any callable object, really) using forward mode automatic differentiation (AD).") (license license:expat))) +(define-public julia-fuzzycompletions + (package + (name "julia-fuzzycompletions") + (version "0.4.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JunoLab/FuzzyCompletions.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "07sv88c472n6w4x7diy952igbcfm1s104ysnnvprld83312siw06")))) + (build-system julia-build-system) + (home-page "https://github.com/JunoLab/FuzzyCompletions.jl") + (synopsis "Fuzzy completion provider for Julia") + (description + "FuzzyCompletions provides fuzzy completions for a Julia runtime session.") + (license license:expat))) + (define-public julia-gumbo (package (name "julia-gumbo") -- cgit 1.4.1 From 40a7da2b14b4704bc1c8c2f5fdeb2451b232113c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 27 May 2021 16:00:21 +0300 Subject: gnu: Add julia-tableiointerface. * gnu/packages/julia-xyz.scm (julia-tableiointerface): New variable. --- gnu/packages/julia-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 52b94a2932..a81aa7f0b7 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1756,6 +1756,27 @@ linear algebra operations.") warnings (stderr) or both streams at the same time.") (license license:expat))) +(define-public julia-tableiointerface + (package + (name "julia-tableiointerface") + (version "0.1.6") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/lungben/TableIOInterface.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0p2fi9jbyfg2j6rysv4if7dx8qw2mssb04i75j1zq607j8707kvn")))) + (build-system julia-build-system) + (home-page "https://github.com/lungben/TableIOInterface.jl") + (synopsis "File formats based on file extensions") + (description "This package determines tabular file formats based on file +extensions. It is intended to be the base both for @code{TableIO.jl} and for +the @code{Pluto.jl} tabular data import functionality.") + (license license:expat))) + (define-public julia-unpack (package (name "julia-unpack") -- cgit 1.4.1 From d54d21d0b28443c5e2906faa07531df27ca73704 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 27 May 2021 16:10:59 +0300 Subject: gnu: Add julia-indexing. * gnu/packages/julia-xyz.scm (julia-indexing): New variable. --- gnu/packages/julia-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index a81aa7f0b7..56bd998429 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -919,6 +919,27 @@ conditional ifelse. It is similar to @code{Core.ifelse} but it is extendable.") (description "This package provides a wrapper for Imagemagick.") (license license:expat))) +(define-public julia-indexing + (package + (name "julia-indexing") + (version "1.1.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/andyferris/Indexing.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1s7bz5aaj9sx753pcaixq83jgbk33adxgybpinjgzb9lzdv1ddgx")))) + (build-system julia-build-system) + (home-page "https://github.com/andyferris/Indexing.jl") + (synopsis "Generalized indexing for Julia") + (description "This package defines functions for getting multiple indices +out of dictionaries, tuples, etc, extending this ability beyond +@code{AbstractArray}.") + (license license:expat))) + (define-public julia-inifile (package (name "julia-inifile") -- cgit 1.4.1 From f74305a011ad43c3c53b34ed9514b27aca7e2c30 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 27 May 2021 16:11:45 +0300 Subject: gnu: Add julia-dictionaries. * gnu/packages/julia-xyz.scm (julia-dictionaries): New variable. --- gnu/packages/julia-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 56bd998429..2977be03e7 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -489,6 +489,28 @@ including, @code{CircularBuffer}, @code{Queue}, @code{Stack}, @code{Accumulators}, @code{LinkedLists}, @code{SortedDicts} and many others.") (license license:expat))) +(define-public julia-dictionaries + (package + (name "julia-dictionaries") + (version "0.3.8") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/andyferris/Dictionaries.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1j88f6qa5hqm64n5q3jy08a02gwp7by401s03n5x7575p58iqqh2")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-indexing" ,julia-indexing))) + (home-page "https://github.com/andyferris/Dictionaries.jl") + (synopsis "Alternative interface for dictionaries in Julia") + (description "This package provides an alternative interface for +dictionaries in Julia, for improved productivity and performance.") + (license license:expat))) + (define-public julia-docstringextensions (package (name "julia-docstringextensions") -- cgit 1.4.1 From a033f81099a9ab9255da73c13e5ba95ef37e0b02 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 27 May 2021 16:18:52 +0300 Subject: gnu: Add julia-colorschemes. * gnu/packages/julia-xyz.scm (julia-colorschemes): New variable. --- gnu/packages/julia-xyz.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 2977be03e7..ebc2bb58ef 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -309,6 +309,31 @@ between colors, simulating color blindness, parsing colors, and generating color scales for graphics.") (license license:expat))) +(define-public julia-colorschemes + (package + (name "julia-colorschemes") + (version "3.12.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGraphics/ColorSchemes.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "08k39hbdf3jn0001f7qxa99xvagrnh9764911hs6cmxkvp061sa4")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-colors" ,julia-colors) + ("julia-colortypes" ,julia-colortypes) + ("julia-fixedpointnumbers" ,julia-fixedpointnumbers) + ("julia-staticarrays" ,julia-staticarrays))) + (home-page "https://github.com/JuliaGraphics/ColorSchemes.jl") + (synopsis "Colorschemes, colormaps, gradients, and palettes") + (description "This package provides a collection of colorschemes.") + (license license:expat))) + (define-public julia-colortypes (package (name "julia-colortypes") -- cgit 1.4.1 From f11621f1221530e81731d069c51c00c45907e92b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 27 May 2021 16:19:37 +0300 Subject: gnu: Add julia-plotutils. * gnu/packages/julia-xyz.scm (julia-plotutils): New variable. --- gnu/packages/julia-xyz.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index ebc2bb58ef..986a7cbc15 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1553,6 +1553,33 @@ algorithms, while ensuring that the most efficient implementation is used in actual computation.") (license license:expat))) +(define-public julia-plotutils + (package + (name "julia-plotutils") + (version "1.0.10") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaPlots/PlotUtils.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1jimdkp590g7s33w7i431nn7mp1phjy9gdjs88zyqsmq5hxldacg")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-colors" ,julia-colors) + ("julia-colorschemes" ,julia-colorschemes) + ("julia-reexport" ,julia-reexport))) + (native-inputs + `(("julia-stablerngs" ,julia-stablerngs))) + (home-page "https://github.com/JuliaPlots/PlotUtils.jl") + (synopsis "Helper algorithms for building plotting components") + (description "This package containts generic helper algorithms for building +plotting components.") + (license license:expat))) + (define-public julia-recipesbase (package (name "julia-recipesbase") -- cgit 1.4.1 From 014421ee271f1790d81c9660d34ac26c4f2bf8b6 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 27 May 2021 16:36:12 +0300 Subject: gnu: Add julia-scratch. * gnu/packages/julia-xyz.scm (julia-scratch): New variable. --- gnu/packages/julia-xyz.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 986a7cbc15..551f016929 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1703,6 +1703,34 @@ other power series in @code{h}.") a loadable module.") (license license:expat)))) +(define-public julia-scratch + (package + (name "julia-scratch") + (version "1.0.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaPackaging/Scratch.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "06n0rc7grlg9igkdlrql83q0zpc97bh2hfzj5mw4spfik8ahw2aa")))) + (build-system julia-build-system) + (arguments + `(#:tests? #f)) ; Test suite tries to access the Julia package registry. + (home-page "https://github.com/JuliaPackaging/Scratch.jl") + (synopsis "Scratch spaces for all your persistent mutable data needs") + (description "This repository implements the scratch spaces API for +package-specific mutable containers of data. These spaces can contain datasets, +text, binaries, or any other kind of data that would be convenient to store in +a location specific to your package. As compared to Artifacts, these containers +of data are mutable. Because the scratch space location on disk is not very +user-friendly, scratch spaces should, in general, not be used for a storing +files that the user must interact with through a file browser.") + (license license:expat))) + (define-public julia-sortingalgorithms (package (name "julia-sortingalgorithms") -- cgit 1.4.1 From 1ce87b8159749f5e3ccf237e62b5b55bdb866740 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 24 May 2021 21:15:22 +0200 Subject: gnu: sassc: Update to 3.6.2. * gnu/packages/web.scm (sassc): Update to 3.6.2. --- gnu/packages/web.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 30216911ce..30a12098a0 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -2008,7 +2008,7 @@ stylesheets, you'll need to use another program that uses this library, (define-public sassc (package (name "sassc") - (version "3.6.1") + (version "3.6.2") (source (origin (method git-fetch) (uri (git-reference @@ -2017,7 +2017,7 @@ stylesheets, you'll need to use another program that uses this library, (file-name (git-file-name name version)) (sha256 (base32 - "1sxm54mkhs9m4vnl7vn11y17mhzamc403hv3966j1c7p2rbzg5pv")))) + "0m7flrs0hz3ivib8kvsgn3d0fgkabqviadkp1dyspa6iibx3gjwd")))) (build-system gnu-build-system) (arguments `(#:make-flags @@ -2036,9 +2036,9 @@ stylesheets, you'll need to use another program that uses this library, (("install: libsass-install-\\$\\(BUILD\\) \\\\") "install: \\")) #t)) - ;; This phase fails for some reason. + ;; This phase fails because… (delete 'bootstrap) - ;; There is no configure script. + ;; …there is no configure script to be generated. (delete 'configure) (add-before 'build 'setup-environment (lambda _ -- cgit 1.4.1 From 3627ac367e1ffdf00b6ac296b863000bf9b3caaf Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 27 May 2021 16:07:38 +0200 Subject: gnu: mpd: Update to 0.22.8. * gnu/packages/mpd.scm (mpd): Update to 0.22.8. --- gnu/packages/mpd.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index 7df0d82805..5ec01dca7b 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -105,7 +105,7 @@ interfacing MPD in the C, C++ & Objective C languages.") (define-public mpd (package (name "mpd") - (version "0.22.6") + (version "0.22.8") (source (origin (method url-fetch) (uri @@ -114,7 +114,7 @@ interfacing MPD in the C, C++ & Objective C languages.") "/mpd-" version ".tar.xz")) (sha256 (base32 - "0pjdd8qwia1dsfkzyxcasfhxiqwk6lcz333z8w9vcg2wi6j4kq9b")))) + "0v980hhrdq9k2323ha6gfd7kzpwhdcgja6aqj9gwzbzzr44fs5wn")))) (build-system meson-build-system) (arguments `(#:configure-flags '("-Ddocumentation=enabled"))) -- cgit 1.4.1 From c59606aa50c7f258b5a3d450107ee4ab3027f0b0 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 27 May 2021 16:16:36 +0200 Subject: gnu: fio: Update to 3.27. * gnu/packages/benchmark.scm (fio): Update to 3.27. --- gnu/packages/benchmark.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm index b7bb332fc7..a75663a1f8 100644 --- a/gnu/packages/benchmark.scm +++ b/gnu/packages/benchmark.scm @@ -52,14 +52,14 @@ (define-public fio (package (name "fio") - (version "3.26") + (version "3.27") (source (origin (method url-fetch) (uri (string-append "https://brick.kernel.dk/snaps/" "fio-" version ".tar.bz2")) (sha256 (base32 - "1114h60vw63bim872an33xpvjfib6sc9dwj9xvk0yw41xjzfpp06")))) + "0akaixip86ycbxr13bjff2121rgfbz35fa9l39677wpwzckp4f4d")))) (build-system gnu-build-system) (arguments '(#:test-target "test" -- cgit 1.4.1 From e6eacc34aa6da3264ab3f6d25aae4cbc529c91ea Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 27 May 2021 16:17:01 +0200 Subject: gnu: xfsprogs: Update to 5.12.0. * gnu/packages/linux.scm (xfsprogs): Update to 5.12.0. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index e2c938beab..24ab210536 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -7322,7 +7322,7 @@ compatible with Python's ConfigParser style of .INI files, including RFC (define-public xfsprogs (package (name "xfsprogs") - (version "5.11.0") + (version "5.12.0") (source (origin (method url-fetch) (uri (string-append @@ -7330,7 +7330,7 @@ compatible with Python's ConfigParser style of .INI files, including RFC "xfsprogs-" version ".tar.gz")) (sha256 (base32 - "1byj53qdwsii35d0f11nz0dl618mpvwy5aa44pc9zg281g2r27ab")))) + "0b5vvwq4rqw7kph23ycd518d31dx3wq7w61znixxpdljx0ig71qn")))) (build-system gnu-build-system) (outputs (list "out" "python")) (arguments -- cgit 1.4.1 From cedcab1da3f5281177743a61e19879cc4ee07adf Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 27 May 2021 16:19:03 +0200 Subject: gnu: libnftnl: Update to 1.2.0. * gnu/packages/linux.scm (libnftnl): Update to 1.2.0. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 24ab210536..406629b6f6 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -6612,14 +6612,14 @@ re-use code and to avoid re-inventing the wheel.") (define-public libnftnl (package (name "libnftnl") - (version "1.1.9") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "mirror://netfilter.org/libnftnl/" "libnftnl-" version ".tar.bz2")) (sha256 - (base32 "16jbp4fs5dz2yf4c3bl1sb48x9x9wi1chv39zwmfgya1k9pimcp9")))) + (base32 "1xblq1cbcxhr6qmjpy98i1qdza148idgz99vbhjc7s4vzvfizc4h")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit 1.4.1 From e2d3f8d48a481fef05327c430609e5f35a0237c5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 27 May 2021 16:19:11 +0200 Subject: gnu: nftables: Update to 0.9.9. * gnu/packages/linux.scm (nftables): Update to 0.9.9. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 406629b6f6..f127e36e36 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -6636,7 +6636,7 @@ used by nftables.") (define-public nftables (package (name "nftables") - (version "0.9.8") + (version "0.9.9") (source (origin (method url-fetch) @@ -6645,7 +6645,7 @@ used by nftables.") (string-append "https://www.nftables.org/projects/nftables" "/files/nftables-" version ".tar.bz2"))) (sha256 - (base32 "1r4g22grhd4s1918wws9vggb8821sv4kkj8197ygxr6sar301z30")))) + (base32 "1d7iwc8xlyfsbgn6qx1sdfcq7jhpl8wpfj39hcd06y8dzp3jvvvn")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--disable-man-doc"))) ; FIXME: Needs docbook2x. -- cgit 1.4.1 From a16ce0b11d32e6344e4a2e148b1bf6ed34b189b3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 27 May 2021 16:19:25 +0200 Subject: gnu: lightspark: Update to 0.8.4.1. * gnu/packages/animation.scm (lightspark): Update to 0.8.4.1. --- gnu/packages/animation.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/animation.scm b/gnu/packages/animation.scm index bf139ac88e..71fc8f20b0 100644 --- a/gnu/packages/animation.scm +++ b/gnu/packages/animation.scm @@ -329,7 +329,7 @@ audio or video backends, ensuring good performance.") (define-public lightspark (package (name "lightspark") - (version "0.8.4") + (version "0.8.4.1") (source (origin (method git-fetch) @@ -338,7 +338,7 @@ audio or video backends, ensuring good performance.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1mkvjmrjdqx4rsvavd619m144pdfkgs3jb6z7i9fmzyvh4i0jp37")))) + (base32 "17l5gzb7p8nivx1a2frca2jklcjdsk2qj4jniv3z8bh307ksz254")))) (build-system cmake-build-system) (arguments `(#:tests? #f ;requires Adobe Flex SDK, see README.tests -- cgit 1.4.1 From f2c66d70fca921c59328cd739eaa039f5edfa4f4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 27 May 2021 17:05:05 +0200 Subject: gnu: iperf: Update to 3.10. * gnu/packages/networking.scm (iperf): Update to 3.10. [source]: Build from git. --- gnu/packages/networking.scm | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 8bcaa98fbb..6cb1cc9f7f 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2347,14 +2347,16 @@ that block port 22.") (define-public iperf (package (name "iperf") - (version "3.9") - (source (origin - (method url-fetch) - (uri (string-append "http://downloads.es.net/pub/iperf" - "/iperf-" version ".tar.gz")) - (sha256 - (base32 - "0f601avdmzpwsa3lbi0ppjhkrdipm5wifhhxy5czf99370k3mdi4")))) + (version "3.10") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/esnet/iperf") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "102wcyl4j7c7lj7z87b5xlhj1ark88v4f3q9pmmljw8ksn2w1m2g")))) (build-system gnu-build-system) (synopsis "TCP, UDP and SCTP bandwidth measurement tool") (description -- cgit 1.4.1 From 80594d6749011e8655a65173ee2ad30b219bbbe5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 27 May 2021 17:05:35 +0200 Subject: gnu: iperf: Omit static library. * gnu/packages/networking.scm (iperf)[arguments]: Add "--disable-static" configure flag. --- gnu/packages/networking.scm | 3 +++ 1 file changed, 3 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 6cb1cc9f7f..ccac1bfc6d 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2358,6 +2358,9 @@ that block port 22.") (sha256 (base32 "102wcyl4j7c7lj7z87b5xlhj1ark88v4f3q9pmmljw8ksn2w1m2g")))) (build-system gnu-build-system) + (arguments + `(#:configure-flags + (list "--disable-static"))) (synopsis "TCP, UDP and SCTP bandwidth measurement tool") (description "iPerf is a tool to measure achievable bandwidth on IP networks. It -- cgit 1.4.1 From 963c235d5046d36600089015073fd51fbe847828 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 27 May 2021 17:06:09 +0200 Subject: gnu: libopenmpt: Update to 0.5.9. * gnu/packages/audio.scm (libopenmpt): Update to 0.5.9. --- gnu/packages/audio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 5e30ed296d..f905a2827c 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -302,7 +302,7 @@ Linux kernel.") (define-public libopenmpt (package (name "libopenmpt") - (version "0.5.8") + (version "0.5.9") (source (origin (method url-fetch) @@ -310,7 +310,7 @@ Linux kernel.") (string-append "https://download.openmpt.org/archive/libopenmpt/src/" "libopenmpt-" version "+release.autotools.tar.gz")) (sha256 - (base32 "1kca5nc870mfv7i4ww2g1q9jn61gsq46irsypbr6fgxpfh8w5qi9")))) + (base32 "0h86p8mnpm98vc4v6jbvrmm02fch7dnn332i26fg3a2s1738m04d")))) (build-system gnu-build-system) (arguments `(#:configure-flags -- cgit 1.4.1 From 9401cb54fc7384bbfd85c57cbeef02d94e804f60 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 27 May 2021 17:06:19 +0200 Subject: gnu: shotwell: Update to 0.30.12. * gnu/packages/gnome.scm (shotwell): Update to 0.30.12. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 7e0ee6d314..dd416be3ed 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -7024,7 +7024,7 @@ metadata in photo and video files of various formats.") (define-public shotwell (package (name "shotwell") - (version "0.30.11") + (version "0.30.12") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/shotwell/" @@ -7032,7 +7032,7 @@ metadata in photo and video files of various formats.") "shotwell-" version ".tar.xz")) (sha256 (base32 - "12d26y40kjlv5x8f5g04wff33vh7mdjb8c41ydqbrwdip0jwy2n2")))) + "1h5crjq59lqi8f8mdkadzi8pc3i9i2ik4lsx2nrhzq486fzdfhw6")))) (build-system meson-build-system) (arguments '(#:glib-or-gtk? #t -- cgit 1.4.1 From f0b925038255e0e6909bad14115007cc34590f3a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 27 May 2021 17:30:25 +0200 Subject: gnu: ccl: Update to 1.12.1. * gnu/packages/lisp.scm (ccl): Update to 1.12.1. [inputs]: Keep using the 1.12 bootstrap for ARM. --- gnu/packages/lisp.scm | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index f6df3ef824..082eb920be 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -598,7 +598,9 @@ statistical profiler, a code coverage tool, and many other extensions.") ;; it, as is the case for SBCL, but I know of no attempt to do so." (package (name "ccl") - (version "1.12") + ;; XXX When updating this package, check whether we can simply append + ;; VERSION to the ccl-bootstrap URL again, instead of per architecture. + (version "1.12.1") (source (origin (method git-fetch) (uri (git-reference @@ -607,7 +609,7 @@ statistical profiler, a code coverage tool, and many other extensions.") (file-name (git-file-name "ccl" version)) (sha256 (base32 - "0kxr24d2fzsmpsilijpwwfl6g89y7fcrwb80kai5nx9pwgxmjbp3")))) + "1zz291lvsrr7pps8wfl2kdxsnzjngqi4v3mil14pga4r5zanmsi7")))) (build-system gnu-build-system) ;; CCL consists of a "lisp kernel" and "heap image", both of which are ;; shipped in precompiled form in source tarballs. The former is a C @@ -619,20 +621,20 @@ statistical profiler, a code coverage tool, and many other extensions.") ,(origin (method url-fetch) (uri (string-append - "https://github.com/Clozure/ccl/releases/download/v" version "/" + "https://github.com/Clozure/ccl/releases/download/v" (match (%current-system) - ("armhf-linux" "linuxarm") + ("armhf-linux" "1.12/linuxarm") ;; XXX: This source only works on x86, but provide it as a ;; catch-all to prevent errors when querying this package ;; on unsupported platforms. - (_ "linuxx86")) + (_ "1.12.1/linuxx86")) ".tar.gz")) (sha256 (base32 (match (%current-system) ("armhf-linux" "0x4bjx6cxsjvxyagijhlvmc7jkyxifdvz5q5zvz37028va65243c") - (_ "15l7cfa4a7jkfwdzsfm4q3n22jnb57imxahpql3h77xin57v1gbz")))))))) + (_ "0ll017ajcfsyx8f7zsy4394y8xxvz40iz0gcsmznp0n3mf0xi67c")))))))) (native-inputs `(("cl-asdf" ,cl-asdf) ("m4" ,m4))) -- cgit 1.4.1 From 49c2e3f69b7e845cbc9ddee0106e04546e2f7043 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 27 May 2021 17:32:52 +0200 Subject: gnu: libndp: Update to 1.8. * gnu/packages/networking.scm (libndp): Update to 1.8. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index ccac1bfc6d..51595720cc 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1154,14 +1154,14 @@ containing both Producer and Consumer support.") (define-public libndp (package (name "libndp") - (version "1.7") + (version "1.8") (source (origin (method url-fetch) (uri (string-append "https://libndp.org/files/" "libndp-" version ".tar.gz")) (sha256 (base32 - "1dlinhl39va00v55qygjc9ap77yqf7xvn4rwmvdr49xhzzxhlj1c")))) + "0ay0n0d85254zdmv8znmn399gfiqpk6ga0jwdwa7ylpbw9pbdzw8")))) (build-system gnu-build-system) (home-page "https://libndp.org/") (synopsis "Library for Neighbor Discovery Protocol") -- cgit 1.4.1 From 0fd84b7f6843332b8014e6f119764aed13831372 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 27 May 2021 17:33:38 +0200 Subject: gnu: lksctp-tools: Edit synopsis & description. * gnu/packages/networking.scm (synopsis, description): Improve. --- gnu/packages/networking.scm | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 51595720cc..6e2128aa12 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -461,11 +461,14 @@ performance across unpredictable networks, such as the Internet.") ("pkg-config" ,pkg-config))) (inputs `(("linux-headers" ,linux-libre-headers))) - (synopsis "Linux SCTP helper library") - (description "Lksctp-tools project provides a user space library for SCTP -(libsctp) including C language header files (netinet/sctp.h) for accessing SCTP -specific application programming interfaces not provided by the standard -sockets, and also some helper utilities around SCTP.") + (synopsis + "@acronym{SCTP, Stream Control Transmission Protocol} helpers for Linux") + (description + "The lksctp-tools project provides a user-space library for @acronym{SCTP, +the Stream Control Transmission Protocol} (@file{libsctp}) and C language header +files (@file{netinet/sctp.h}) for accessing SCTP-specific @acronym{APIs, +application programming interfaces} not provided by the standard sockets. +It also includes some SCTP-related helper utilities.") (home-page "http://lksctp.sourceforge.net/") (license (list -- cgit 1.4.1 From 32acea79fa9b87221b95f41b90c7783b8ee04012 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 27 May 2021 17:34:27 +0200 Subject: gnu: lksctp-tools: Update to 1.0.19. * gnu/packages/networking.scm (lksctp-tools): Update to 1.0.19. [source]: Remove patch. * gnu/packages/patches/lksctp-tools-1.0.18-fix-header-file-name.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/networking.scm | 6 ++-- .../lksctp-tools-1.0.18-fix-header-file-name.patch | 32 ---------------------- 3 files changed, 2 insertions(+), 37 deletions(-) delete mode 100644 gnu/packages/patches/lksctp-tools-1.0.18-fix-header-file-name.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 8355a208ea..792ebac1e1 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1278,7 +1278,6 @@ dist_patch_DATA = \ %D%/packages/patches/libffi-float128-powerpc64le.patch \ %D%/packages/patches/libvirt-add-install-prefix.patch \ %D%/packages/patches/libziparchive-add-includes.patch \ - %D%/packages/patches/lksctp-tools-1.0.18-fix-header-file-name.patch \ %D%/packages/patches/localed-xorg-keyboard.patch \ %D%/packages/patches/kdiagram-Fix-missing-link-libraries.patch \ %D%/packages/patches/kiki-level-selection-crash.patch \ diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 6e2128aa12..3da10a2990 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -440,7 +440,7 @@ performance across unpredictable networks, such as the Internet.") (define-public lksctp-tools (package (name "lksctp-tools") - (version "1.0.18") + (version "1.0.19") (source (origin (method git-fetch) @@ -449,10 +449,8 @@ performance across unpredictable networks, such as the Internet.") (url "https://github.com/sctp/lksctp-tools") (commit (string-append "v" version)))) (file-name (git-file-name name version)) - (patches - (search-patches "lksctp-tools-1.0.18-fix-header-file-name.patch")) (sha256 - (base32 "1x4fwzrlzvfa3vcpja97m8w5g9ir2zrh4zs7zksminrnmdrs0dsr")))) + (base32 "1jfq58j365mlgssavyw5wcal42n0xjkr40vmj9b8w265wgs28j20")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) diff --git a/gnu/packages/patches/lksctp-tools-1.0.18-fix-header-file-name.patch b/gnu/packages/patches/lksctp-tools-1.0.18-fix-header-file-name.patch deleted file mode 100644 index 1ebe6c803d..0000000000 --- a/gnu/packages/patches/lksctp-tools-1.0.18-fix-header-file-name.patch +++ /dev/null @@ -1,32 +0,0 @@ -From 378560050a8f93786c590cc99a55461666205b61 Mon Sep 17 00:00:00 2001 -From: Xin Long -Date: Fri, 24 Aug 2018 01:13:32 +0800 -Subject: [PATCH] build: fix netinet/sctp.h not to be installed - -After libcnetinet_HEADERS was set to sctp.h.in, netinet/sctp.h can -no longer be installed into ${includedir}. - -Since "AC_CONFIG_HEADERS([src/include/netinet/sctp.h])" is already -added into configure.ac, there's no need to generate sctp.h by -automake. - -So we simply set libcnetinet_HEADERS back to sctp.h. - -Fixes: 9607dd85e70a ("netinet/sctp.h: dynamically build based on system setup") -Signed-off-by: Xin Long -Signed-off-by: Marcelo Ricardo Leitner ---- - src/include/netinet/Makefile.am | 3 +-- - 1 file changed, 1 insertion(+), 2 deletions(-) - -diff --git a/src/include/netinet/Makefile.am b/src/include/netinet/Makefile.am -index ca0aac2..965db8c 100644 ---- a/src/include/netinet/Makefile.am -+++ b/src/include/netinet/Makefile.am -@@ -11,5 +11,4 @@ libcnetinetdir = $(includedir)/netinet - # API. - include_HEADERS = - --libcnetinet_HEADERS = sctp.h.in --BUILT_SOURCES = sctp.h -+libcnetinet_HEADERS = sctp.h -- cgit 1.4.1 From 847af45d0eba726418482b1b146a5ece2dbbb2c2 Mon Sep 17 00:00:00 2001 From: Solene Rapenne Date: Thu, 27 May 2021 18:17:32 +0200 Subject: gnu: phodav: Add gsettings-desktop-schemas input. * gnu/packages/gnome.scm (phodav)[native-inputs]: Add gsettings-desktop-schemas. Fixes: https://issues.guix.gnu.org/48414 Signed-off-by: Tobias Geerinckx-Rice --- gnu/packages/gnome.scm | 2 ++ 1 file changed, 2 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index dd416be3ed..2b9fb0c6d7 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -59,6 +59,7 @@ ;;; Copyright © 2020, 2021 Andy Tai ;;; Copyright © 2020, 2021 Sébastien Lerique ;;; Copyright © 2021 Trevor Hass +;;; Copyright © 2021 Solene Rapenne ;;; ;;; This file is part of GNU Guix. ;;; @@ -1176,6 +1177,7 @@ Library reference documentation.") `(("docbook-xml" ,docbook-xml-4.3) ("gettext" ,gettext-minimal) ("glib:bin" ,glib "bin") + ("gsettings-desktop-schemas" ,gsettings-desktop-schemas) ("gtk-doc" ,gtk-doc/stable) ("pkg-config" ,pkg-config))) (inputs -- cgit 1.4.1 From 5f1c4692a551abed8139f701d91611c85cd63607 Mon Sep 17 00:00:00 2001 From: Jack Hill Date: Fri, 21 May 2021 15:40:38 -0400 Subject: gnu: botan: Update to 2.18.1. * gnu/packages/crypto.scm (botan): Update to 2.18.1. Signed-off-by: Leo Famulari --- gnu/packages/crypto.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index 2658c38cb4..f333aced1b 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -944,14 +944,14 @@ SHA256, SHA512, SHA3, AICH, ED2K, Tiger, DC++ TTH, BitTorrent BTIH, GOST R (define-public botan (package (name "botan") - (version "2.17.3") + (version "2.18.1") (source (origin (method url-fetch) (uri (string-append "https://botan.randombit.net/releases/" "Botan-" version ".tar.xz")) (sha256 (base32 - "121vn1aryk36cpks70kk4c4cfic5g0qs82bf92xap9258ijkn4kr")))) + "0adf53drhk1hlpfih0175c9081bqpclw6p2afn51cmx849ib9izq")))) (build-system gnu-build-system) (arguments '(#:phases -- cgit 1.4.1 From d1b3b5b73da9a87991246ec40f6fd64e70b4e33a Mon Sep 17 00:00:00 2001 From: Jack Hill Date: Fri, 21 May 2021 15:40:39 -0400 Subject: gnu: botan: Respect #:tests?. * gnu/packages/crypto.scm (botan)[arguments]: Respect #:tests? in the custom 'check' phase. Signed-off-by: Leo Famulari --- gnu/packages/crypto.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index f333aced1b..674cb05801 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -976,7 +976,9 @@ SHA256, SHA512, SHA3, AICH, ED2K, Tiger, DC++ TTH, BitTorrent BTIH, GOST R (add-before 'check 'library-path-for-tests (lambda _ (setenv "LD_LIBRARY_PATH" (getcwd)))) (replace 'check - (lambda _ (invoke "./botan-test")))))) + (lambda* (#:key tests? #:allow-other-keys) + (if tests? + (invoke "./botan-test"))))))) (native-inputs `(("python" ,python-wrapper) ("python-docutils" ,python-docutils))) -- cgit 1.4.1 From 8d4d32d1d189624a1a238d54ae8e29fceef42680 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Thu, 27 May 2021 19:00:15 +0100 Subject: gnu: guix-build-coordinator: Update to 0-29.8c98f47. * gnu/packages/package-management.scm (guix-build-coordinator): Update to 0-29.8c98f47. --- gnu/packages/package-management.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 1ff9f4908c..efafbb704b 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -1061,8 +1061,8 @@ environments.") (license (list license:gpl3+ license:agpl3+ license:silofl1.1)))) (define-public guix-build-coordinator - (let ((commit "675c52d732f504232c0764ba1f03c5c54fd47763") - (revision "28")) + (let ((commit "8c98f47714fb1c1898ffa7b54966eaf913a0ae1d") + (revision "29")) (package (name "guix-build-coordinator") (version (git-version "0" revision commit)) @@ -1073,7 +1073,7 @@ environments.") (commit commit))) (sha256 (base32 - "1mbhpvrws4vf2ln3kj0a1j2p9zqvgn3nw3a85zff376s02937yqn")) + "09llhpv3ni8m24i4v37mgjcmaabaj6cy9fxgci7pch6dsi3rkc1r")) (file-name (string-append name "-" version "-checkout")))) (build-system gnu-build-system) (arguments -- cgit 1.4.1 From 11ac8ac6fabf3c244881bb770f47c437984591cb Mon Sep 17 00:00:00 2001 From: Solene Rapenne Date: Thu, 27 May 2021 00:00:13 +0200 Subject: gnu: entr: Update to 4.9. Signed-off-by: Leo Famulari --- gnu/packages/entr.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/entr.scm b/gnu/packages/entr.scm index 49e1060b5f..5ca40690dd 100644 --- a/gnu/packages/entr.scm +++ b/gnu/packages/entr.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2019 Ricardo Wurmus ;;; Copyright © 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2020 Jakub Kądziołka +;;; Copyright © 2021 Solene Rapenne ;;; ;;; This file is part of GNU Guix. ;;; @@ -33,14 +34,14 @@ (define-public entr (package (name "entr") - (version "4.6") + (version "4.9") (source (origin (method url-fetch) (uri (string-append "http://entrproject.org/code/entr-" version ".tar.gz")) (sha256 (base32 - "0vcflgagna2gdlpjsd6748c73j2829xlhm276mi838zl1n121phn")))) + "18h58k69f0qmqkknbcnhm5dz7mv5gr2blcq88qr62vz4zg9a8mp2")))) (build-system gnu-build-system) (arguments `(#:test-target "test" -- cgit 1.4.1 From 0b31e45b49af76d02ad760162ffe69d6c3cb854f Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 27 May 2021 20:58:45 +0200 Subject: gnu: Add python-logutils. * gnu/packages/python-xyz.scm (python-logutils): New variable. --- gnu/packages/python-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b10b55357f..973da15cad 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -25194,6 +25194,27 @@ query Watchman to discover file changes.") environment.") (license license:expat))) +(define-public python-logutils + (package + (name "python-logutils") + (version "0.3.5") + (source + (origin + (method url-fetch) + (uri (pypi-uri "logutils" version)) + (sha256 + (base32 + "10lsi5wv5ysnvf9ya4ncbix6mmipnv5067sf2cglc2f2sljql1dw")))) + (build-system python-build-system) + (home-page "https://bitbucket.org/vinay.sajip/logutils/") + (synopsis "Logging utilities") + (description "This package provides a set of handlers for the Python +standard library logging package. Some of these handlers are out-of-scope +for the standard library, and so they are packaged here. Others are updated +versions which have appeared in recent Python releases, but are usable with +older versions of Python and so are packaged here.") + (license license:bsd-3))) + (define-public python-qtsass (package (name "python-qtsass") -- cgit 1.4.1 From 167fc141d4e6f054e546322eb06e07dacb3309a3 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 27 May 2021 20:59:16 +0200 Subject: gnu: Add python-helper. * gnu/packages/python-xyz.scm (python-helper): New variable. --- gnu/packages/python-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 973da15cad..3540d8fb05 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -25215,6 +25215,29 @@ versions which have appeared in recent Python releases, but are usable with older versions of Python and so are packaged here.") (license license:bsd-3))) +(define-public python-helper + (package + (name "python-helper") + (version "2.5.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "helper" version)) + (sha256 + (base32 + "1d2j64wgbggzv5rhvil10zndp2w78wa5np5w0psj122ws9qr9wsa")))) + (build-system python-build-system) + (native-inputs + `(("python-mock" ,python-mock))) + (propagated-inputs + `(("python-logutils" ,python-logutils) + ("python-pyyaml" ,python-pyyaml))) + (home-page "https://github.com/gmr/helper") + (synopsis "Library for writing configurable applications and daemons") + (description + "This package provides procedures for quickly writing configurable +applications and daemons.") + (license license:bsd-3))) + (define-public python-qtsass (package (name "python-qtsass") -- cgit 1.4.1 From a30e616cccc850f0c9ad809be7db82729f46d0d8 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 27 May 2021 22:50:46 +0200 Subject: gnu: Add python-htsget. * gnu/packages/bioinformatics.scm (python-htsget): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index af1010f853..6f3bc96c9e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -846,6 +846,30 @@ input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.") (license license:x11))) +(define-public python-htsget + (package + (name "python-htsget") + (version "0.2.5") + (source (origin + (method url-fetch) + (uri (pypi-uri "htsget" version)) + (sha256 + (base32 + "0ic07q85vhw9djf23k57b21my7i5xp400m8gfqgr5gcryqvdr0yk")))) + (build-system python-build-system) + (native-inputs + `(("python-setuptools-scm" ,python-setuptools-scm))) + (propagated-inputs + `(("python-humanize" ,python-humanize) + ("python-requests" ,python-requests) + ("python-six" ,python-six))) + (home-page "https://pypi.org/project/htsget/") + (synopsis "Python API and command line interface for the GA4GH htsget API") + (description "This package is a client implementation of the GA4GH htsget +protocol. It provides a simple and reliable way to retrieve genomic data from +servers supporting the protocol.") + (license license:asl2.0))) + (define-public python-pybedtools (package (name "python-pybedtools") -- cgit 1.4.1 From 87c9f63fce05063c190e277a8d79803fa3693e11 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 27 May 2021 23:01:35 +0200 Subject: gnu: Add python-pyega3. * gnu/packages/bioinformatics.scm (python-pyega3): New variable. --- gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6f3bc96c9e..f38c0c07ef 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1994,6 +1994,45 @@ multiple sequence alignments.") (define-public python2-bx-python (package-with-python2 python-bx-python)) +(define-public python-pyega3 + (package + (name "python-pyega3") + (version "3.4.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "pyega3" version)) + (sha256 + (base32 + "1k736in8g27rarx65ym9xk50x53zjg75h37bb8ljynxv04rypx2q")))) + (build-system python-build-system) + (arguments + `(#:tests? #f)) ; The tests require network access. + (native-inputs + `(("python-psutil" ,python-psutil) + ("python-htsget" ,python-htsget))) + (propagated-inputs + `(("python-requests" ,python-requests) + ("python-tqdm" ,python-tqdm) + ("python-urllib3" ,python-urllib3) + ("python-responses" ,python-responses))) + (home-page "https://github.com/EGA-archive/ega-download-client") + (synopsis "Python client for EGA") + (description "This package is a python-based tool for viewing and +downloading files from authorized EGA datasets. It uses the EGA data API and +has several key features: +@itemize +@item Files are transferred over secure https connections and received + unencrypted, so no need for decryption after download. +@item Downloads resume from where they left off in the event that the + connection is interrupted. +@item Supports file segmenting and parallelized download of segments, + improving overall performance. +@item After download completes, file integrity is verified using checksums. +@item Implements the GA4GH-compliant htsget protocol for download of genomic + ranges for data files with accompanying index files. +@end itemize\n") + (license license:asl2.0))) + (define-public python-pysam (package (name "python-pysam") -- cgit 1.4.1 From bb5a3e91e93830622026084af909aabe53693d25 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Fri, 28 May 2021 10:09:10 +0200 Subject: gnu: Add python-argopt. * gnu/packages/python-xyz.scm (python-argopt): New variable. --- gnu/packages/python-xyz.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3540d8fb05..c4f19b4c6f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -219,6 +219,31 @@ #:use-module (srfi srfi-1) #:use-module (srfi srfi-26)) +(define-public python-argopt + (package + (name "python-argopt") + (version "0.7.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "argopt" version)) + (sha256 + (base32 + "0ybs7kkp0cpl8zn1lvf7481xhssg1bbhh5la2cjzdm5yibashyxa")))) + (build-system python-build-system) + (native-inputs + `(("python-coverage" ,python-coverage) + ("python-nose" ,python-nose) + ("python-setuptools" ,python-setuptools) ; Won't build without this. + ("python-setuptools-scm" ,python-setuptools-scm))) + (propagated-inputs + `(("python-toml" ,python-toml) + ("python-flake8" ,python-flake8))) + (home-page "https://github.com/casperdcl/argopt") + (synopsis "Generate a command-line interface from a docstring") + (description "This package provides tools to define a command line interface +from a docstring rather than the other way around.") + (license license:mpl2.0))) + (define-public python-colorful (package (name "python-colorful") -- cgit 1.4.1 From bd32bcca56ae4a27e754e43ace9bf28b0cae298e Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Fri, 28 May 2021 10:05:27 +0200 Subject: gnu: gnuradio: Add python-matplotlib dependency explicitly. * gnu/packages/radio.scm (gnuradio)[inputs]: Add python-matplotlib. --- gnu/packages/radio.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 72f0618313..c2886cd1ac 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -375,6 +375,7 @@ used by RDS Spy, and audio files containing @dfn{multiplex} signals (MPX).") ("python-click" ,python-click) ("python-click-plugins" ,python-click-plugins) ("python-lxml" ,python-lxml) + ("python-matplotlib" ,python-matplotlib) ("python-numpy" ,python-numpy) ("python-pycairo" ,python-pycairo) ("python-pygobject" ,python-pygobject) -- cgit 1.4.1 From 4ad3f818c9e2d200bf5c9cf0cf986b1a185d9d5b Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Fri, 28 May 2021 10:47:16 +0200 Subject: gnu: Add python-cachetools. * gnu/packages/python-xyz.scm (python-cachetools): New variable. --- gnu/packages/python-xyz.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c4f19b4c6f..d978942402 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -244,6 +244,24 @@ from a docstring rather than the other way around.") (license license:mpl2.0))) +(define-public python-cachetools + (package + (name "python-cachetools") + (version "4.2.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "cachetools" version)) + (sha256 + (base32 + "1zqc098gk6y614lxwqd9z2gm8lldgvrpid133pnlm4m048gfvdb1")))) + (build-system python-build-system) + (home-page "https://github.com/tkem/cachetools/") + (synopsis "Extensible memoizing collections and decorators") + (description "This module provides various memoizing collections and +decorators, including variants of the Python standard library's +@code{lru_cache} function decorator.") + (license license:expat))) + (define-public python-colorful (package (name "python-colorful") -- cgit 1.4.1 From 5e0b11fbe8e60f1ba690b7c579c44814ab1ef92f Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Fri, 28 May 2021 11:15:21 +0200 Subject: gnu: hackrf: Update to 2021.03.1. * gnu/packages/radio.scm (hackrf): Update to 2021.03.1. --- gnu/packages/radio.scm | 87 ++++++++++++++++++++++++-------------------------- 1 file changed, 41 insertions(+), 46 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index c2886cd1ac..8f9e180723 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -799,61 +799,56 @@ for correctness.") (license license:gpl3+))) (define-public hackrf - ;; Using a git commit because there have been many many commits - ;; since the relase two years ago, but no sign of a promised - ;; release for many months now. - (let ((commit "43e6f99fe8543094d18ff3a6550ed2066c398862") - (revision "0")) - (package - (name "hackrf") - (version (git-version "2018.01.1" revision commit)) - (source - (origin + (package + (name "hackrf") + (version "2021.03.1") + (source + (origin (method git-fetch) (uri (git-reference (url "https://github.com/mossmann/hackrf") - (commit commit))) + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0avnv693xi0zsnrvkbfn0ln1r3s1iyj0bz7sc3gxay909av0pvbc")))) - (build-system cmake-build-system) - (arguments - '(#:configure-flags - (list "-DUDEV_RULES_GROUP=dialout" - (string-append "-DUDEV_RULES_PATH=" - (assoc-ref %outputs "out") - "/lib/udev/rules.d")) - #:phases - (modify-phases %standard-phases - (add-before 'configure 'enter-source-directory - (lambda _ - (chdir "host") - #t)) - (add-after 'install 'delete-static-library - (lambda* (#:key outputs #:allow-other-keys) - (delete-file (string-append (assoc-ref outputs "out") - "/lib/libhackrf.a")) - #t)) - (add-before 'install-license-files 'leave-source-directory - (lambda _ - (chdir "..") - #t))) - #:tests? #f)) ; no test suite - (native-inputs - `(("pkg-config" ,pkg-config))) - (inputs - `(("fftw" ,fftw) - ("fftwf" ,fftwf) - ("libusb" ,libusb))) - (home-page "https://greatscottgadgets.com/hackrf/") - (synopsis "User-space library and utilities for HackRF SDR") - (description - "Command line utilities and a C library for controlling the HackRF + (base32 "12fkgimjy5ia291c1rn4y59pn9r5wdvz5x9z5xc8zr1xr96iyhfs")))) + (build-system cmake-build-system) + (arguments + '(#:configure-flags + (list "-DUDEV_RULES_GROUP=dialout" + (string-append "-DUDEV_RULES_PATH=" + (assoc-ref %outputs "out") + "/lib/udev/rules.d")) + #:phases + (modify-phases %standard-phases + (add-before 'configure 'enter-source-directory + (lambda _ + (chdir "host") + #t)) + (add-after 'install 'delete-static-library + (lambda* (#:key outputs #:allow-other-keys) + (delete-file (string-append (assoc-ref outputs "out") + "/lib/libhackrf.a")) + #t)) + (add-before 'install-license-files 'leave-source-directory + (lambda _ + (chdir "..") + #t))) + #:tests? #f)) ; no test suite + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("fftw" ,fftw) + ("fftwf" ,fftwf) + ("libusb" ,libusb))) + (home-page "https://greatscottgadgets.com/hackrf/") + (synopsis "User-space library and utilities for HackRF SDR") + (description + "Command line utilities and a C library for controlling the HackRF Software Defined Radio (SDR) over USB. Installing this package installs the userspace hackrf utilities and C library. To install the hackrf udev rules, you must extend 'udev-service-type' with this package. E.g.: @code{(udev-rules-service 'hackrf hackrf #:groups '(\"dialout\"))}.") - (license license:gpl2)))) + (license license:gpl2))) (define-public hamlib (package -- cgit 1.4.1 From 90e1f9cbe1de92346cf609d3f2b60fee8e1358b0 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Fri, 28 May 2021 11:28:16 +0200 Subject: gnu: cuirass: Update to 1.0.0-21.65ae16b. * gnu/packages/ci.scm (cuirass): Update to 1.0.0-21.65ae16b. --- gnu/packages/ci.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm index 22c11a8c7a..f223f372b7 100644 --- a/gnu/packages/ci.scm +++ b/gnu/packages/ci.scm @@ -73,8 +73,8 @@ (file-name (string-append name "-" version "-checkout"))))))) (define-public cuirass - (let ((commit "524b81d9ca6334dc322930a0ccc1d6830a81899b") - (revision "20")) + (let ((commit "65ae16b3c8bc5f7c062fd62b723fdca763b25e3b") + (revision "21")) (package (name "cuirass") (version (git-version "1.0.0" revision commit)) @@ -87,7 +87,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0jq4pdamqv7p85049na9344pr4q3j8zxm5p6k4yl6fq87k096frs")))) + "1kmfsybnbg3fr8fbc15fwf5ynw2737ci5qyaj9wdgzmh6756q3pn")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build utils) -- cgit 1.4.1 From c82b374979ce6d3c2883b9cc6842711779903f15 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Fri, 28 May 2021 09:13:38 +0200 Subject: gnu: intel-mpi-benchmarks: Remove top-level reference to 'openmpi'. This circular dependency could lead to "unbound variable" errors when running 'guix show openmpi' or similar. * gnu/packages/benchmark.scm (intel-mpi-benchmarks/openmpi): Inline code formerly in 'intel-mpi-benchmarks' procedure. (intel-mpi-benchmarks): Remove. --- gnu/packages/benchmark.scm | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm index a75663a1f8..681408a4e6 100644 --- a/gnu/packages/benchmark.scm +++ b/gnu/packages/benchmark.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2018, 2019 Ricardo Wurmus ;;; Copyright © 2019 Eric Bavier ;;; Copyright © 2019 Gábor Boskovits -;;; Copyright © 2019 Ludovic Courtès +;;; Copyright © 2019, 2021 Ludovic Courtès ;;; Copyright © 2020 Vincent Legoll ;;; Copyright © 2020 malte Frank Gerdes ;;; Copyright © 2020, 2021 Maxim Cournoyer @@ -126,13 +126,9 @@ is to write a job file matching the I/O load one wants to simulate.") (license (list license:gpl2 license:gpl2+ license:bsd-2 license:public-domain)))) -;; Parameterized in anticipation of m(va)pich support -(define (intel-mpi-benchmarks mpi) +(define-public intel-mpi-benchmarks/openmpi (package - (name (string-append "intel-mpi-benchmarks" - (if (string=? (package-name mpi) "openmpi") - "" - (string-append "-" (package-name mpi))))) + (name "intel-mpi-benchmarks") (version "2019.6") (source (origin (method git-fetch) @@ -154,7 +150,7 @@ is to write a job file matching the I/O load one wants to simulate.") #t)))) (build-system gnu-build-system) (inputs - `(("mpi" ,mpi))) + `(("openmpi" ,openmpi))) (arguments `(#:phases (modify-phases %standard-phases @@ -194,9 +190,6 @@ Efficiency of the MPI implementation. @end itemize") (license license:cpl1.0))) -(define-public intel-mpi-benchmarks/openmpi - (intel-mpi-benchmarks openmpi)) - (define-public imb-openmpi (deprecated-package "imb-openmpi" intel-mpi-benchmarks/openmpi)) -- cgit 1.4.1 From a800224260b5c005307fce6c0c3d85a2ea3095dd Mon Sep 17 00:00:00 2001 From: Dion Mendel Date: Wed, 26 May 2021 16:21:06 +0800 Subject: gnu: libraft: Update to 0.10.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/cluster.scm (libraft): Update to 0.10.1 Signed-off-by: Ludovic Courtès --- gnu/packages/cluster.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cluster.scm b/gnu/packages/cluster.scm index 01996591c7..18f2707469 100644 --- a/gnu/packages/cluster.scm +++ b/gnu/packages/cluster.scm @@ -186,7 +186,7 @@ independently or together to provide resilient infrastructures.") (define-public libraft (package (name "libraft") - (version "0.9.11") + (version "0.10.1") (home-page "https://github.com/canonical/raft") (source (origin (method git-fetch) @@ -195,7 +195,7 @@ independently or together to provide resilient infrastructures.") (file-name (git-file-name name version)) (sha256 (base32 - "00rsq4z9nykmf7r5rlpv1y6bvckcmg3zv57vh1h681y5pij6cch1")))) + "18idj53vnl5fx1ja1zlp8kiwmdxgwjxsi88rdql0pbh0484b92a3")))) (arguments '(#:configure-flags '("--enable-uv") #:phases (modify-phases %standard-phases -- cgit 1.4.1 From 45a96b3f03e1876e4172d4408cdb53fa904bd274 Mon Sep 17 00:00:00 2001 From: Maxime Devos Date: Mon, 24 May 2021 21:07:15 +0200 Subject: gnu: tryton: Factor out custom ‘check’ phase. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/tryton.scm (tryton-phases): New procedure. (tryton-arguments): New procedure. (python-trytond-account)[arguments]: Use 'tryton-phases'. (python-trytond-account-invoice)[arguments]: Likewise. (python-trytond-account-invoice-stock)[arguments]: Likewise. (python-trytond-account-product)[arguments]: Likewise. (python-trytond-analytic-account)[arguments]: Likewise. (python-trytond-company)[arguments]: Likewise. (python-trytond-country)[arguments]: Likewise. (python-trytond-currency)[arguments]: Likewise. (python-trytond-party)[arguments]: Likewise. (python-trytond-product)[arguments]: Likewise. (python-trytond-purchase)[arguments]: Likewise. (python-trytond-purchase-request)[arguments]: Likewise. (python-trytond-stock)[arguments]: Likewise. (python-trytond-stock-lot)[arguments]: Likewise. Signed-off-by: Ludovic Courtès --- gnu/packages/tryton.scm | 238 ++++++++---------------------------------------- 1 file changed, 39 insertions(+), 199 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/tryton.scm b/gnu/packages/tryton.scm index e9484aa487..800e19d827 100644 --- a/gnu/packages/tryton.scm +++ b/gnu/packages/tryton.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017 Adriano Peluso ;;; Copyright © 2020 Vinicius Monego +;;; Copyright © 2021 Maxime Devos ;;; ;;; This file is part of GNU Guix. ;;; @@ -144,6 +145,26 @@ and security.") "This package provides a library to access Tryton server as a client.") (license license:lgpl3+))) +(define (tryton-phases module . extra-arguments) + "Return the phases for building and testing a Tryton module named MODULE. +If present, pass EXTRA-ARGUMENTS to runtest as well." + `(modify-phases %standard-phases + (replace 'check + (let ((runtest + (string-append + (assoc-ref %build-inputs "trytond") + "/lib/python" + ,(version-major+minor (package-version python)) + "/site-packages/trytond/tests/run-tests.py"))) + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (invoke "python" runtest "-m" ,module ,@extra-arguments)))))) + +(define (tryton-arguments module . extra-arguments) + "Like ’tryton-phases’, but directly return all arguments for +the build system." + `(#:phases ,(apply tryton-phases module extra-arguments))) + ;;; ;;; Tryton modules - please sort alphabetically ;;; @@ -159,19 +180,7 @@ and security.") (sha256 (base32 "16ny67vcnxk9ngcxd56cfixm441vs9jxv3apmb16xsi47yk2xd7w")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (let ((runtest - (string-append - (assoc-ref %build-inputs "trytond") - "/lib/python" - ,(version-major+minor (package-version python)) - "/site-packages/trytond/tests/run-tests.py"))) - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "python" runtest "-m" "account"))))))) + (arguments (tryton-arguments "account")) (native-inputs `(("python-genshi" ,python-genshi) ("python-lxml" ,python-lxml) @@ -210,19 +219,7 @@ most of accounting needs.") (sha256 (base32 "0drccambg6855p7ai8654c7f9v85jzwicwpxmagyrr09qz6qzgcz")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (let ((runtest - (string-append - (assoc-ref %build-inputs "trytond") - "/lib/python" - ,(version-major+minor (package-version python)) - "/site-packages/trytond/tests/run-tests.py"))) - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "python" runtest "-m" "account_invoice"))))))) + (arguments (tryton-arguments "account_invoice")) (native-inputs `(("python-genshi" ,python-genshi) ("python-lxml" ,python-lxml) @@ -268,19 +265,7 @@ term.") (sha256 (base32 "02m6ikcc38ac41ddzg5xp5l9jz0k6j7j1g2xa62ki4v093yn4z5v")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (let ((runtest - (string-append - (assoc-ref %build-inputs "trytond") - "/lib/python" - ,(version-major+minor (package-version python)) - "/site-packages/trytond/tests/run-tests.py"))) - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "python" runtest "-m" "account_invoice_stock"))))))) + (arguments (tryton-arguments "account_invoice_stock")) (native-inputs `(("python-dateutil" ,python-dateutil) ("python-genshi" ,python-genshi) @@ -319,19 +304,7 @@ average price of the posted invoice lines that are linked to it.") (sha256 (base32 "10bpbkkmllbh9lm5ajydmc5nvqm9bbdn9rmm03jqgik23s5kyx2z")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (let ((runtest - (string-append - (assoc-ref %build-inputs "trytond") - "/lib/python" - ,(version-major+minor (package-version python)) - "/site-packages/trytond/tests/run-tests.py"))) - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "python" runtest "-m" "account_product"))))))) + (arguments (tryton-arguments "account_product")) (native-inputs `(("python-dateutil" ,python-dateutil) ("python-genshi" ,python-genshi) @@ -372,19 +345,7 @@ and category.") (sha256 (base32 "10rn2rf1ji7d1gxmgca368yvabql1ahklqg7p8sh5bl79vn5qx5x")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (let ((runtest - (string-append - (assoc-ref %build-inputs "trytond") - "/lib/python" - ,(version-major+minor (package-version python)) - "/site-packages/trytond/tests/run-tests.py"))) - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "python" runtest "-m" "analytic_account"))))))) + (arguments (tryton-arguments "analytic_account")) (native-inputs `(("python-dateutil" ,python-dateutil) ("python-genshi" ,python-genshi) @@ -424,19 +385,7 @@ required to analyse accounting using multiple different axes.") (sha256 (base32 "1bwy2rkgfw32cwhq5fh3rpy7bx425h44ap10i9kjx5ak86bfnpz9")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (let ((runtest - (string-append - (assoc-ref %build-inputs "trytond") - "/lib/python" - ,(version-major+minor (package-version python)) - "/site-packages/trytond/tests/run-tests.py"))) - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "python" runtest "-m" "company"))))))) + (arguments (tryton-arguments "company")) (native-inputs `(("python-dateutil" ,python-dateutil) ("python-genshi" ,python-genshi) @@ -472,20 +421,8 @@ company and employee and extend the user model.") (sha256 (base32 "1lkspk5w5pb0gg2h27zb7vwcj993gkm1f84qdxmqlpkc8raqvicj")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (let ((runtest - (string-append - (assoc-ref %build-inputs "trytond") - "/lib/python" - ,(version-major+minor (package-version python)) - "/site-packages/trytond/tests/run-tests.py"))) - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - ;; Doctest contains one test that requires internet access. - (invoke "python" runtest "-m" "country" "--no-doctest"))))))) + ;; Doctest contains one test that requires internet access. + (arguments (tryton-arguments "country" "--no-doctest")) (native-inputs `(("python-dateutil" ,python-dateutil) ("python-genshi" ,python-genshi) @@ -518,19 +455,7 @@ company and employee and extend the user model.") (sha256 (base32 "0b5p7ibil7nlsv7f31j69rka4xj5za798262algx7xa88a6h7mmx")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (let ((runtest - (string-append - (assoc-ref %build-inputs "trytond") - "/lib/python" - ,(version-major+minor (package-version python)) - "/site-packages/trytond/tests/run-tests.py"))) - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "python" runtest "-m" "currency"))))))) + (arguments (tryton-arguments "currency")) (native-inputs `(("python-dateutil" ,python-dateutil) ("python-genshi" ,python-genshi) @@ -565,20 +490,8 @@ currency and rate.") (sha256 (base32 "1hapfq7ip99s4qp9xra1m40q4n379p9pmfnz2x4ggd79ss76bghc")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (let ((runtest - (string-append - (assoc-ref %build-inputs "trytond") - "/lib/python" - ,(version-major+minor (package-version python)) - "/site-packages/trytond/tests/run-tests.py"))) - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - ;; Doctest 'scenario_party_phone_number.rst' fails. - (invoke "python" runtest "-m" "party" "--no-doctest"))))))) + ;; Doctest 'scenario_party_phone_number.rst' fails. + (arguments (tryton-arguments "party" "--no-doctest")) (native-inputs `(("python-dateutil" ,python-dateutil) ("python-genshi" ,python-genshi) @@ -613,19 +526,7 @@ addresses.") (sha256 (base32 "0x18ngpjyrdwjwg17bz98jph4jv5gcv0qc0p2kxpam4lqsy34ic2")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (let ((runtest - (string-append - (assoc-ref %build-inputs "trytond") - "/lib/python" - ,(version-major+minor (package-version python)) - "/site-packages/trytond/tests/run-tests.py"))) - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "python" runtest "-m" "product"))))))) + (arguments (tryton-arguments "product")) (native-inputs `(("python-dateutil" ,python-dateutil) ("python-genshi" ,python-genshi) @@ -661,19 +562,7 @@ Template and Product.") (sha256 (base32 "0na74zijj46b12gypy9si3las02a96rh5ygl503c7razha61g1b0")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (let ((runtest - (string-append - (assoc-ref %build-inputs "trytond") - "/lib/python" - ,(version-major+minor (package-version python)) - "/site-packages/trytond/tests/run-tests.py"))) - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "python" runtest "-m" "purchase"))))))) + (arguments (tryton-arguments "purchase")) (native-inputs `(("python-dateutil" ,python-dateutil) ("python-genshi" ,python-genshi) @@ -721,21 +610,8 @@ Template and Product.") (sha256 (base32 "1m92snnvgisnv083nml6cz5qgnfdg539rd5bwg3lqrknm7343w16")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (let ((runtest - (string-append - (assoc-ref %build-inputs "trytond") - "/lib/python" - ,(version-major+minor (package-version python)) - "/site-packages/trytond/tests/run-tests.py"))) - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - ;; Doctest 'scenario_purchase_request.rst' fails. - (invoke "python" runtest - "-m" "purchase_request" "--no-doctest"))))))) + ;; Doctest 'scenario_purchase_request.rst' fails. + (arguments (tryton-arguments "purchase_request" "--no-doctest")) (native-inputs `(("python-dateutil" ,python-dateutil) ("python-genshi" ,python-genshi) @@ -773,19 +649,7 @@ generated by other process from Tryton.") (sha256 (base32 "0yb8kd3alwqkivrlpx0ni4jxv3x14i37lmwism9yi81xwchyrcjk")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (let ((runtest - (string-append - (assoc-ref %build-inputs "trytond") - "/lib/python" - ,(version-major+minor (package-version python)) - "/site-packages/trytond/tests/run-tests.py"))) - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "python" runtest "-m" "stock"))))))) + (arguments (tryton-arguments "stock")) (native-inputs `(("python-genshi" ,python-genshi) ("python-lxml" ,python-lxml) @@ -827,19 +691,7 @@ inventory to control and update stock levels.") (sha256 (base32 "0w2f62cfzm7j8wnw8igmjslpxc1a8s82dkdizyvim5qhjg6mrsym")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (let ((runtest - (string-append - (assoc-ref %build-inputs "trytond") - "/lib/python" - ,(version-major+minor (package-version python)) - "/site-packages/trytond/tests/run-tests.py"))) - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "python" runtest "-m" "stock_lot"))))))) + (arguments (tryton-arguments "stock_lot")) (native-inputs `(("python-dateutil" ,python-dateutil) ("python-genshi" ,python-genshi) @@ -874,19 +726,7 @@ inventory to control and update stock levels.") (sha256 (base32 "01cgpxlznldrba79a3xmj4d0csyfc3ccgs66c490j8v8rdnqpbww")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (let ((runtest - (string-append - (assoc-ref %build-inputs "trytond") - "/lib/python" - ,(version-major+minor (package-version python)) - "/site-packages/trytond/tests/run-tests.py"))) - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "python" runtest "-m" "stock_supply"))))))) + (arguments (tryton-arguments "stock_supply")) (native-inputs `(("python-dateutil" ,python-dateutil) ("python-genshi" ,python-genshi) -- cgit 1.4.1 From 0ab7796f4d8989619c8091a5e3c36507161b6743 Mon Sep 17 00:00:00 2001 From: Maxime Devos Date: Mon, 24 May 2021 22:17:09 +0200 Subject: gnu: tryton: Use local 'inputs' instead of global '%build-inputs'. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The former is preferred above the latter. * gnu/packages/tryton.scm (tryton-phases): Look up "trytond" in the 'inputs' argument instead of in '%build-inputs'. Signed-off-by: Ludovic Courtès --- gnu/packages/tryton.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/tryton.scm b/gnu/packages/tryton.scm index 800e19d827..107d5b4a7c 100644 --- a/gnu/packages/tryton.scm +++ b/gnu/packages/tryton.scm @@ -150,13 +150,13 @@ and security.") If present, pass EXTRA-ARGUMENTS to runtest as well." `(modify-phases %standard-phases (replace 'check - (let ((runtest - (string-append - (assoc-ref %build-inputs "trytond") - "/lib/python" - ,(version-major+minor (package-version python)) - "/site-packages/trytond/tests/run-tests.py"))) - (lambda* (#:key inputs outputs #:allow-other-keys) + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((runtest + (string-append + (assoc-ref inputs "trytond") + "/lib/python" + ,(version-major+minor (package-version python)) + "/site-packages/trytond/tests/run-tests.py"))) (add-installed-pythonpath inputs outputs) (invoke "python" runtest "-m" ,module ,@extra-arguments)))))) -- cgit 1.4.1 From 416f7843c48496fa3cbca2c2fffb9f661751cbe0 Mon Sep 17 00:00:00 2001 From: Maxime Devos Date: Mon, 24 May 2021 22:36:06 +0200 Subject: gnu: tryton: Allow disabling the test suite. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/tryton.scm (tryton-phases): Respect 'tests?' in the 'check' phase. Signed-off-by: Ludovic Courtès --- gnu/packages/tryton.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/tryton.scm b/gnu/packages/tryton.scm index 107d5b4a7c..5fbbeb53be 100644 --- a/gnu/packages/tryton.scm +++ b/gnu/packages/tryton.scm @@ -150,15 +150,16 @@ and security.") If present, pass EXTRA-ARGUMENTS to runtest as well." `(modify-phases %standard-phases (replace 'check - (lambda* (#:key inputs outputs #:allow-other-keys) + (lambda* (#:key inputs outputs tests? #:allow-other-keys) (let ((runtest (string-append (assoc-ref inputs "trytond") "/lib/python" ,(version-major+minor (package-version python)) "/site-packages/trytond/tests/run-tests.py"))) - (add-installed-pythonpath inputs outputs) - (invoke "python" runtest "-m" ,module ,@extra-arguments)))))) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "python" runtest "-m" ,module ,@extra-arguments))))))) (define (tryton-arguments module . extra-arguments) "Like ’tryton-phases’, but directly return all arguments for -- cgit 1.4.1 From 45b98751ffec9c74b1bc466a09dceada14ebf2a1 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Fri, 28 May 2021 14:25:12 +0200 Subject: gnu: cuirass: Update to 1.0.0-22.3ac739b. * gnu/packages/ci.scm (cuirass): Update to 1.0.0-22.3ac739b. --- gnu/packages/ci.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm index f223f372b7..f3fae20383 100644 --- a/gnu/packages/ci.scm +++ b/gnu/packages/ci.scm @@ -73,8 +73,8 @@ (file-name (string-append name "-" version "-checkout"))))))) (define-public cuirass - (let ((commit "65ae16b3c8bc5f7c062fd62b723fdca763b25e3b") - (revision "21")) + (let ((commit "3ac739b97dbf3684f925eac7a5d609e79ec1ac5f") + (revision "22")) (package (name "cuirass") (version (git-version "1.0.0" revision commit)) @@ -87,7 +87,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "1kmfsybnbg3fr8fbc15fwf5ynw2737ci5qyaj9wdgzmh6756q3pn")))) + "1nl171qmxhcb0sq39khk7knapvlzm26z2lmzqwdmj65vyyg9inrc")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build utils) -- cgit 1.4.1 From 4ec964ec38d511ca203cd3c29b194d0cfb99667a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 28 May 2021 08:06:45 -0400 Subject: gnu: jami-gnome: Include phases from the glib-or-gtk-build-system. This makes Jami less dependent on the environment it is run within; for example when using Jami on a foreign distributions. * gnu/packages/jami.scm (jami-gnome)[imported-modules]: New argument. [modules]: New argument. [phases]{glib-or-gtk-compile-schemas, glib-or-gtk-wrap}: New phases. Reported-by: Simon Tournier --- gnu/packages/jami.scm | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/jami.scm b/gnu/packages/jami.scm index 0adc3ed81e..ff14373bf3 100644 --- a/gnu/packages/jami.scm +++ b/gnu/packages/jami.scm @@ -546,12 +546,21 @@ decentralized calling using P2P-DHT.") ; automatically started by DBus. ("adwaita-icon-theme" ,adwaita-icon-theme))) (arguments - `(#:tests? #f ; There is no testsuite. + `(#:tests? #f ;no test suite + #:imported-modules (,@%cmake-build-system-modules + (guix build glib-or-gtk-build-system)) + #:modules ((guix build cmake-build-system) + ((guix build glib-or-gtk-build-system) #:prefix gtk:) + (guix build utils)) #:phases (modify-phases %standard-phases (add-after 'unpack 'change-directory (lambda _ - (chdir "client-gnome")))))) + (chdir "client-gnome"))) + (add-after 'install 'glib-or-gtk-compile-schemas + (assoc-ref gtk:%standard-phases 'glib-or-gtk-compile-schemas)) + (add-after 'glib-or-gtk-compile-schemas 'glib-or-gtk-wrap + (assoc-ref gtk:%standard-phases 'glib-or-gtk-wrap))))) (synopsis "Jami client for GNOME") (description "This package provides a Jami client for the GNOME desktop. Jami is a secure and distributed voice, video and chat communication platform -- cgit 1.4.1 From 0b70eb03cbcf5df7de9f468d9e2a3b53379779fe Mon Sep 17 00:00:00 2001 From: Solene Rapenne Date: Fri, 28 May 2021 19:05:23 +0200 Subject: gnu: gnutls: Replace with 3.6.16 [fixes CVE-2021-20305]. * gnu/packages/tls.scm (gnutls)[replacement]: New field. (gnutls-3.6.16): New variable. Signed-off-by: Leo Famulari --- gnu/packages/tls.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 174438ad87..55410f3911 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -15,6 +15,7 @@ ;;; Copyright © 2018 Clément Lassieur ;;; Copyright © 2019 Mathieu Othacehe ;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen +;;; Copyright © 2021 Solene Rapenne ;;; ;;; This file is part of GNU Guix. ;;; @@ -165,6 +166,7 @@ living in the same process.") (package (name "gnutls") (version "3.6.15") + (replacement gnutls-3.6.16) (source (origin (method url-fetch) ;; Note: Releases are no longer on ftp.gnu.org since the @@ -258,6 +260,22 @@ required structures.") (properties '((ftp-server . "ftp.gnutls.org") (ftp-directory . "/gcrypt/gnutls"))))) +;; Replacement package to fix CVE-2021-20305. +(define gnutls-3.6.16 + (package + (inherit gnutls) + (version "3.6.16") + (source (origin + (method url-fetch) + (uri (string-append "mirror://gnupg/gnutls/v" + (version-major+minor version) + "/gnutls-" version ".tar.xz")) + (patches (search-patches "gnutls-skip-trust-store-test.patch" + "gnutls-cross.patch")) + (sha256 + (base32 + "1czk511pslz367shf32f2jvvkp7y1323bcv88c2qng98mj0v6y8v")))))) + (define-public gnutls/guile-2.0 ;; GnuTLS for Guile 2.0. (package/inherit gnutls -- cgit 1.4.1 From b1ae0f30d856503fa311d380584a6d7c80559332 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 28 May 2021 17:33:37 +0200 Subject: gnu: Add mosaicatcher. * gnu/packages/bioinformatics.scm (mosaicatcher): New variable. --- gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f38c0c07ef..2a7443314a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6170,6 +6170,46 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") ;; 2. MD5 implementation - RSA Data Security, RFC 1321 (license (list license:gpl2+ license:public-domain))))) +(define-public mosaicatcher + (package + (name "mosaicatcher") + (version "0.3.1") + (source (origin + ;; There are no release tarballs nor tags. + (method git-fetch) + (uri (git-reference + (url "https://github.com/friendsofstrandseq/mosaicatcher") + (commit (string-append version "-dev")))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1n2s5wvvj2y0vfgjkg1q11xahpbagxz7h2vf5q7qyy25s12kbzbd")) + (patches (search-patches "mosaicatcher-unbundle-htslib.patch")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #false ; there are no tests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "src"))) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((target (assoc-ref outputs "out")) + (bin (string-append target "/bin")) + (share (string-append target "/share/mosaicatcher"))) + (install-file "mosaic" bin) + (mkdir-p share) + (copy-recursively "../R" share))))))) + (inputs + `(("boost" ,boost) + ("htslib" ,htslib))) + (home-page "https://github.com/friendsofstrandseq/mosaicatcher") + (synopsis "Count and classify Strand-seq reads") + (description + "Mosaicatcher counts Strand-seq reads and classifies strand states of +each chromosome in each cell using a Hidden Markov Model.") + (license license:expat))) + (define-public ngs-sdk (package (name "ngs-sdk") -- cgit 1.4.1 From f5871b19cc32593149b91ca3f33075200844b4c0 Mon Sep 17 00:00:00 2001 From: Eric Brown Date: Tue, 25 May 2021 00:58:50 -0500 Subject: gnu: Add cbc. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/maths.scm (cbc): New variable. Co-authored-by: Ludovic Courtès --- gnu/packages/maths.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 3d7248417b..59598a242d 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1798,6 +1798,35 @@ large-scale nonlinear optimization. It provides C++, C, and Fortran interfaces.") (license license:epl1.0))) +(define-public cbc + (package + (name "cbc") + (version "2.10.5") + (source (origin + (method url-fetch) + (uri (string-append "https://www.coin-or.org/download/source/" + "Cbc/Cbc-" version ".tgz")) + (sha256 + (base32 + "0wk9vr6zc62gw71v7gnra5wxqlcljcgbhm5lasx236v791b986ns")) + (modules '((guix build utils))) + (snippet + ;; Make sure we don't use the bundled software. + '(delete-file-recursively "ThirdParty")))) + (build-system gnu-build-system) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (inputs + `(("openblas" ,openblas))) + (home-page "https://www.coin-or.org") + (synopsis "Branch-and-cut solver") + (description + "Cbc (Coin-or branch and cut) is a mixed integer linear programming +solver written in C++. It can be used as a library or as a standalone +executable.") + (license license:epl1.0))) + (define-public clp (package (name "clp") -- cgit 1.4.1 From 30713c2c2ac8a01931516017dc70f797d6f1a0dd Mon Sep 17 00:00:00 2001 From: Eric Brown Date: Tue, 25 May 2021 00:45:31 -0500 Subject: gnu: ipopt: Update to 3.13.4 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/maths.scm (ipopt): Update to 3.13.4, update URL. [license]: Change to LICENSE:EPL2.0. Co-authored-by: Ludovic Courtès --- gnu/packages/maths.scm | 24 ++++++++++-------------- 1 file changed, 10 insertions(+), 14 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 59598a242d..747ad1ddfd 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1752,21 +1752,16 @@ online as well as original implementations of various other algorithms.") (define-public ipopt (package (name "ipopt") - (version "3.12.12") + (version "3.13.4") (source (origin - (method url-fetch) - (uri (string-append - "https://www.coin-or.org/download/source/Ipopt/Ipopt-" - version".tgz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/coin-or/Ipopt") + (commit (string-append "releases/" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "07yn9rzdswjk8n246qq6ci9ssf2bcplkifcpsfz9j6cdxw9vgbkv")) - (modules '((guix build utils))) - (snippet - ;; Make sure we don't use the bundled software. - '(begin - (delete-file-recursively "ThirdParty") - #t)))) + "08gznhwhqv1x4baksz350ih8q16r5rd0k8vals6078m3h94khr4b")))) (build-system gnu-build-system) (arguments '(#:phases (modify-phases %standard-phases @@ -1786,7 +1781,8 @@ online as well as original implementations of various other algorithms.") after "\n"))) #t)))))) (native-inputs - `(("gfortran" ,gfortran))) + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) (inputs ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL. `(("lapack" ,lapack))) ;for both libblas and liblapack @@ -1796,7 +1792,7 @@ online as well as original implementations of various other algorithms.") "The Interior Point Optimizer (IPOPT) is a software package for large-scale nonlinear optimization. It provides C++, C, and Fortran interfaces.") - (license license:epl1.0))) + (license license:epl2.0))) (define-public cbc (package -- cgit 1.4.1 From 02f6144344d34ce24a821a6f6ab5e3c9e4bd2e7d Mon Sep 17 00:00:00 2001 From: Stefan Reichör Date: Tue, 18 May 2021 21:38:48 +0200 Subject: gnu: Add mbuffer. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/networking.scm (mbuffer): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/networking.scm | 34 +++++++++++++++++++++++++++++++++- 1 file changed, 33 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 3da10a2990..f65c8a7f13 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2014, 2017, 2018 Ludovic Courtès ;;; Copyright © 2015, 2016, 2017, 2018, 2020 Ricardo Wurmus ;;; Copyright © 2015 Mark H Weaver -;;; Copyright © 2015, 2016, 2017 Stefan Reichör +;;; Copyright © 2015, 2016, 2017, 2021 Stefan Reichör ;;; Copyright © 2016 Raimon Grau ;;; Copyright © 2016–2021 Tobias Geerinckx-Rice ;;; Copyright © 2016 John Darrington @@ -909,6 +909,38 @@ establish a relatively secure environment (su and chroot) for running client or server shell scripts with network connections.") (license license:gpl2))) +(define-public mbuffer + (package + (name "mbuffer") + (version "20210328") + (source (origin + (method url-fetch) + (uri (string-append + "http://www.maier-komor.de/software/mbuffer/mbuffer-" + version ".tgz")) + (sha256 + (base32 + "0pfw9xw4ph18yss07fl6w8fbqiwy1w9r1knzw5gsb4c993cbidai")))) + (build-system gnu-build-system) + (inputs `(("openssl" ,openssl))) + (home-page "http://www.maier-komor.de/mbuffer.html") + (synopsis + "Swiss army knife for data stream buffering (network aware)") + (description + "mbuffer is a tool for buffering data streams with a large set of features: + +@itemize +@item direct support for TCP based network targets (IPv4 and IPv6) +@item ability to send to multiple targets in parallel (distribution mode) +@item support for multiple volumes +@item I/O rate limitation +@item high/low watermark based restart criteria +@item configurable buffer size +@item on the fly MD5 hash calculation +@item highly efficient, multi-threaded implementation +@end itemize") + (license license:gpl3+))) + (define-public tcp-wrappers (package (name "tcp-wrappers") -- cgit 1.4.1 From 803be0975dbd31d16d75e6bc7154e8caa07cacb0 Mon Sep 17 00:00:00 2001 From: Stefan Reichör Date: Tue, 18 May 2021 22:33:08 +0200 Subject: gnu: Add hostscope. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/monitoring.scm (hostscope): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/monitoring.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm index 22b02a561b..f0a25e57a6 100644 --- a/gnu/packages/monitoring.scm +++ b/gnu/packages/monitoring.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2020 Alex ter Weele ;;; Copyright © 2020 Lars-Dominik Braun ;;; Copyright © 2021 Marius Bakke +;;; Copyright © 2021 Stefan Reichör ;;; ;;; This file is part of GNU Guix. ;;; @@ -622,3 +623,29 @@ future system load (i.e., capacity planning).") ;; license:gpl2 for other plugins (license (list license:expat license:gpl2)))) +(define-public hostscope + (package + (name "hostscope") + (version "8.0") + (source (origin + (method url-fetch) + (uri (string-append + "http://www.maier-komor.de/hostscope/hostscope-V" + version ".tgz")) + (sha256 + (base32 + "0jw6yij8va0f292g4xkf9lp9sxkzfgv67ajw49g3vq42q47ld7cv")))) + (build-system gnu-build-system) + (inputs `(("ncurses" ,ncurses))) + (arguments '(#:tests? #f)) ;; No included tests. + (home-page "http://www.maier-komor.de/hostscope.html") + (synopsis + "System monitoring tool for multiple hosts") + (description + "HostScope displays key system metrics of Linux hosts, such as detailed +CPU load, speed and temperature, I/O rates of network interfaces, I/O rates of +disks, and user process summary information. All metrics are multicast on the +LAN, if wanted, and clients can switch between multiple hosts on the network. +Hostscope features a bridge to Influx DB. So Grafana can be used to visualize +the recorded data over time.") + (license license:gpl3+))) -- cgit 1.4.1 From ca1caf9cf157df58dd7b080ad7795b6cf11e47bf Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Fri, 28 May 2021 22:57:46 +0200 Subject: gnu: hostscope: Add 'release-monitoring-url' property. * gnu/packages/monitoring.scm (hostscope)[properties]: New field. --- gnu/packages/monitoring.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm index f0a25e57a6..d2aef0eaab 100644 --- a/gnu/packages/monitoring.scm +++ b/gnu/packages/monitoring.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016 Ludovic Courtès +;;; Copyright © 2016, 2021, 2021 Ludovic Courtès ;;; Copyright © 2018 Sou Bunnbu ;;; Copyright © 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2018, 2020, 2021 Tobias Geerinckx-Rice @@ -639,6 +639,7 @@ future system load (i.e., capacity planning).") (inputs `(("ncurses" ,ncurses))) (arguments '(#:tests? #f)) ;; No included tests. (home-page "http://www.maier-komor.de/hostscope.html") + (properties `((release-monitoring-url . ,home-page))) (synopsis "System monitoring tool for multiple hosts") (description -- cgit 1.4.1 From 9d439e3ba05e99f33cf95ee3c3f8729caed4791e Mon Sep 17 00:00:00 2001 From: Stefan Reichör Date: Tue, 18 May 2021 22:57:43 +0200 Subject: gnu: Add xjobs. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/parallel.scm (xjobs): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/parallel.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm index d950fa9014..1108d6f457 100644 --- a/gnu/packages/parallel.scm +++ b/gnu/packages/parallel.scm @@ -41,6 +41,7 @@ #:use-module (gnu packages admin) #:use-module (gnu packages autotools) #:use-module (gnu packages base) + #:use-module (gnu packages flex) #:use-module (gnu packages freeipmi) #:use-module (gnu packages linux) #:use-module (gnu packages mpi) @@ -135,6 +136,32 @@ execution is also possible.") (home-page "https://github.com/leahneukirchen/xe") (license license:public-domain))) +(define-public xjobs + (package + (name "xjobs") + (version "20200726") + (source (origin + (method url-fetch) + (uri (string-append + "http://www.maier-komor.de/xjobs/xjobs-" + version ".tgz")) + (sha256 + (base32 + "0ay6gn43pnm7r1jamwgpycl67bjg5n87ncl27jb01w2x6x70z0i3")))) + (build-system gnu-build-system) + (arguments `(#:tests? #f)) ;; No tests + (native-inputs + `(("flex" ,flex) + ("which" ,which))) + (home-page "http://www.maier-komor.de/xjobs.html") + (synopsis + "Parallel execution of jobs with several useful options") + (description + "xjobs reads job descriptions line by line and executes them in +parallel. It limits the number of parallel executing jobs and starts new jobs +when jobs finish.") + (license license:gpl2+))) + (define-public slurm (package (name "slurm") -- cgit 1.4.1 From cefa260fb42693b87545b1baab8cef9723827f80 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Fri, 28 May 2021 23:03:12 +0200 Subject: gnu: xjobs: Add 'release-monitoring-url' property. * gnu/packages/parallel.scm (xjobs)[properties]: New field. --- gnu/packages/parallel.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm index 1108d6f457..d523d75a82 100644 --- a/gnu/packages/parallel.scm +++ b/gnu/packages/parallel.scm @@ -154,6 +154,7 @@ execution is also possible.") `(("flex" ,flex) ("which" ,which))) (home-page "http://www.maier-komor.de/xjobs.html") + (properties `((release-monitoring-url . ,home-page))) (synopsis "Parallel execution of jobs with several useful options") (description -- cgit 1.4.1 From 63ee9215273ca1a5bf5f526d6dbb0dcce3a21c5f Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Fri, 28 May 2021 23:35:41 +0200 Subject: gnu: emacs-amx: Update to 3.4. * gnu/packages/emacs-xyz.scm (emacs-amx): Update to 3.4. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 5ddeb09230..87184b202d 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -22341,7 +22341,7 @@ Later you can insert it into an Org buffer using the command (define-public emacs-amx (package (name "emacs-amx") - (version "3.3") + (version "3.4") (source (origin (method git-fetch) @@ -22350,7 +22350,7 @@ Later you can insert it into an Org buffer using the command (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0ikjzs119g57cwh2v3jmy63lggqc0ib99q5gsl93slkk4y2ihavw")))) + (base32 "0h1cxqqf0hixh25j679r57bq9dv0b20icf268wbnsim5xp88ngf8")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-s" ,emacs-s))) -- cgit 1.4.1 From 6860b15257548e91d8d19fe4e7eb1d195a093eb3 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Fri, 28 May 2021 23:37:21 +0200 Subject: gnu: emacs-auto-sudoedit: Update to 1.1.0. * gnu/packages/emacs-xyz.scm (emacs-auto-sudoedit): Update to 1.1.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 87184b202d..30d90f5892 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -2082,7 +2082,7 @@ letter to each link using avy.") (define-public emacs-auto-sudoedit (package (name "emacs-auto-sudoedit") - (version "1.0.0") + (version "1.1.0") (source (origin (method git-fetch) @@ -2091,7 +2091,7 @@ letter to each link using avy.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "10p0hc95j382km8655pqld9wxg10j1f36czzppkdd6a55cxarv9f")))) + (base32 "1rhdvrj2rjbvl7vkb0wcp6krqxcaigl7jk9z8yvhx6s4cm2qli6q")))) (propagated-inputs `(("emacs-f" ,emacs-f))) (build-system emacs-build-system) -- cgit 1.4.1 From c6499461da48865a74008c4c4bf3a9da5bdaf61c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Fri, 28 May 2021 23:40:33 +0200 Subject: gnu: emacs-chronometrist: Update to 0.7.0. * gnu/packages/emacs-xyz.scm (emacs-chronometrist): Update to 0.7.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 30d90f5892..46f6d8ecc4 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -2591,7 +2591,7 @@ Lock key.") (define-public emacs-chronometrist (package (name "emacs-chronometrist") - (version "0.6.5") + (version "0.7.0") (source (origin (method git-fetch) @@ -2600,7 +2600,7 @@ Lock key.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1k7r5rc6vzrnhp9j5bkv45yzqz7zbqrkiry4fzc8w6f36pcw862f")))) + (base32 "0s483ca4f8192gr9ix9jxjfcmxp30b7qk2jiaqzprkrn9kcgw544")))) (build-system emacs-build-system) (arguments `(#:phases -- cgit 1.4.1 From c8fc1e4f7ab4ff9b46c61ddfad6cf12ed75811a0 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Fri, 28 May 2021 23:42:31 +0200 Subject: gnu: emacs-cider: Update to 1.1.1. * gnu/packages/emacs-xyz.scm (emacs-cider): Update to 1.1.1. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 46f6d8ecc4..b287419db6 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -10462,7 +10462,7 @@ target will call @code{compile} on it.") (define-public emacs-cider (package (name "emacs-cider") - (version "1.1.0") + (version "1.1.1") (source (origin (method git-fetch) @@ -10471,7 +10471,7 @@ target will call @code{compile} on it.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0wigprg45n6q6jmkw2a9s7mr4h500l2ky9244rrdvkjsgj6af8q8")))) + (base32 "0psd8zrhs5w1cfmksd5sjgy9xzfs9i9zp55g97rp7zp6y5als0lx")))) (build-system emacs-build-system) (arguments '(#:exclude ;don't exclude 'cider-test.el' -- cgit 1.4.1 From f95a062f95cc9037a2d6ac928bb896c7e9688566 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 00:02:36 +0200 Subject: gnu: emacs-counsel-jq: Update to 1.1. * gnu/packages/emacs-xyz.scm (emacs-counsel-jq): Update to 1.1. --- gnu/packages/emacs-xyz.scm | 45 +++++++++++++++++++++------------------------ 1 file changed, 21 insertions(+), 24 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index b287419db6..9978d7c989 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -8796,31 +8796,28 @@ The purpose of this library is to wrap all the quirks and hassle of (license license:gpl3+))) (define-public emacs-counsel-jq - (let ((release "1.0.0") - (revision "0") - (commit "aaf33fc2447096cd0d03b77395fe2a95c9fe1481")) - (package - (name "emacs-counsel-jq") - (version (git-version release revision commit)) - (home-page "https://github.com/200ok-ch/counsel-jq") - (source - (origin - (method git-fetch) - (uri (git-reference - (url home-page) - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "10rz0qm8a4bl0m86kx19zq8lri047p4sxqyny08bgm9pbam0wvwn")))) - (build-system emacs-build-system) - (propagated-inputs - `(("emacs-swiper" ,emacs-swiper) - ("jq" ,jq))) - (synopsis "Live preview @code{jq} queries using counsel") - (description - "This Emacs package provides the ability to live preview @code{jq} + (package + (name "emacs-counsel-jq") + (version "1.1") + (home-page "https://github.com/200ok-ch/counsel-jq") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit "aaf33fc2447096cd0d03b77395fe2a95c9fe1481"))) + (file-name (git-file-name name version)) + (sha256 + (base32 "10rz0qm8a4bl0m86kx19zq8lri047p4sxqyny08bgm9pbam0wvwn")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-swiper" ,emacs-swiper) + ("jq" ,jq))) + (synopsis "Live preview @code{jq} queries using counsel") + (description + "This Emacs package provides the ability to live preview @code{jq} queries using counsel.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public emacs-counsel-notmuch ;; Upstream provides no release. Extract version for main file. -- cgit 1.4.1 From a37159c03645cbbaa076e93e0b83bd48c935528c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 00:04:00 +0200 Subject: gnu: emacs-csharp-mode: Update to 0.11.0. * gnu/packages/emacs-xyz.scm (emacs-csharp-mode): Update to 0.11.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 9978d7c989..f4ba9cd94d 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -12863,7 +12863,7 @@ reached with the right hand.") (define-public emacs-csharp-mode (package (name "emacs-csharp-mode") - (version "0.10.0") + (version "0.11.0") (source (origin (method git-fetch) @@ -12872,7 +12872,7 @@ reached with the right hand.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0vwkbla2gkfa9dzxfvrvr7hd2z16769iwbycl7k6l701dnwli1fw")))) + (base32 "0aq6ln92jr3hcrd1592n4s5cb079fly7qaj2hm510p9zckyfx230")))) (build-system emacs-build-system) (home-page "https://github.com/josteink/csharp-mode") (synopsis "Major mode for C# code") -- cgit 1.4.1 From 12489ee005c3c27b99388d5866bdbb3ca28d68e1 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 00:05:23 +0200 Subject: gnu: emacs-cwl-mode: Update to 0.2.6. * gnu/packages/emacs-xyz.scm (emacs-cwl-mode): Update to 0.2.6. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index f4ba9cd94d..d33133ab63 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -28128,7 +28128,7 @@ shorter than usual, using mostly unprefixed keys.") (define-public emacs-cwl-mode (package (name "emacs-cwl-mode") - (version "0.2.5") + (version "0.2.6") (source (origin (method git-fetch) @@ -28138,7 +28138,7 @@ shorter than usual, using mostly unprefixed keys.") (file-name (git-file-name name version)) (sha256 (base32 - "0x9rvyhgy7ijq2r9pin94jz7nisrw6z91jch7d27lkhrmyb1rwk3")))) + "0507acyr9h4646scx316niq27vir6hl2gsgz7wdbiw0cb2drfkd1")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-yaml-mode" ,emacs-yaml-mode))) -- cgit 1.4.1 From 6417b97c7e10de8592ac9fda15774ee711d3dc25 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sat, 29 May 2021 01:21:14 +0100 Subject: Revert "gnu: Add mosaicatcher." mosaicatcher-unbundle-htslib.patch is missing. This reverts commit b1ae0f30d856503fa311d380584a6d7c80559332. --- gnu/packages/bioinformatics.scm | 40 ---------------------------------------- 1 file changed, 40 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2a7443314a..f38c0c07ef 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6170,46 +6170,6 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") ;; 2. MD5 implementation - RSA Data Security, RFC 1321 (license (list license:gpl2+ license:public-domain))))) -(define-public mosaicatcher - (package - (name "mosaicatcher") - (version "0.3.1") - (source (origin - ;; There are no release tarballs nor tags. - (method git-fetch) - (uri (git-reference - (url "https://github.com/friendsofstrandseq/mosaicatcher") - (commit (string-append version "-dev")))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1n2s5wvvj2y0vfgjkg1q11xahpbagxz7h2vf5q7qyy25s12kbzbd")) - (patches (search-patches "mosaicatcher-unbundle-htslib.patch")))) - (build-system cmake-build-system) - (arguments - `(#:tests? #false ; there are no tests - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'chdir - (lambda _ (chdir "src"))) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((target (assoc-ref outputs "out")) - (bin (string-append target "/bin")) - (share (string-append target "/share/mosaicatcher"))) - (install-file "mosaic" bin) - (mkdir-p share) - (copy-recursively "../R" share))))))) - (inputs - `(("boost" ,boost) - ("htslib" ,htslib))) - (home-page "https://github.com/friendsofstrandseq/mosaicatcher") - (synopsis "Count and classify Strand-seq reads") - (description - "Mosaicatcher counts Strand-seq reads and classifies strand states of -each chromosome in each cell using a Hidden Markov Model.") - (license license:expat))) - (define-public ngs-sdk (package (name "ngs-sdk") -- cgit 1.4.1 From 64907645ec86be4a12db66c98343a9e1ea6f781d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 29 May 2021 07:22:30 +0200 Subject: gnu: nyacc: Update to 1.04.0. * gnu/packages/mes.scm (nyacc): Update to 1.04.0. --- gnu/packages/mes.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/mes.scm b/gnu/packages/mes.scm index 750ec2e67a..2defb45ff1 100644 --- a/gnu/packages/mes.scm +++ b/gnu/packages/mes.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Jan (janneke) Nieuwenhuizen ;;; Copyright © 2017, 2018 Efraim Flashner ;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2020, 2021 Ricardo Wurmus ;;; Copyright © 2021 Xinglu Chen ;;; ;;; This file is part of GNU Guix. @@ -99,14 +100,14 @@ extensive examples, including parsers for the Javascript and C99 languages.") (define-public nyacc (package (inherit nyacc-0.99) - (version "1.03.6") + (version "1.04.0") (source (origin (method url-fetch) (uri (string-append "mirror://savannah/nyacc/nyacc-" version ".tar.gz")) (sha256 (base32 - "1s7kli288l4pizjaarx8m6jg7g0mgfy8rpbs9lpzg8la7wr5rvp4")) + "0m3mcdaslvvr2iav8ga146hzsja2hdj4656pszljb4q2q7h25ip5")) (modules '((guix build utils))) (snippet '(begin -- cgit 1.4.1 From e3cde9aaf8dfef17299987590db11aa1f4df418b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 29 May 2021 07:25:08 +0200 Subject: gnu: Add mosaicatcher. * gnu/packages/patches/mosaicatcher-unbundle-htslib.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/bioinformatics.scm (mosaicatcher): New variable. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++ .../patches/mosaicatcher-unbundle-htslib.patch | 49 ++++++++++++++++++++++ 3 files changed, 90 insertions(+) create mode 100644 gnu/packages/patches/mosaicatcher-unbundle-htslib.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 792ebac1e1..cf13d672bd 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1432,6 +1432,7 @@ dist_patch_DATA = \ %D%/packages/patches/module-init-tools-moduledir.patch \ %D%/packages/patches/monero-use-system-miniupnpc.patch \ %D%/packages/patches/mono-mdoc-timestamping.patch \ + %D%/packages/patches/mosaicatcher-unbundle-htslib.patch \ %D%/packages/patches/mozjs17-aarch64-support.patch \ %D%/packages/patches/mozjs24-aarch64-support.patch \ %D%/packages/patches/mozjs38-pkg-config-version.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f38c0c07ef..2a7443314a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6170,6 +6170,46 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") ;; 2. MD5 implementation - RSA Data Security, RFC 1321 (license (list license:gpl2+ license:public-domain))))) +(define-public mosaicatcher + (package + (name "mosaicatcher") + (version "0.3.1") + (source (origin + ;; There are no release tarballs nor tags. + (method git-fetch) + (uri (git-reference + (url "https://github.com/friendsofstrandseq/mosaicatcher") + (commit (string-append version "-dev")))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1n2s5wvvj2y0vfgjkg1q11xahpbagxz7h2vf5q7qyy25s12kbzbd")) + (patches (search-patches "mosaicatcher-unbundle-htslib.patch")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #false ; there are no tests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "src"))) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((target (assoc-ref outputs "out")) + (bin (string-append target "/bin")) + (share (string-append target "/share/mosaicatcher"))) + (install-file "mosaic" bin) + (mkdir-p share) + (copy-recursively "../R" share))))))) + (inputs + `(("boost" ,boost) + ("htslib" ,htslib))) + (home-page "https://github.com/friendsofstrandseq/mosaicatcher") + (synopsis "Count and classify Strand-seq reads") + (description + "Mosaicatcher counts Strand-seq reads and classifies strand states of +each chromosome in each cell using a Hidden Markov Model.") + (license license:expat))) + (define-public ngs-sdk (package (name "ngs-sdk") diff --git a/gnu/packages/patches/mosaicatcher-unbundle-htslib.patch b/gnu/packages/patches/mosaicatcher-unbundle-htslib.patch new file mode 100644 index 0000000000..262895ddcf --- /dev/null +++ b/gnu/packages/patches/mosaicatcher-unbundle-htslib.patch @@ -0,0 +1,49 @@ +--- a/src/CMakeLists.txt 2021-05-28 13:07:25.655107983 +0200 ++++ b/src/CMakeLists.txt 2021-05-28 13:09:55.764025497 +0200 +@@ -21,24 +21,6 @@ + + + +-### Link HTSlib +- +-ExternalProject_Add(htslib +- PREFIX ${CMAKE_BINARY_DIR}/htslib +- GIT_REPOSITORY "https://github.com/samtools/htslib.git" +- GIT_TAG "1.3.1" +- UPDATE_COMMAND "" +- BUILD_IN_SOURCE 1 +- CONFIGURE_COMMAND "" +- BUILD_COMMAND make +- INSTALL_COMMAND make install prefix=${CMAKE_BINARY_DIR}/htslib +- LOG_DOWNLOAD 1 +-) +-link_directories (${CMAKE_BINARY_DIR}/htslib/lib) +-include_directories (${CMAKE_BINARY_DIR}/htslib/include) +- +- +- + ### Set version + + # Get the current working branch +@@ -64,13 +46,6 @@ + + # 2. Boost version from find_package (Boost_VERSION) + +-# 3. Get HTSlib version from git +-execute_process( +- COMMAND git describe --always +- WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/htslib +- OUTPUT_VARIABLE HTSLIB_VERSION +- OUTPUT_STRIP_TRAILING_WHITESPACE +-) + set(HTSLIB_VERSION "1.3.1 ${HTSLIB_VERSION}") + + # 4. write version.hpp file +@@ -105,7 +80,6 @@ + add_executable (mosaic main.cpp ${HEADER_FILES}) + target_link_libraries (mosaic LINK_PUBLIC ${Boost_LIBRARIES}) + target_link_libraries (mosaic LINK_PUBLIC hts) +-add_dependencies (mosaic htslib) + + + ### Doxygen API documentation -- cgit 1.4.1 From 6e1cf434d75c3d6db377ea260b90c596e9d8a554 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Sat, 29 May 2021 15:58:56 +0200 Subject: gnu: cuirass: Update to 1.0.0-23.58e3551. * gnu/packages/ci.scm (cuirass): Update to 1.0.0-23.58e3551. --- gnu/packages/ci.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm index f3fae20383..588f52ae56 100644 --- a/gnu/packages/ci.scm +++ b/gnu/packages/ci.scm @@ -73,8 +73,8 @@ (file-name (string-append name "-" version "-checkout"))))))) (define-public cuirass - (let ((commit "3ac739b97dbf3684f925eac7a5d609e79ec1ac5f") - (revision "22")) + (let ((commit "58e3551d6dcc3cf4a9d072d6c56531ae3b6e7bbe") + (revision "23")) (package (name "cuirass") (version (git-version "1.0.0" revision commit)) @@ -87,7 +87,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "1nl171qmxhcb0sq39khk7knapvlzm26z2lmzqwdmj65vyyg9inrc")))) + "0m2w0258m9mb1gq1522z4mhinhs3xgbmdas4aaqnf50hsnxmh7h5")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build utils) -- cgit 1.4.1 From ef5c6f9097367d45225bf6ca994cd2b51153da6d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 15:01:13 +0200 Subject: gnu: mc: Support mice. * gnu/packages/mc.scm (mc)[inputs]: Add gpm. --- gnu/packages/mc.scm | 2 ++ 1 file changed, 2 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/mc.scm b/gnu/packages/mc.scm index 7369dcf800..73ffc14e57 100644 --- a/gnu/packages/mc.scm +++ b/gnu/packages/mc.scm @@ -31,6 +31,7 @@ #:use-module (gnu packages ssh) #:use-module (gnu packages pkg-config) #:use-module (gnu packages check) + #:use-module (gnu packages linux) #:use-module (gnu packages perl) #:use-module (gnu packages compression)) @@ -49,6 +50,7 @@ (native-inputs `(("pkg-config" ,pkg-config) ("perl" ,perl))) (inputs `(("aspell" ,aspell) + ("gpm" ,gpm) ("ncurses" ,ncurses) ("libssh2" ,libssh2) ("glib" ,glib) -- cgit 1.4.1 From 11e4ccc6fb8f10f4d7c81e663eb4933c915572aa Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 15:04:33 +0200 Subject: Sort module imports in (gnu packages mc). * gnu/packages/mc.scm: Order module imports alphabetically. --- gnu/packages/mc.scm | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/mc.scm b/gnu/packages/mc.scm index 73ffc14e57..9b5a0c4830 100644 --- a/gnu/packages/mc.scm +++ b/gnu/packages/mc.scm @@ -20,20 +20,20 @@ ;;; along with GNU Guix. If not, see . (define-module (gnu packages mc) - #:use-module (guix packages) - #:use-module (guix licenses) - #:use-module (guix download) - #:use-module (guix build-system gnu) - #:use-module (gnu packages) #:use-module (gnu packages aspell) - #:use-module (gnu packages ncurses) - #:use-module (gnu packages glib) - #:use-module (gnu packages ssh) - #:use-module (gnu packages pkg-config) #:use-module (gnu packages check) + #:use-module (gnu packages compression) + #:use-module (gnu packages glib) #:use-module (gnu packages linux) + #:use-module (gnu packages ncurses) #:use-module (gnu packages perl) - #:use-module (gnu packages compression)) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages ssh) + #:use-module (gnu packages) + #:use-module (guix build-system gnu) + #:use-module (guix download) + #:use-module (guix licenses) + #:use-module (guix packages)) (define-public mc (package -- cgit 1.4.1 From 38e8ffe25582aa9ffb5196bcd46a201571961591 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 15:05:05 +0200 Subject: gnu: mc: Order inputs alphabetically. * gnu/packages/mc.scm (mc)[native-inputs, inputs]: Order alphabetically. --- gnu/packages/mc.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/mc.scm b/gnu/packages/mc.scm index 9b5a0c4830..b9dea3b446 100644 --- a/gnu/packages/mc.scm +++ b/gnu/packages/mc.scm @@ -47,14 +47,14 @@ (sha256 (base32 "09vc2vf6k12a8k5gdss6hcskwfcbyalrkhn65nidkwlm0p2svpn6")))) (build-system gnu-build-system) - (native-inputs `(("pkg-config" ,pkg-config) - ("perl" ,perl))) + (native-inputs `(("perl" ,perl) + ("pkg-config" ,pkg-config))) (inputs `(("aspell" ,aspell) + ("check" ,check) + ("glib" ,glib) ("gpm" ,gpm) - ("ncurses" ,ncurses) ("libssh2" ,libssh2) - ("glib" ,glib) - ("check" ,check) + ("ncurses" ,ncurses) ("unzip" ,unzip))) (arguments `(#:configure-flags -- cgit 1.4.1 From 947398c70a382762eac6e22a214f282301c1af71 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 15:44:23 +0200 Subject: gnu: emacs: Support console mice. * gnu/packages/emacs.scm (emacs)[inputs]: Add gpm. --- gnu/packages/emacs.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 1a2b98bec2..1edbaa463a 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -59,7 +59,7 @@ #:use-module (gnu packages gtk) #:use-module (gnu packages guile) #:use-module (gnu packages image) - #:use-module (gnu packages linux) ; alsa-lib + #:use-module (gnu packages linux) ; alsa-lib, gpm #:use-module (gnu packages mail) ; for mailutils #:use-module (gnu packages multiprecision) #:use-module (gnu packages ncurses) @@ -247,6 +247,7 @@ ("mailutils" ,mailutils) ;; TODO: Add the optional dependencies. + ("gpm" ,gpm) ("libx11" ,libx11) ("gtk+" ,gtk+) ("cairo" ,cairo) -- cgit 1.4.1 From 9e632a55546e9b6bb8098e5743678daf86a2c855 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 16:05:00 +0200 Subject: gnu: isc-dhcp: Update to 4.4.2-P1 [fixes CVE-2021-25217]. * gnu/packages/admin.scm (isc-dhcp): Update to 4.4.2-P1. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 001c6db414..a3d260818e 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1147,14 +1147,14 @@ connection alive.") bind-release-version))) (package (name "isc-dhcp") - (version "4.4.2") + (version "4.4.2-P1") (source (origin (method url-fetch) (uri (string-append "https://ftp.isc.org/isc/dhcp/" version "/dhcp-" version ".tar.gz")) (sha256 (base32 - "08a5003zdxgl41b29zjkxa92h2i40zyjgxg0npvnhpkfl5jcsz0s")))) + "06jsr0cg5rsmyibshrpcb9za0qgwvqccashdma7mlm1rflrh8pmh")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f -- cgit 1.4.1 From ee206133de2100bd872e493710a0b28995744b21 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 16:05:31 +0200 Subject: gnu: isc-dhcp: Update home page. * gnu/packages/admin.scm (isc-dhcp)[home-page]: Update. --- gnu/packages/admin.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index a3d260818e..8bc02f5ee3 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1277,7 +1277,7 @@ connection alive.") ("coreutils*" ,coreutils) ("sed*" ,sed))) - (home-page "https://www.isc.org/products/DHCP/") + (home-page "https://www.isc.org/dhcp/") (synopsis "Dynamic Host Configuration Protocol (DHCP) tools") (description "ISC's Dynamic Host Configuration Protocol (DHCP) distribution provides a -- cgit 1.4.1 From 38c892f6057d3a9331be19af496bc5c5a87b4b6d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 28 May 2021 22:57:46 +0200 Subject: gnu: libjcat: Update to 0.1.8. * gnu/packages/compression.scm (libjcat): Update to 0.1.8. --- gnu/packages/compression.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index c1996edbec..33d05173e9 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -1015,7 +1015,7 @@ tarballs.") (define-public libjcat (package (name "libjcat") - (version "0.1.7") + (version "0.1.8") (source (origin (method git-fetch) @@ -1025,7 +1025,7 @@ tarballs.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "110c8h3p7m4ibrfvgja592z7j5h88qqanllxsvmxkjz3b129i02r")))) + (base32 "18qkyg19r7fxzv93kar5n808n3582ygjmqwa7rnyg5y4b6hnwihl")))) (build-system meson-build-system) (native-inputs `(("gobject-introspection" ,gobject-introspection) -- cgit 1.4.1 From 1374347ddbdde476703a2d98666897e7c5f22a34 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 28 May 2021 23:08:32 +0200 Subject: gnu: libolm: Update to 3.2.3. * gnu/packages/crypto.scm (libolm): Update to 3.2.3. --- gnu/packages/crypto.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index 674cb05801..99455dc632 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -1299,7 +1299,7 @@ Trusted comments are signed, thus verified, before being displayed.") (define-public libolm (package (name "libolm") - (version "3.2.2") + (version "3.2.3") (source (origin (method git-fetch) (uri (git-reference @@ -1307,7 +1307,7 @@ Trusted comments are signed, thus verified, before being displayed.") (commit version))) (sha256 (base32 - "0qji25wiwmkxyfpraxj96c54hyayqmjkvwh0gsy5gb5pz5bp4mcy")) + "0bixly6jqpwfx3p37c1qp1j685yg6m429r1nazwh43w4n527bs3y")) (file-name (git-file-name name version)))) (build-system cmake-build-system) (arguments -- cgit 1.4.1 From f3a15e5450e2f8d47334d90b4fb4e0a3d2425331 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:10:28 +0200 Subject: gnu: emacs-datetime: Update to 0.7. * gnu/packages/emacs-xyz.scm (emacs-datetime): Update to 0.7. --- gnu/packages/emacs-xyz.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index d33133ab63..7218faa4b6 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -17042,7 +17042,7 @@ navigate and display hierarchy structures.") (define-public emacs-datetime (package (name "emacs-datetime") - (version "0.6.6") + (version "0.7") (source (origin (method git-fetch) @@ -17051,8 +17051,7 @@ navigate and display hierarchy structures.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 - "0a3q667pybpmsjkbgf6287jwgpnx8brp5314wb8zbczw6ncygnbi")))) + (base32 "0g6qgp6zvrbiaq6yfzqs3bmnry43xspp3ra3hm17x80b6izdsn90")))) (build-system emacs-build-system) (arguments `(#:include (cons "^[^/]*\\.extmap$" %default-include))) -- cgit 1.4.1 From f22c1cb0eee9f2e600c588446cd6a3d7af47f63b Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:15:08 +0200 Subject: gnu: emacs-dired-sidebar: Update to 0.2.0. * gnu/packages/emacs-xyz.scm (emacs-dired-sidebar): Update to 0.2.0. --- gnu/packages/emacs-xyz.scm | 40 ++++++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 20 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 7218faa4b6..13966ea8c7 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13930,27 +13930,27 @@ additions: (license license:gpl3+)))) (define-public emacs-dired-sidebar - (let ((commit "da77919081d9a4e73c2df63542353319381e4f89") - (revision "2")) - (package - (name "emacs-dired-sidebar") - (home-page "https://github.com/jojojames/dired-sidebar") - (version (git-version "0.1.0" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference (url home-page) (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "05h56wdl2xvc8davnx83ypg20fl7wlks97cafa4r2yf141xjc05h")))) - (build-system emacs-build-system) - (propagated-inputs - `(("emacs-dired-subtree" ,emacs-dired-hacks))) - (synopsis "Sidebar for Emacs using Dired") - (description - "This package provides a sidebar for Emacs similar to @code{NeoTree} + (package + (name "emacs-dired-sidebar") + (home-page "https://github.com/jojojames/dired-sidebar") + (version "0.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "090dqaqyjmkzrz4szjpk1iip0bdvb0frp4l79393f8ki8w7c16c1")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-dired-subtree" ,emacs-dired-hacks))) + (synopsis "Sidebar for Emacs using Dired") + (description + "This package provides a sidebar for Emacs similar to @code{NeoTree} or @code{treemacs}, but leveraging @code{Dired} to do the job of display.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public emacs-which-key (package -- cgit 1.4.1 From d7c61c3acad947f83d69e2375129bf0d057b9fae Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:16:01 +0200 Subject: gnu: emacs-d-mode: Update to 2.0.11. * gnu/packages/emacs-xyz.scm (emacs-d-mode): Update to 2.0.11. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 13966ea8c7..1bd56b22be 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -3295,7 +3295,7 @@ evaluations. The entry point is @code{M-x build-farm} command.") (define-public emacs-d-mode (package (name "emacs-d-mode") - (version "2.0.10") + (version "2.0.11") (source (origin (method git-fetch) @@ -3304,7 +3304,7 @@ evaluations. The entry point is @code{M-x build-farm} command.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0915kb9jcaixgindhj85fmykkhvj31ckp1yg6746fznwdgfrlifv")))) + (base32 "0vkl470vvmxap8ca773a0jvjvalmvdbbax3qvgjdclp54ml75al4")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-undercover" ,emacs-undercover))) -- cgit 1.4.1 From a8aafa39c664059df11ddb3025550665202382de Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:16:13 +0200 Subject: gnu: emacs-d-mode: Clean up description. * gnu/packages/emacs-xyz.scm (emacs-d-mode)[description]: Remove unnecessary information. --- gnu/packages/emacs-xyz.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 1bd56b22be..677112889b 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -3311,8 +3311,7 @@ evaluations. The entry point is @code{M-x build-farm} command.") (home-page "https://github.com/Emacs-D-Mode-Maintainers/Emacs-D-Mode") (synopsis "Emacs major mode for editing D code") (description "This package provides an Emacs major mode for highlighting -code written in the D programming language. This mode is currently known to -work with Emacs 24 and 25.") +code written in the D programming language.") (license license:gpl2+))) (define-public emacs-extempore-mode -- cgit 1.4.1 From d936eee8bc3780b32a2c81ff888eee96eded1b66 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:19:29 +0200 Subject: gnu: emacs-dockerfile-mode: Update to 1.4. * gnu/packages/emacs-xyz.scm (emacs-dockerfile-mode): Update to 1.4. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 677112889b..1a95216fa7 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -22458,7 +22458,7 @@ constant expressions.") (define-public emacs-dockerfile-mode (package (name "emacs-dockerfile-mode") - (version "1.3") + (version "1.4") (source (origin (method git-fetch) @@ -22468,7 +22468,7 @@ constant expressions.") (file-name (git-file-name name version)) (sha256 (base32 - "1br73dsls42fn4rwagljkpa3l4wwj6f7jxfn3gmgl6c54z81av3v")))) + "1ypkihd9si769r6k0lfrv8jq8mjv4gyhiwyi820sayfppvma5rj0")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-s" ,emacs-s))) -- cgit 1.4.1 From 23fb3fa28004f7570a63b1a7cabce8dd0afac784 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:20:06 +0200 Subject: gnu: emacs-doom-modeline: Update to 3.1.1. * gnu/packages/emacs-xyz.scm (emacs-doom-modeline): Update to 3.1.1. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 1a95216fa7..fdc26b489e 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -25673,7 +25673,7 @@ Telegram messaging platform.") (define-public emacs-doom-modeline (package (name "emacs-doom-modeline") - (version "3.0.0") + (version "3.1.1") (source (origin (method git-fetch) (uri (git-reference @@ -25681,7 +25681,7 @@ Telegram messaging platform.") (commit (string-append "v" version)))) (sha256 (base32 - "08m75rl5i812pa87zcsjvb4mm3jjhpwzgx9mf2m7sxj807airz5d")) + "1dkgh87sv25mdlzdfihp6gp0asvwplx9yrn7nfsqzsfc3kpajkck")) (file-name (git-file-name name version)))) (build-system emacs-build-system) (arguments -- cgit 1.4.1 From 9a254d5ccb87f767af3ca54e12213e87190d277c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:22:27 +0200 Subject: gnu: emacs-ebib: Update to 2.32.1. * gnu/packages/emacs-xyz.scm (emacs-ebib): Update to 2.32.1. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index fdc26b489e..6d75c19ed0 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -16621,7 +16621,7 @@ files to be expanded upon opening them.") (define-public emacs-ebib (package (name "emacs-ebib") - (version "2.29") + (version "2.32.1") (source (origin (method git-fetch) @@ -16630,7 +16630,7 @@ files to be expanded upon opening them.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1d0xnhdcsz2ysq145k2l0f2r4vb0pkai1v6wl6sfba7xi5fc323i")))) + (base32 "1xgpdw0sxl2c9dn6x6fk0rqpqlqxsjlj0vyag611blj600br7dqr")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-parsebib" ,emacs-parsebib))) -- cgit 1.4.1 From bc068d3e829d3f611da2a613bc955f730aa2a2a5 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:22:59 +0200 Subject: gnu: emacs-eldev: Update to 0.9.1. * gnu/packages/emacs-xyz.scm (emacs-eldev): Update to 0.9.1. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 6d75c19ed0..2cf1bfdea5 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -16433,7 +16433,7 @@ according to a parsing expression grammar.") (define-public emacs-eldev (package (name "emacs-eldev") - (version "0.8.1") + (version "0.9.1") (source (origin (method git-fetch) (uri (git-reference @@ -16442,7 +16442,7 @@ according to a parsing expression grammar.") (file-name (git-file-name name version)) (sha256 (base32 - "19s45hdhcg5l608awfxvmhd61xzp7dd5pvviv89xzzksx74l1188")))) + "1jfj4f5w20qd12k6ygv0jazn2x9pxjrmqmlmibppc4ybrhhgmg0s")))) (build-system emacs-build-system) (arguments `(#:tests? #t -- cgit 1.4.1 From 13ab81d94d0f9176ab97f3c0daea25ff9086b47b Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:23:34 +0200 Subject: gnu: emacs-elfeed-score: Update to 0.7.8. * gnu/packages/emacs-xyz.scm (emacs-elfeed-score): Update to 0.7.8. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 2cf1bfdea5..91f639d9de 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -9574,7 +9574,7 @@ with Elfeed.") (define-public emacs-elfeed-score (package (name "emacs-elfeed-score") - (version "0.7.7") + (version "0.7.8") (source (origin (method git-fetch) @@ -9584,7 +9584,7 @@ with Elfeed.") (file-name (git-file-name name version)) (sha256 (base32 - "07xid0a31ghknbfwj8dxzbqkg4sfayjhlqvp17p2bzlf1mj0zjyd")))) + "0lcpj2vp947kbfk6fq7xz7j71mcpjs9086pqh690w4mzv1253gra")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-elfeed" ,emacs-elfeed))) -- cgit 1.4.1 From 218bea8b5f25240cefda27133ee548257f5497b0 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:25:36 +0200 Subject: gnu: emacs-esxml: Update to 0.3.7. * gnu/packages/emacs-xyz.scm (emacs-esxml): Update to 0.3.7. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 91f639d9de..a47ff26db3 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -15289,7 +15289,7 @@ Lisp.") (define-public emacs-esxml (package (name "emacs-esxml") - (version "0.3.5") + (version "0.3.7") (source (origin (method git-fetch) (uri (git-reference @@ -15298,7 +15298,7 @@ Lisp.") (file-name (git-file-name name version)) (sha256 (base32 - "16jn404vfmsvm12wrf8iczqlgdf2iycbxrvalvzxnm2gr5dfzp7z")))) + "1xzxmgsg0j72sf1vjh9gjswz3c29js0kqhm7r3jrqrh3a5agdnml")))) (build-system emacs-build-system) (arguments `(#:phases -- cgit 1.4.1 From 1a597afd96e942953affaaca28c3d2d98e4c731f Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:26:23 +0200 Subject: gnu: emacs-evil-commentary: Update to 2.2.0. * gnu/packages/emacs-xyz.scm (emacs-evil-commentary): Update to 2.2.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a47ff26db3..b0da921690 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13421,7 +13421,7 @@ addition of surrounding pairs, such as parentheses and quotes, in evil mode.") (define-public emacs-evil-commentary (package (name "emacs-evil-commentary") - (version "2.1.1") + (version "2.2.0") (source (origin (method git-fetch) @@ -13430,7 +13430,7 @@ addition of surrounding pairs, such as parentheses and quotes, in evil mode.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0zjs9zyqfygnpxapvf0ymmiid40i06cxbhjzd81zw33nafgkf6r4")))) + (base32 "1l8zi9wlg1f7ffm8gh92qwk3q7h6cdl8b8zkd9hcda53mq6klpjr")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-evil" ,emacs-evil))) -- cgit 1.4.1 From fac09678e7b219fddf1ee5c5e99e035b60bbd44a Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:26:56 +0200 Subject: gnu: emacs-evil-matchit: Update to 2.3.11. * gnu/packages/emacs-xyz.scm (emacs-evil-matchit): Update to 2.3.11. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index b0da921690..561b7bfd2f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -15030,7 +15030,7 @@ Features: (define-public emacs-evil-matchit (package (name "emacs-evil-matchit") - (version "2.3.10") + (version "2.3.11") (source (origin (method git-fetch) @@ -15039,7 +15039,7 @@ Features: (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "14nrc46290q54y7wv25251f2kqc0z8i9byl09xkgjijqldl9vdxa")))) + (base32 "1990g1b6v0i7jaiv35bdssdn601rjifzg4fy9s3sxk0drqm1xiss")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-evil" ,emacs-evil))) -- cgit 1.4.1 From 838835dd8645fe9b398ee17bb96c218345e7089b Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:27:45 +0200 Subject: gnu: emacs-evil-nerd-commenter: Update to 3.5.4. * gnu/packages/emacs-xyz.scm (emacs-evil-nerd-commenter): Update to 3.5.4. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 561b7bfd2f..245a63b1c7 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -11250,7 +11250,7 @@ pasting into and from @code{tmux} paste buffers.") (define-public emacs-evil-nerd-commenter (package (name "emacs-evil-nerd-commenter") - (version "3.5.3") + (version "3.5.4") (source (origin (method git-fetch) @@ -11260,7 +11260,7 @@ pasting into and from @code{tmux} paste buffers.") (file-name (git-file-name name version)) (sha256 (base32 - "1y5pn3rkqj8dxp5c7dsci621vnv6hsia74w2c1hybkkrjbka851q")))) + "1vyl8lidhjph7k86n8q09mwqpasaxsmwb8vi5i2gcd6klds9hg0d")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-evil" ,emacs-evil))) (home-page "https://github.com/redguardtoo/evil-nerd-commenter") -- cgit 1.4.1 From e1e7cb650dcf5a103835734cef96511e39c8fc65 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:30:05 +0200 Subject: gnu: emacs-ewmctrl: Update to 1.0.0. * gnu/packages/emacs-xyz.scm (emacs-ewmctrl): Update to 1.0.0. The previous commit was exactly matching "1.0.0" tag, so the hash did not change. --- gnu/packages/emacs-xyz.scm | 63 +++++++++++++++++++++++----------------------- 1 file changed, 31 insertions(+), 32 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 245a63b1c7..79b3ea9629 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -16724,39 +16724,38 @@ arXiv, Google Scholar, Library of Congress, etc. (license license:gpl3+)))) (define-public emacs-ewmctrl - (let ((commit "3d0217c4d6cdb5c308b6cb4293574f470d4faacf")) - (package - (name "emacs-ewmctrl") - (version (git-version "0.0.1" "1" commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/flexibeast/ewmctrl") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0ilwvx0qryv3v6xf0gxqwnfm6pf96gxap8h9g3f6z6lk9ff4n1wi")))) - (build-system emacs-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-ewmctrl - ;; This build phase makes sure ‘ewmctrl’ looks - ;; for ‘wmctrl’ in the right place. - (lambda _ - (let ((file "ewmctrl.el")) - (chmod file #o644) - (emacs-substitute-sexps file - ("(defcustom ewmctrl-wmctrl-path" (which "wmctrl"))))))))) - (inputs - `(("wmctrl" ,wmctrl))) - (home-page "https://github.com/flexibeast/ewmctrl") - (synopsis "Emacs interface to @code{wmctrl}") - (description "@code{ewmctrl} provides an Emacs interface to + (package + (name "emacs-ewmctrl") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/flexibeast/ewmctrl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ilwvx0qryv3v6xf0gxqwnfm6pf96gxap8h9g3f6z6lk9ff4n1wi")))) + (build-system emacs-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-ewmctrl + ;; This build phase makes sure ‘ewmctrl’ looks + ;; for ‘wmctrl’ in the right place. + (lambda _ + (let ((file "ewmctrl.el")) + (chmod file #o644) + (emacs-substitute-sexps file + ("(defcustom ewmctrl-wmctrl-path" (which "wmctrl"))))))))) + (inputs + `(("wmctrl" ,wmctrl))) + (home-page "https://github.com/flexibeast/ewmctrl") + (synopsis "Emacs interface to @code{wmctrl}") + (description "@code{ewmctrl} provides an Emacs interface to @code{wmctrl} command-line window-management program.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public emacs-erc-image (let ((commit "82fb3871f02e24b1e880770b9a3d187aab43d0f0") -- cgit 1.4.1 From da71f7466b7686953a083121b472ba2bce4f760d Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:31:14 +0200 Subject: gnu: emacs-exwm-x: Update to 2.0.2. * gnu/packages/emacs-xyz.scm (emacs-exwm-x): Update to 2.0.2. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 79b3ea9629..1ab31521d6 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13238,7 +13238,7 @@ other operations.") (define-public emacs-exwm-x (package (name "emacs-exwm-x") - (version "1.9.0") + (version "2.0.2") (synopsis "Derivative window manager based on EXWM") (source (origin @@ -13249,7 +13249,7 @@ other operations.") (file-name (git-file-name name version)) (sha256 (base32 - "03l3dl7s1qys1kkh40rm1sfx7axy1b8sf5f6nyksj9ps6d30p5i4")))) + "0h248mma7kky30jr9bbhmp95wchl2cx5p6kh0gxmzpbc247dn2cc")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-counsel" ,emacs-counsel) -- cgit 1.4.1 From c899ed0ca75bc7a80d98d115650403d58c18b8d7 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:32:13 +0200 Subject: gnu: emacs-find-file-in-project: Update to 6.0.7. * gnu/packages/emacs-xyz.scm (emacs-find-file-in-project): Update to 6.0.7. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 1ab31521d6..27d1984188 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -9663,7 +9663,7 @@ maximizes flexibility (at the expense of conciseness).") (define-public emacs-find-file-in-project (package (name "emacs-find-file-in-project") - (version "6.0.0") + (version "6.0.7") (source (origin (method git-fetch) (uri (git-reference @@ -9672,7 +9672,7 @@ maximizes flexibility (at the expense of conciseness).") (file-name (git-file-name name version)) (sha256 (base32 - "1iagywiihwv96y9p811xlx4cmbsj8h76niymprv1vm4fj6cmihr6")))) + "1qkfijqr839y605ssyalr2v9n6b86hr64mxikc96lx6nzdyjyyl0")))) (build-system emacs-build-system) (arguments `(#:tests? #t -- cgit 1.4.1 From 8691ea2ab7b9af98b9e5d5d5b52cda3daaa75108 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:35:27 +0200 Subject: gnu: emacs-geiser-racket: Remove ".git" suffix from origin URI. * gnu/packages/emacs-xyz.scm (emacs-geiser-racket)[source]: Remove ".git" suffix. --- gnu/packages/emacs-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 27d1984188..33890eb8f2 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -367,7 +367,7 @@ a generic Scheme interaction mode for the GNU Emacs editor.") (origin (method git-fetch) (uri (git-reference - (url "https://gitlab.com/emacs-geiser/racket.git") + (url "https://gitlab.com/emacs-geiser/racket") (commit version))) (file-name (git-file-name name version)) (sha256 -- cgit 1.4.1 From feb9ae939eefc391751ed50d8cbf1d9b0ea1112f Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:36:29 +0200 Subject: gnu: emacs-ghub: Update to 3.5.3. * gnu/packages/emacs-xyz.scm (emacs-ghub): Update to 3.5.3. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 33890eb8f2..eb8d2a7cd8 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1073,7 +1073,7 @@ organizing remote Go repository clones.") (define-public emacs-ghub (package (name "emacs-ghub") - (version "3.4.1") + (version "3.5.3") (source (origin (method git-fetch) @@ -1082,7 +1082,7 @@ organizing remote Go repository clones.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "07iy4203ppvzkh67sb0v968hnypnvy4dpfy0qpqrp8zmc455dxq5")))) + (base32 "1sn7rzfkm75vj3whhisrjk1s34lz6hc08hmf4nnznbdvyimnd013")))) (build-system emacs-build-system) (arguments `(#:phases -- cgit 1.4.1 From e1e4684552a6201ec91fcb51f90f27dbc1d2e28c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:37:48 +0200 Subject: gnu: emacs-gitlab-ci-mode: Update to 20190824.12.2. * gnu/packages/emacs-xyz.scm (emacs-gitlab-ci-mode): Update to 20190824.12.2. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index eb8d2a7cd8..f4e87f7384 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -10112,7 +10112,7 @@ behavior very similar to that of Python mode.") (define-public emacs-gitlab-ci-mode (package (name "emacs-gitlab-ci-mode") - (version "20190425.11.10") + (version "20190824.12.2") (source (origin (method git-fetch) (uri (git-reference @@ -10121,7 +10121,7 @@ behavior very similar to that of Python mode.") (file-name (git-file-name name version)) (sha256 (base32 - "1jkp9mnbiccqnha9zs646znqyqvy5jjb81kah7ghbkzdqqk2avm0")))) + "16fb4r3vq8xkzl911v7gaky95w1agfxjlpaxpjmidwx48rbcar59")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-yaml-mode" ,emacs-yaml-mode))) -- cgit 1.4.1 From 649d9bccef910c042fa02a771ffce73b9c6c649d Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:38:00 +0200 Subject: gnu: emacs-gitlab-ci-mode: Drop ".git" suffix in source URI. * gnu/packages/emacs-xyz.scm (emacs-gitlab-ci-mode)[source]: Drop ".git" suffix. --- gnu/packages/emacs-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index f4e87f7384..4fc323521b 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -10116,7 +10116,7 @@ behavior very similar to that of Python mode.") (source (origin (method git-fetch) (uri (git-reference - (url "https://gitlab.com/joewreschnig/gitlab-ci-mode.git") + (url "https://gitlab.com/joewreschnig/gitlab-ci-mode") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 -- cgit 1.4.1 From e35f0c463486b73fa52871858e24332ed619b3a0 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:39:02 +0200 Subject: gnu: emacs-god-mode: Update to 2.17.3. * gnu/packages/emacs-xyz.scm (emacs-god-mode): Update to 2.17.3. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 4fc323521b..b08ca3bf4f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6805,7 +6805,7 @@ linting of manifests and integration with Puppet Debugger.") (define-public emacs-god-mode (package (name "emacs-god-mode") - (version "2.17.0") + (version "2.17.3") (source (origin (method git-fetch) @@ -6815,7 +6815,7 @@ linting of manifests and integration with Puppet Debugger.") (file-name (git-file-name name version)) (sha256 (base32 - "1d2nrj35fzhnycchi0b7m5mbk5fyq7bgpbkkvc5xzqafclrsnapi")))) + "1wsc04l5j5a9y5439qx85pcchxjnjgcgwbffw3l30q9zlblvc58b")))) (build-system emacs-build-system) (home-page "https://github.com/chrisdone/god-mode") (synopsis "Minor mode for entering commands without modifier keys") -- cgit 1.4.1 From b273527eb7af1a38fc23e3ffef9f0804aecfbc0e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:39:37 +0200 Subject: gnu: emacs-helm: Update to 3.7.1. * gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.7.1. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index b08ca3bf4f..c3fad3a7a2 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -10228,7 +10228,7 @@ ack, ag, helm and pt.") (define-public emacs-helm (package (name "emacs-helm") - (version "3.7.0") + (version "3.7.1") (source (origin (method git-fetch) @@ -10237,7 +10237,7 @@ ack, ag, helm and pt.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0lxq13bsbh7xawgsq08kjm7s28x9yl8mid3538flv5kcc1rv2b9y")))) + (base32 "0b8sfpvy02ijk9xi9b44762b718jqfq063wcg75dk3q452d27s1h")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-async" ,emacs-async) -- cgit 1.4.1 From 7c45ad24832403986a4de0f650f36cb1fca4003e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:40:28 +0200 Subject: gnu: emacs-helm-ag: Update to 0.64. * gnu/packages/emacs-xyz.scm (emacs-helm-ag): Update to 0.64. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index c3fad3a7a2..992257c0ca 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -10305,7 +10305,7 @@ for search-based navigation of buffers.") (define-public emacs-helm-ag (package (name "emacs-helm-ag") - (version "0.62") + (version "0.64") (source (origin (method git-fetch) @@ -10314,7 +10314,7 @@ for search-based navigation of buffers.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0xgbpp8xqdiyvfs64x0q909g77ml28z3irw2lnasvpsg0dfdm2zy")))) + (base32 "0ml9yp3qaiwn7iixyxvsj3fxn7gw913qxisr47df57q4ka912law")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-helm" ,emacs-helm))) -- cgit 1.4.1 From d4037e781cf6b4439c04006638a943353ca6e3e7 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:41:09 +0200 Subject: gnu: emacs-helm-org-rifle: Update to 1.7.1. * gnu/packages/emacs-xyz.scm (emacs-helm-org-rifle): Update to 1.7.1. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 992257c0ca..1ebf84963a 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -12216,7 +12216,7 @@ above over the network.") (define-public emacs-helm-org-rifle (package (name "emacs-helm-org-rifle") - (version "1.7.0") + (version "1.7.1") (source (origin (method git-fetch) @@ -12226,7 +12226,7 @@ above over the network.") (file-name (git-file-name name version)) (sha256 (base32 - "058zvh7cdall7dl3xay9ibcjvs13fbqp8fli3lz980pinmsds3r2")))) + "0pm6va26kadjvbai4qsnjc2bk379w2nk6h3b5f0c2yv3q5na0p49")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-dash" ,emacs-dash) -- cgit 1.4.1 From 71fd285657894c568e353980dfeb022963ae1a27 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:41:46 +0200 Subject: gnu: emacs-highlight-defined: Update to 0.1.6. * gnu/packages/emacs-xyz.scm (emacs-highlight-defined): Update to 0.1.6. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 1ebf84963a..394c89b2d9 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -18721,7 +18721,7 @@ decrease the number at point.") (define-public emacs-highlight-defined (package (name "emacs-highlight-defined") - (version "0.1.5") + (version "0.1.6") (source (origin (method git-fetch) @@ -18730,7 +18730,7 @@ decrease the number at point.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "08czwa165rnd5z0dwwdddn7zi5w63sdk31l47bj0598kbly01n7r")))) + (base32 "0a9nn1jnbgv93kz1iz5iay34d0p7lkpd8ic619ysk8qcksc0yn2i")))) (build-system emacs-build-system) (home-page "https://github.com/Fanael/highlight-defined") (synopsis "Syntax highlighting of known Elisp symbols") -- cgit 1.4.1 From 57b9db9caa46159f910efb461830e693c796a56e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:42:20 +0200 Subject: gnu: emacs-hl-todo: Update to 3.3.0. * gnu/packages/emacs-xyz.scm (emacs-hl-todo): Update to 3.3.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 394c89b2d9..cc1f65625e 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -7894,7 +7894,7 @@ between symbols.") (define-public emacs-hl-todo (package (name "emacs-hl-todo") - (version "3.1.2") + (version "3.3.0") (source (origin (method git-fetch) (uri (git-reference @@ -7903,7 +7903,7 @@ between symbols.") (file-name (git-file-name name version)) (sha256 (base32 - "1i5mdmkbrxqx75grwl01pywbgl8pasr00mq6fidspp0aligsbg6w")))) + "0bdwdp8d0g7n0kv6l4h7alya3z6fsfi618dzw5x8f2az3r87yg8y")))) (build-system emacs-build-system) (home-page "https://github.com/tarsius/hl-todo") (synopsis "Emacs mode to highlight TODO and similar keywords") -- cgit 1.4.1 From 73275048b41a87a633d742e0700975ef87544c5c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:43:10 +0200 Subject: gnu: emacs-ido-completing-read+: Update to 4.13. * gnu/packages/emacs-xyz.scm (emacs-ido-completing-read+): Update to 4.13. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index cc1f65625e..cf558a173b 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -10041,7 +10041,7 @@ a file, or a complete directory.") (define-public emacs-ido-completing-read+ (package (name "emacs-ido-completing-read+") - (version "4.13") + (version "4.14") (source (origin (method url-fetch) (uri (string-append "https://raw.githubusercontent.com" @@ -10050,7 +10050,7 @@ a file, or a complete directory.") (file-name (string-append "ido-completing-read+-" version ".el")) (sha256 (base32 - "0g2ixvw2sxpvrgz78745zi6iql4501pqi85zi6j31dnc1hx1i0r6")))) + "1wn94nkfv6qyyj6clvms7m7ncqf09bgszv67may530y75kylivav")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-s" ,emacs-s))) -- cgit 1.4.1 From e11cb6b5d2f00783c378d029ea0a3e051fa404a4 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:44:09 +0200 Subject: gnu: emacs-jsonnet-mode: Update to 0.1.3. * gnu/packages/emacs-xyz.scm (emacs-jsonnet-mode): Update to 0.1.3. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index cf558a173b..fc319ed746 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13752,7 +13752,7 @@ JSON objects.") (define-public emacs-jsonnet-mode (package (name "emacs-jsonnet-mode") - (version "0.1.2") + (version "0.1.3") (source (origin (method git-fetch) @@ -13762,7 +13762,7 @@ JSON objects.") (file-name (git-file-name name version)) (sha256 (base32 - "0vi7415n90d1z2ww1hld0gdp6v7z4rd6f70h476dp2x4hydk293i")))) + "14nxfa91yg2243v4d5kvynp2645x3811ispmhmpgil3x9qbl9jg9")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-dash" ,emacs-dash))) -- cgit 1.4.1 From 9921102f117a0dc25d820399b47aac67b015a2ed Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:45:49 +0200 Subject: gnu: emacs-magit-annex: Update to 1.8.0. * gnu/packages/emacs-xyz.scm (emacs-magit-annex): Update to 1.8.0. --- gnu/packages/emacs-xyz.scm | 48 ++++++++++++++++++++++------------------------ 1 file changed, 23 insertions(+), 25 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index fc319ed746..fbd2d14811 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -795,29 +795,27 @@ process, passing on the arguments as command line arguments.") (license license:gpl3+))) (define-public emacs-magit-annex - (let ((commit "ef5dce6267e9118a5eca82a22bcad0b67826c23a") - (revision "1")) - (package - (name "emacs-magit-annex") - (version (git-version "1.7.1" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/magit/magit-annex") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0vzkydgl889cq173zjl89g2vrddb9abc4a8gljiz3b4a7n5b1nrd")))) - (build-system emacs-build-system) - (propagated-inputs - `(("magit" ,emacs-magit) - ("transient" ,emacs-transient))) - (home-page "https://github.com/magit/magit-annex/") - (synopsis "Git-annex support for Magit") - (description - "Magit-annex adds a few git-annex operations to the Magit interface.") - (license license:gpl3+)))) + (package + (name "emacs-magit-annex") + (version "1.8.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/magit/magit-annex") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ak4chfn95p2vj3y0wiyimj609a4jfzrfpsc1kn0is1jv3dlkl6c")))) + (build-system emacs-build-system) + (propagated-inputs + `(("magit" ,emacs-magit) + ("transient" ,emacs-transient))) + (home-page "https://github.com/magit/magit-annex/") + (synopsis "Git-annex support for Magit") + (description + "Magit-annex adds a few git-annex operations to the Magit interface.") + (license license:gpl3+))) (define-public emacs-minions (package @@ -3455,7 +3453,7 @@ kmonad's configuration files (@file{.kbd}).") (define-public emacs-keycast (package (name "emacs-keycast") - (version "1.0.4") + (version "1.1.0") (source (origin (method git-fetch) @@ -3464,7 +3462,7 @@ kmonad's configuration files (@file{.kbd}).") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1g9arjdhdpvsw47ny9gi5k758ya37yza4mr0rhbf02yvrqyfsrgr")))) + (base32 "0093v1c5nl2bh1lvccqq6fzpgjald3yypp87dsim982aywl2vlv1")))) (build-system emacs-build-system) (home-page "https://github.com/tarsius/keycast") (synopsis "Show current command and its key in the mode line") -- cgit 1.4.1 From bf9e2fe1859eb76cd1eb181f8dbec0eb26b21dbf Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:46:42 +0200 Subject: gnu: emacs-magit-svn: Update to 2.2.3. * gnu/packages/emacs-xyz.scm (emacs-magit-svn): Update to 2.2.3. --- gnu/packages/emacs-xyz.scm | 45 ++++++++++++++++++++++----------------------- 1 file changed, 22 insertions(+), 23 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index fbd2d14811..61006ee8cd 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -736,30 +736,29 @@ rebasing, and other common Git operations.") (license license:gpl3+))) (define-public emacs-magit-svn - (let ((commit "9e33ceee32f665db59909e1c00a667ccdd04178f")) - (package - (name "emacs-magit-svn") - (version (git-version "2.2.1" "2" commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/magit/magit-svn") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1mlqz8dh6jy5rv72lgkxv253dgh73fmbaidskicypapvbl3lr6xy")))) - (build-system emacs-build-system) - (propagated-inputs `(("dash" ,emacs-dash) - ("with-editor" ,emacs-with-editor) - ("magit" ,emacs-magit) - ("transient" ,emacs-transient))) - (home-page "https://github.com/magit/magit-svn") - (synopsis "Git-SVN extension to Magit") - (description - "This package is an extension to Magit, the Git Emacs mode, providing + (package + (name "emacs-magit-svn") + (version "2.2.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/magit/magit-svn") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1v1y4fir1plz4kj0cvkcd29wibli4dw7vp4fmbxq4df76d8iy8yd")))) + (build-system emacs-build-system) + (propagated-inputs `(("dash" ,emacs-dash) + ("with-editor" ,emacs-with-editor) + ("magit" ,emacs-magit) + ("transient" ,emacs-transient))) + (home-page "https://github.com/magit/magit-svn") + (synopsis "Git-SVN extension to Magit") + (description + "This package is an extension to Magit, the Git Emacs mode, providing support for Git-SVN.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public emacs-magit-popup (package -- cgit 1.4.1 From 20f0027325f85ac47ebfef635d8944dea440fb90 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:47:23 +0200 Subject: gnu: emacs-markdown-preview-mode: Update to 0.9.4. * gnu/packages/emacs-xyz.scm (emacs-markdown-preview-mode): Update to 0.9.4. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 61006ee8cd..121bd94e66 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -23550,7 +23550,7 @@ url-encoded parameters, as well as web sockets.") (define-public emacs-markdown-preview-mode (package (name "emacs-markdown-preview-mode") - (version "0.9.2") + (version "0.9.4") (source (origin (method git-fetch) @@ -23560,7 +23560,7 @@ url-encoded parameters, as well as web sockets.") (file-name (git-file-name name version)) (sha256 (base32 - "1d1id99gagymvzdfa1mwqh8y3szm8ii47rpijkfi1qnifjg5jaq9")))) + "0a0qskhy6jil583hq3mgbzdsi3m1schzyzrd46yfxdsvqiczg170")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-markdown-mode" ,emacs-markdown-mode) -- cgit 1.4.1 From 130f4070d769a0fb375758ab0dadb5572447d5f7 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:48:42 +0200 Subject: gnu: emacs-minitest: Update to 0.9.2. * gnu/packages/emacs-xyz.scm (emacs-minitest): Update to 0.9.2. --- gnu/packages/emacs-xyz.scm | 50 ++++++++++++++++++++++------------------------ 1 file changed, 24 insertions(+), 26 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 121bd94e66..8398cb2769 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -3923,36 +3923,34 @@ of files under Git version control from within Emacs.") (license license:gpl3+))) (define-public emacs-minitest - (let ((commit "1aadb7865c1dc69c201cecee275751ecec33a182") - (revision "1")) - (package - (name "emacs-minitest") - (version (git-version "0.8.0" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/arthurnn/minitest-emacs") - (commit commit))) - (file-name (git-file-name name commit)) - (sha256 - (base32 - "1l18zqpdzbnqj2qawq8hj7z7pl8hr8z9d8ihy8jaiqma915hmhj1")))) - (build-system emacs-build-system) - (arguments - '(#:include (cons "^snippets\\/minitest-mode\\/" %default-include) - #:exclude (delete "^[^/]*tests?\\.el$" %default-exclude))) - (propagated-inputs - `(("emacs-dash" ,emacs-dash) - ("emacs-f" ,emacs-f))) - (home-page "https://github.com/arthurnn/minitest-emacs") - (synopsis "Emacs minitest mode") - (description - "The minitest mode provides commands to run the tests for the current + (package + (name "emacs-minitest") + (version "0.9.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/arthurnn/minitest-emacs") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0d8kg68yy5x1y3ivj43vzcakb3gii6bh8jm40g4sah5f53bbrs16")))) + (build-system emacs-build-system) + (arguments + '(#:include (cons "^snippets\\/minitest-mode\\/" %default-include) + #:exclude (delete "^[^/]*tests?\\.el$" %default-exclude))) + (propagated-inputs + `(("emacs-dash" ,emacs-dash) + ("emacs-f" ,emacs-f))) + (home-page "https://github.com/arthurnn/minitest-emacs") + (synopsis "Emacs minitest mode") + (description + "The minitest mode provides commands to run the tests for the current file or line, as well as rerunning the previous tests, or all the tests for a project. This package also includes relevant snippets for yasnippet.") - (license license:expat)))) + (license license:expat))) (define-public emacs-gdscript-mode (package -- cgit 1.4.1 From 6f7b3027559fd861756877a4cb523ab4222581c4 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:49:30 +0200 Subject: gnu: emacs-no-littering: Update to 1.2.2. * gnu/packages/emacs-xyz.scm (emacs-no-littering): Update to 1.2.2. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 8398cb2769..bf2191f1b6 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -26675,7 +26675,7 @@ launching other commands/applications from within Emacs, similar to the (define-public emacs-no-littering (package (name "emacs-no-littering") - (version "1.2.1") + (version "1.2.2") (source (origin (method git-fetch) @@ -26684,7 +26684,7 @@ launching other commands/applications from within Emacs, similar to the (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "00chkzpjcdll907vpzfzmf9p3jprisnr8i0h1x5gixidwbfc2whi")))) + (base32 "1kbbbx1agzcxc5n1b6cavdx3wjxz6mgi9rafja8mk8cyaaiz0rkd")))) (build-system emacs-build-system) (home-page "https://github.com/emacscollective/no-littering") (synopsis "Help keep @file{~/.emacs.d/} clean") -- cgit 1.4.1 From c0ea8d84e5b4f7d05b6951eb53501f64e9a97d13 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:50:05 +0200 Subject: gnu: emacs-olivetti: Update to 1.11.4. * gnu/packages/emacs-xyz.scm (emacs-olivetti): Update to 1.11.4. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index bf2191f1b6..78f54cf565 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -3493,7 +3493,7 @@ a command.") (define-public emacs-olivetti (package (name "emacs-olivetti") - (version "1.11.3") + (version "1.11.4") (source (origin (method git-fetch) @@ -3502,7 +3502,7 @@ a command.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0zcph7l0hxisbvsyzb1dw3paq5a5sjp5lrq5nq9zggvgc6zvx7sh")))) + (base32 "1pw1zc0pdwwi9dv8fypfxgn6xbfvm88qzhss880lspialff1wcxn")))) (build-system emacs-build-system) (home-page "https://github.com/rnkn/olivetti") (synopsis "Emacs minor mode for a nice writing environment") -- cgit 1.4.1 From 400a2a6296d0a3358380068f0adfce8ad4074d23 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:50:37 +0200 Subject: gnu: emacs-org-fragtog: Update to 0.3.2. * gnu/packages/emacs-xyz.scm (emacs-org-fragtog): Update to 0.3.2. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 78f54cf565..684b6505a1 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -4702,7 +4702,7 @@ displays the priority part of a heading as your preferred string value.") (define-public emacs-org-fragtog (package (name "emacs-org-fragtog") - (version "0.3.1") + (version "0.3.2") (source (origin (method git-fetch) @@ -4711,7 +4711,7 @@ displays the priority part of a heading as your preferred string value.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1szkx3n9gk6799rxv0jb3096pn2ssz82536x9a98xqwbimy4kvn6")))) + (base32 "0cw8903nw0mrn9kppwlypsb6h9m54zrb6y969yj0gnkza6gqy36c")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-org" ,emacs-org))) -- cgit 1.4.1 From 42178c86f0d9f3c1a6b7306a16035d1e2b2cb82b Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:51:14 +0200 Subject: gnu: emacs-orgit: Update to 1.7.0. * gnu/packages/emacs-xyz.scm (emacs-orgit): Update to 1.7.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 684b6505a1..3bbeba1168 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -22304,7 +22304,7 @@ recursively. The results are cached for speed.") (define-public emacs-orgit (package (name "emacs-orgit") - (version "1.6.3") + (version "1.7.0") (home-page "https://github.com/magit/orgit") (source (origin (method git-fetch) @@ -22314,7 +22314,7 @@ recursively. The results are cached for speed.") (file-name (git-file-name name version)) (sha256 (base32 - "08amzcvw483dpfq5r34ysn84wzd538qk0jblc94vgcaidspx6481")))) + "1xd58yqqsb79lgxkhxs4s50jq8f3639k6fhlza9hsy53apfczkal")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-dash" ,emacs-dash) -- cgit 1.4.1 From b037cac225769c8e8f1868d0448a775b5fcac972 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:51:52 +0200 Subject: gnu: emacs-org-re-reveal: Update to 3.9.0. * gnu/packages/emacs-xyz.scm (emacs-org-re-reveal): Update to 3.9.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 3bbeba1168..f0090acabd 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -17924,7 +17924,7 @@ powerful Org contents.") (define-public emacs-org-re-reveal (package (name "emacs-org-re-reveal") - (version "3.7.0") + (version "3.9.0") (source (origin (method git-fetch) (uri (git-reference @@ -17933,7 +17933,7 @@ powerful Org contents.") (file-name (git-file-name name version)) (sha256 (base32 - "1vzn0l8ig4rzh5h8j7kxn8kslqrij97qqv98fbnlwmrw4z87v8dr")))) + "1w6zvgfcyjqlxy4s13h7w66vv0fcid57s6vigzgnzi666w86fdyh")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-htmlize" ,emacs-htmlize) -- cgit 1.4.1 From 57e6d4e37e5c917a563f739321cdd9ae156563fa Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:53:12 +0200 Subject: gnu: emacs-org-roam-bibtex: Update to 0.6.0-pre.2. * gnu/packages/emacs-xyz.scm (emacs-org-roam-bibtex): Update to 0.6.0-pre.2. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index f0090acabd..ca165daeda 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -27168,7 +27168,7 @@ personal wiki.") (define-public emacs-org-roam-bibtex (package (name "emacs-org-roam-bibtex") - (version "0.4.0") + (version "0.6.0-pre.2") (source (origin (method git-fetch) @@ -27177,7 +27177,7 @@ personal wiki.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "13pll793khyfncpwm2dg24w747sqp7kgf7m3fqw2xzhv9cx2g7nq")))) + (base32 "0cjj7lx73qg4yw84r3b8fqhp5r74bzi57nvnvbvbck4i33ywqwx5")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-helm-bibtex" ,emacs-helm-bibtex) -- cgit 1.4.1 From 55c812c070f0c5a0e973f2e1190227667db67713 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:54:06 +0200 Subject: gnu: emacs-org-static-blog: Update to 1.5.0. * gnu/packages/emacs-xyz.scm (emacs-org-static-blog): Update to 1.5.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index ca165daeda..2f2412d2f1 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -26988,7 +26988,7 @@ All entries in a specified TODO state will be carried over to the next day.") (define-public emacs-org-static-blog (package (name "emacs-org-static-blog") - (version "1.4.0") + (version "1.5.0") (source (origin (method git-fetch) @@ -26997,7 +26997,7 @@ All entries in a specified TODO state will be carried over to the next day.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "00yhgxg87mfaflrkh0i905hr873yd03a7znw5hkrps43zxha9kb9")))) + (base32 "1p9v40mm8p25b9xgfahwqqx4c36aqnl9yyjjdhkp6x5xkhkdf7by")))) (build-system emacs-build-system) (home-page "https://github.com/bastibe/org-static-blog") (synopsis -- cgit 1.4.1 From 868982186559c9866239336dc773b704e9f2370d Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:54:35 +0200 Subject: gnu: emacs-org-trello: Update to 0.8.2. * gnu/packages/emacs-xyz.scm (emacs-org-trello): Update to 0.8.2. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 2f2412d2f1..0eb026e845 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -7218,7 +7218,7 @@ overview of tasks in a subtree.") (define-public emacs-org-trello (package (name "emacs-org-trello") - (version "0.8.1") + (version "0.8.2") (source (origin (method git-fetch) @@ -7228,7 +7228,7 @@ overview of tasks in a subtree.") (file-name (git-file-name name version)) (sha256 (base32 - "02gx3kv4mkij69ln8x8wf9n28x17pbb4kv85v78d3lxph7ykqimc")))) + "18y5zdjc7zh4jlwz6k1nl13i721rknqm0vp4mxfnmq0sc5a0qva0")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-dash" ,emacs-dash) -- cgit 1.4.1 From b7a9b63a70c248b3419bc7abd8ecc4392e33de40 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:55:30 +0200 Subject: gnu: emacs-package-lint: Update to 0.15. * gnu/packages/emacs-xyz.scm (emacs-package-lint): Update to 0.15. --- gnu/packages/emacs-xyz.scm | 47 +++++++++++++++++++++------------------------- 1 file changed, 21 insertions(+), 26 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 0eb026e845..af1011b4a8 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -20063,36 +20063,31 @@ image, rotate it, save modified images, and more.") (license license:gpl3+)))) (define-public emacs-package-lint - ;; The commit below includes a fix for a missing file, "stdlib-changes", - ;; preventing build. - (let ((commit "14c216f4889e71eec2a9da64e36ab8990337e82d") - (version "0.13") - (revision "0")) - (package - (name "emacs-package-lint") - (version (git-version version revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/purcell/package-lint") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1zifiqmpj9j14fnrm3jxapady25m1nlm514nfry0jfrhhikvj6i8")))) - (arguments - '(#:include (cons "^data/" %default-include))) - (build-system emacs-build-system) - (home-page "https://github.com/purcell/package-lint") - (synopsis "Linting library for elisp package authors") - (description - "This provides a list of issues with the Emacs package metadata of a file, + (package + (name "emacs-package-lint") + (version "0.15") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/purcell/package-lint") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1cn713g90zyjfq225yvg14c1qshslpi4466m3w102l5g57p8xv44")))) + (arguments + '(#:include (cons "^data/" %default-include))) + (build-system emacs-build-system) + (home-page "https://github.com/purcell/package-lint") + (synopsis "Linting library for elisp package authors") + (description + "This provides a list of issues with the Emacs package metadata of a file, e.g. the package dependencies it requires. See function @code{package-lint-buffer}. Checks will currently be enabled only if a \"Package-Requires:\" or \"Package-Version:\" header is present in the file.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public emacs-picpocket (let ((version "41") -- cgit 1.4.1 From 8fd54b9434b7cdade5d6e3b6969f829eac9ffcc3 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:56:02 +0200 Subject: gnu: emacs-pandoc-mode: Update to 2.31. * gnu/packages/emacs-xyz.scm (emacs-pandoc-mode): Update to 2.31. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index af1011b4a8..e155cc78e3 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -20297,7 +20297,7 @@ text in neighboring sections.") (define-public emacs-pandoc-mode (package (name "emacs-pandoc-mode") - (version "2.30.1") + (version "2.31") (source (origin (method git-fetch) @@ -20307,7 +20307,7 @@ text in neighboring sections.") (file-name (git-file-name name version)) (sha256 (base32 - "1k31pkvd9m798i6phcr0y3wd34fgq6ii41hx3lszmikvxb1yvm2y")))) + "1c3gay9fkikg7h46djw1nf86fzckmv7w1zbz5fbar20klcr12pbm")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-dash" ,emacs-dash) -- cgit 1.4.1 From eb00037407f1a7b26c23817b1c1107250c0485c0 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:56:49 +0200 Subject: gnu: emacs-parsec: Update to 0.1.4. * gnu/packages/emacs-xyz.scm (emacs-parsec): Update to 0.1.4. --- gnu/packages/emacs-xyz.scm | 39 ++++++++++++++++++--------------------- 1 file changed, 18 insertions(+), 21 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index e155cc78e3..e3184a9dcd 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -16832,32 +16832,29 @@ and @code{erc-send-modify-hook} to download and show images.") (license license:gpl3+))) (define-public emacs-parsec - ;; Last release is too old (2016). - (let ((revision "0") - (commit "2cbbbc2254aa7bcaa4fb5e07c8c1bf2f381dba26")) - (package - (name "emacs-parsec") - (version (git-version "0.1.3" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/cute-jumper/parsec.el") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1g1s8s45g3kkbi3h7w0pmadmzdswb64mkdvdpg2lihg341kx37gm")))) - (build-system emacs-build-system) - (home-page "https://github.com/cute-jumper/parsec.el") - (synopsis "Parser combinator library for Emacs Lisp") - (description - "Parsec is a parser combinator library for Emacs Lisp, similar to + (package + (name "emacs-parsec") + (version "0.1.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cute-jumper/parsec.el") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1g1s8s45g3kkbi3h7w0pmadmzdswb64mkdvdpg2lihg341kx37gm")))) + (build-system emacs-build-system) + (home-page "https://github.com/cute-jumper/parsec.el") + (synopsis "Parser combinator library for Emacs Lisp") + (description + "Parsec is a parser combinator library for Emacs Lisp, similar to Haskell's Parsec library. It contains most of the parser combinators in Text.Parsec.Combinator, and more combinators can be added if necessary! Most of the parser combinators have the same behavior as their Haskell counterparts. Parsec also comes with a simple error handling mechanism so that it can display an error message showing how the parser fails.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public emacs-move-text (package -- cgit 1.4.1 From 39eb5a1829d1e0d4df2d80915428011f7205c7b0 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:57:30 +0200 Subject: gnu: emacs-perspective: Update to 2.15. * gnu/packages/emacs-xyz.scm (emacs-perspective): Update to 2.15. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index e3184a9dcd..cb87123855 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -7912,7 +7912,7 @@ regexp that matches all known keywords.") (define-public emacs-perspective (package (name "emacs-perspective") - (version "2.14") + (version "2.15") (source (origin (method git-fetch) @@ -7921,7 +7921,7 @@ regexp that matches all known keywords.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "04r5h5zs5r6s22p5ynhpr860r2r552z9pyf4kbabfg1gz9jag7yp")))) + (base32 "0l9i7ky25d9ii04w2brgxc8dk2rky50naba8lbfqi7hcc34z8pp6")))) (build-system emacs-build-system) (arguments `(#:tests? #t -- cgit 1.4.1 From c85289a6a8692fca04d5b0cb04b572c3df9f8ee9 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:58:31 +0200 Subject: gnu: emacs-projectile: Update to 2.4.0. * gnu/packages/emacs-xyz.scm (emacs-projectile): Update to 2.4.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index cb87123855..45e5d18440 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -9400,7 +9400,7 @@ like @code{org-edit-src-code} but for arbitrary regions.") (define-public emacs-projectile (package (name "emacs-projectile") - (version "2.3.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (string-append "https://raw.githubusercontent.com/bbatsov" @@ -9408,7 +9408,7 @@ like @code{org-edit-src-code} but for arbitrary regions.") (file-name (string-append "projectile-" version ".el")) (sha256 (base32 - "1a2drmvx80076d52w46rgynwndj78l3ljr71pdzp9g9hh71mr27y")))) + "1vawbngfdcp6isqf74kwvk438wh6da2liqqxgzilw1qbhqg7z7aw")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-dash" ,emacs-dash) -- cgit 1.4.1 From b4f579b07f44cd1f2c9d102d14c44cd1a3b4749f Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 15:59:29 +0200 Subject: gnu: emacs-pubmed: Update to 0.5. * gnu/packages/emacs-xyz.scm (emacs-pubmed): Update to 0.5. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 45e5d18440..982826fb78 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -14516,7 +14516,7 @@ included by default, and more can be readily added.") (define-public emacs-pubmed (package (name "emacs-pubmed") - (version "0.2.1") + (version "0.5") (source (origin (method git-fetch) @@ -14526,7 +14526,7 @@ included by default, and more can be readily added.") (file-name (git-file-name name version)) (sha256 (base32 - "15bwjxc7g43m5pi8z17anaqqkvi209r7kk1chmf175477gvrv7c0")))) + "17d2v7q6sfafk8j1ish053xsmihi4f1hbk53fkkmhwan6sw9c4sc")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-deferred" ,emacs-deferred) -- cgit 1.4.1 From 9e29523a44afa55b317f4f87ab68e4caaecbad1f Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 16:01:32 +0200 Subject: gnu: emacs-puppet-mode: Update to 0.4. * gnu/packages/emacs-xyz.scm (emacs-puppet-mode): Update to 0.4. [source]: Switch to `git-fetch' method. --- gnu/packages/emacs-xyz.scm | 43 ++++++++++++++++++++----------------------- 1 file changed, 20 insertions(+), 23 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 982826fb78..95465b0458 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6739,31 +6739,28 @@ the locations of docstrings, arguments, and functions.") (license license:gpl3+))) (define-public emacs-puppet-mode - (let ((commit "b3ed5057166a4f49dfa9be638523a348b55a2fd2") - (revision "1")) - (package - (name "emacs-puppet-mode") - ;; The last release, 0.3 was several years ago, and there have been many - ;; commits since - (version (git-version "0.3" revision commit)) - (source - (origin - (method url-fetch) - (uri (string-append - "https://raw.githubusercontent.com/voxpupuli/puppet-mode/" - commit "/puppet-mode.el")) - (sha256 - (base32 - "1indycxawsl0p2aqqg754f6735q3cmah9vd886rpn0ncc3ipi1xm")))) - (build-system emacs-build-system) - (home-page "https://github.com/voxpupuli/puppet-mode") - (synopsis "Emacs major mode for the Puppet configuration language") - (description - "This package provides support for the Puppet configuration language, + (package + (name "emacs-puppet-mode") + (version "0.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/voxpupuli/puppet-mode") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0c5q8qmbligzjsn05di4wh6ggpd3944j4yqb78vzd441b8ssq70i")))) + (build-system emacs-build-system) + (home-page "https://github.com/voxpupuli/puppet-mode") + (synopsis "Emacs major mode for the Puppet configuration language") + (description + "This package provides support for the Puppet configuration language, including syntax highlighting, indentation of expressions and statements, linting of manifests and integration with Puppet Debugger.") - ;; Also incorporates work covered by the Apache License, Version 2.0 - (license license:gpl3+)))) + ;; Also incorporates work covered by the Apache License, Version 2.0 + (license license:gpl3+))) (define-public emacs-purescript-mode ;; Retrieved on 2021-05-18. -- cgit 1.4.1 From ea9276dea3b1bc52a7c61a6478dda3e37e743af5 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 16:02:29 +0200 Subject: gnu: emacs-pyim: Update to 3.7.9. * gnu/packages/emacs-xyz.scm (emacs-pyim): Update to 3.7.9. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 95465b0458..2274b5dcbb 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -12957,13 +12957,13 @@ containing words from the Rime project.") (define-public emacs-pyim (package (name "emacs-pyim") - (version "3.7.6") + (version "3.7.9") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/pyim-" version ".tar")) (sha256 - (base32 "1crimmvyppjmds9shfvxy9j5zi3mk133bv5av0fgicm7ddkivksr")))) + (base32 "00ff1izdwcy53dcwpdn18wwndnw2jsw4bhg8gkqaa60xm468xzkl")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-async" ,emacs-async) -- cgit 1.4.1 From b6c3e2463eea0da62317f37bb93358d3ffb417c7 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 16:03:10 +0200 Subject: gnu: emacs-python-black: Update to 1.1.0. * gnu/packages/emacs-xyz.scm (emacs-python-black): Update to 1.1.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 2274b5dcbb..fc8615f33e 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6616,7 +6616,7 @@ and popup menus.") (define-public emacs-python-black (package (name "emacs-python-black") - (version "1.0.0") + (version "1.1.0") (source (origin (method git-fetch) @@ -6626,7 +6626,7 @@ and popup menus.") (file-name (git-file-name name version)) (sha256 (base32 - "0fjnd85nlkck156dj6cahk8chhgkbgl2kwywqzi8bl4yj700m4dk")))) + "1cmzc0fa3jj7ajxbqhbsc8jx47k6g223sfd42c4lrqdnmh95760m")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-dash" ,emacs-dash) -- cgit 1.4.1 From d40adbae6129c61614c272bb8ab6eaffc229f31d Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 16:03:50 +0200 Subject: gnu: emacs-rainbow-delimiters: Update to 2.1.5. * gnu/packages/emacs-xyz.scm (emacs-rainbow-delimiters): Update to 2.1.5. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index fc8615f33e..b089e28805 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -9855,7 +9855,7 @@ completion, interactive development and more.") (define-public emacs-rainbow-delimiters (package (name "emacs-rainbow-delimiters") - (version "2.1.4") + (version "2.1.5") (source (origin (method git-fetch) (uri (git-reference @@ -9864,7 +9864,7 @@ completion, interactive development and more.") (file-name (git-file-name name version)) (sha256 (base32 - "1zr2669savnmkc68hiqsq9wccm6bs1j6jbmlac1xqh6nq7xgq36g")))) + "179mzsd8nvlr0ym9zf9fgdngsgxj3kdgbjblynliirsyk05ssrwc")))) (build-system emacs-build-system) (home-page "https://github.com/Fanael/rainbow-delimiters") (arguments -- cgit 1.4.1 From 997573fccee4cfb182cc76cbfe2fff3f937a179e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 16:04:25 +0200 Subject: gnu: emacs-robe: Update to 0.8.3. * gnu/packages/emacs-xyz.scm (emacs-robe): Update to 0.8.3. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index b089e28805..442ef63dea 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -4819,7 +4819,7 @@ mode-line.") (define-public emacs-robe (package (name "emacs-robe") - (version "0.8.2") + (version "0.8.3") (source (origin (method git-fetch) @@ -4828,7 +4828,7 @@ mode-line.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0qw18wi54yg971n4wnjqkd8lqj5lbs9ra8bvmngif2bzhqlfdsbn")))) + (base32 "1xbj7wi389n6pxfvxrakvhylkdlqg8ll9ad2zmxggcchygwah6nl")))) (build-system emacs-build-system) (arguments '(#:include (cons "^lib\\/" %default-include))) -- cgit 1.4.1 From 368887faa465f7460af5c46585fb44cb29f1c0f8 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 16:05:28 +0200 Subject: gnu: emacs-roguel-ike: Update to 0.1.1. * gnu/packages/emacs-xyz.scm (emacs-roguel-ike): Update to 0.1.1. --- gnu/packages/emacs-xyz.scm | 59 ++++++++++++++++++++++------------------------ 1 file changed, 28 insertions(+), 31 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 442ef63dea..d1eaf22a36 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -4869,40 +4869,37 @@ completing keywords and smart indentation.") (license license:gpl3+)))) (define-public emacs-roguel-ike - ;; Tagged branch is outdated. - (let ((revision "0") - (commit "706dcb0687e8016d7d776f9d9e5ace9fdbbca43c")) - (package - (name "emacs-roguel-ike") - (version (git-version "0.1.0" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/stevenremot/roguel-ike") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0rgv4y9aa5cc2ddz3y5z8d22xmr8kf5c60h0r3g8h91jmcw3rb4z")))) - (build-system emacs-build-system) - (propagated-inputs - `(("emacs-popup" ,emacs-popup))) - (arguments - `(#:include (cons* "^roguel-ike/" "^roguel-ike-lib/" %default-include) - #:phases - (modify-phases %standard-phases - (add-before 'check 'set-test-environment - (lambda _ - (setenv "HOME" "/tmp") - #t))))) - (home-page "https://github.com/stevenremot/roguel-ike.git") - (synopsis "Coffee-break roguelike for Emacs") - (description - "Roguel-ike is an attempt to develop a coffee-break roguelike for + (package + (name "emacs-roguel-ike") + (version "0.1.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/stevenremot/roguel-ike") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0rgv4y9aa5cc2ddz3y5z8d22xmr8kf5c60h0r3g8h91jmcw3rb4z")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-popup" ,emacs-popup))) + (arguments + `(#:include (cons* "^roguel-ike/" "^roguel-ike-lib/" %default-include) + #:phases + (modify-phases %standard-phases + (add-before 'check 'set-test-environment + (lambda _ + (setenv "HOME" "/tmp") + #t))))) + (home-page "https://github.com/stevenremot/roguel-ike.git") + (synopsis "Coffee-break roguelike for Emacs") + (description + "Roguel-ike is an attempt to develop a coffee-break roguelike for Emacs. The complete game would allow the player to create various characters and to make them fulfill challenges like arena fight and short dungeon explorations.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public emacs-rspec (let ((commit "66ea7cc9699d6edc6115daa024818adbd85efc20") -- cgit 1.4.1 From 0fc6f38e900ad981bd515c2761ce9519fc53b09a Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 16:06:53 +0200 Subject: gnu: emacs-simple-modeline: Update to 1.4. * gnu/packages/emacs-xyz.scm (emacs-simple-modeline): Update to 1.4. --- gnu/packages/emacs-xyz.scm | 40 +++++++++++++++++++--------------------- 1 file changed, 19 insertions(+), 21 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index d1eaf22a36..48a43e0455 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -25700,27 +25700,25 @@ replicate some of the features of the Doom modeline package.") (license license:gpl2+))) (define-public emacs-simple-modeline - (let ((commit "38973dec2912e2136d8fde5f2667063863fee15a") - (revision "1")) - (package - (name "emacs-simple-modeline") - (version (git-version"1.2" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/gexplorer/simple-modeline") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0y70hc3x8rxr8b5x8d0a23gpcadzrn43wmrsvqqxmmkqqp45n7gj")))) - (build-system emacs-build-system) - (home-page "https://github.com/gexplorer/simple-modeline") - (synopsis "Simple mode-line configuration for Emacs") - (description - "This package provides a simple mode-line configuration for Emacs.") - (license license:gpl3+)))) + (package + (name "emacs-simple-modeline") + (version "1.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/gexplorer/simple-modeline") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1rnzrx7gcaw056cqvnb1wai4hala0r0gpk3a4kyyghyp9hmrxbb5")))) + (build-system emacs-build-system) + (home-page "https://github.com/gexplorer/simple-modeline") + (synopsis "Simple mode-line configuration for Emacs") + (description + "This package provides a simple mode-line configuration for Emacs.") + (license license:gpl3+))) (define-public emacs-frames-only-mode (package -- cgit 1.4.1 From b1f613fb17bfd862c458e54176fa8a268d642217 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 16:08:36 +0200 Subject: gnu: emacs-solaire-mode: Update to 1.1.5. * gnu/packages/emacs-xyz.scm (emacs-solaire-mode): Update to 1.1.5. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 48a43e0455..3e7a527090 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -7602,7 +7602,7 @@ single theme but a set of guidelines with numerous implementations.") (define-public emacs-solaire-mode (package (name "emacs-solaire-mode") - (version "1.0.9") + (version "1.1.5") (source (origin (method git-fetch) @@ -7611,7 +7611,7 @@ single theme but a set of guidelines with numerous implementations.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "011m4r7s6i9lgjymh7jgq5jwwrpz4vmpvp3c8d4ix96v5hi04kzg")))) + (base32 "1l2w06w8b904h55xchs3dnjm4ry7xnpmyc4fg2vvrw1hr69q6mda")))) (build-system emacs-build-system) (home-page "https://github.com/hlissner/emacs-solaire-mode") (synopsis "Change background of file-visiting buffers in Emacs") -- cgit 1.4.1 From e4f8ae21400e359d9bff0c609123dff9bf8437aa Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 16:10:02 +0200 Subject: gnu: emacs-templatel: Update to 0.1.6. * gnu/packages/emacs-xyz.scm (emacs-templatel): Update to 0.1.6. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 3e7a527090..10d3061384 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -10173,7 +10173,7 @@ Dust.js, React/JSX, Angularjs, ejs, etc.") (define-public emacs-templatel (package (name "emacs-templatel") - (version "0.1.4") + (version "0.1.6") (source (origin (method git-fetch) @@ -10182,7 +10182,7 @@ Dust.js, React/JSX, Angularjs, ejs, etc.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1k33h503038l2bcr8gs020z2cjxfs94lamkdgv52cvd9i20d0kqq")))) + (base32 "03n7amd2mfr4jmc4s1ar5ckm86knr7qarxxlkdhbnw3svy5kbc57")))) (build-system emacs-build-system) (home-page "https://clarete.li/templatel") (synopsis "Jinja inspired template language for Emacs Lisp") -- cgit 1.4.1 From 71fe50b5de9ab5fbcb398049d1a0d0cd193d4a35 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 16:10:41 +0200 Subject: gnu: emacs-tide: Update to 4.2.3. * gnu/packages/emacs-xyz.scm (emacs-tide): Update to 4.2.3. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 10d3061384..6399bbbeef 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -9286,7 +9286,7 @@ indentation and filling of comments and C preprocessor fontification.") (define-public emacs-tide (package (name "emacs-tide") - (version "4.0.2") + (version "4.2.3") (source (origin (method git-fetch) (uri (git-reference @@ -9295,7 +9295,7 @@ indentation and filling of comments and C preprocessor fontification.") (file-name (git-file-name name version)) (sha256 (base32 - "1n2dihpl53a48jis3l4rry581wpr5lxjd433drlkaa4lqgx8cw67")))) + "1fj2fghiycnzds2zxfxgj1d9mdzsvs9rvl9bwy2f1vwawqk1m48w")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-dash" ,emacs-dash) -- cgit 1.4.1 From c4e6b6e990724b843ba8f1d473135f43f60bc971 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 16:11:19 +0200 Subject: gnu: emacs-visual-fill-column: Update to 2.4. * gnu/packages/emacs-xyz.scm (emacs-visual-fill-column): Update to 2.4. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 6399bbbeef..f809e98709 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -9946,7 +9946,7 @@ keybindings in Emacs, and does not come with any predefined bindings.") (define-public emacs-visual-fill-column (package (name "emacs-visual-fill-column") - (version "2.2") + (version "2.4") (source (origin (method git-fetch) @@ -9955,7 +9955,7 @@ keybindings in Emacs, and does not come with any predefined bindings.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1wjb4zm9mx07v0qx2fxmclg4pg0ssgnf8lp89wc56kmc0s40jhii")))) + (base32 "1wfww6bqdphv871in80fc84ml8gkl04il6w51z2ycx99km8b723l")))) (build-system emacs-build-system) (home-page "https://github.com/joostkremers/visual-fill-column") (synopsis "Fill-column for visual-line-mode") -- cgit 1.4.1 From e579aeb7a477e6c80b916fc8e5ad5affdff2365f Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 16:12:02 +0200 Subject: gnu: emacs-wc-mode: Update to 1.4.1. * gnu/packages/emacs-xyz.scm (emacs-wc-mode): Update to 1.4.1. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index f809e98709..9091fbd43d 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -24775,7 +24775,7 @@ files to numerous other formats via Pandoc.") (define-public emacs-wc-mode (package (name "emacs-wc-mode") - (version "1.4") + (version "1.4.1") (source (origin (method git-fetch) (uri (git-reference @@ -24784,7 +24784,7 @@ files to numerous other formats via Pandoc.") (file-name (git-file-name name version)) (sha256 (base32 - "01icd63mb2hg1bgbmkq3jm8kc3ic8whfy2awcgx53zqkmyz87qxc")))) + "1wzgb4z2qyyv223x5fc7ff2fn5xpz4s7lr1q1y33q8878a7w9d45")))) (build-system emacs-build-system) (home-page "https://github.com/bnbeckwith/wc-mode") (synopsis "Running word count with goals (minor mode)") -- cgit 1.4.1 From 28e6e48f4b6fc2a19dc7bddfd188dde2d3f8eedf Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 16:12:35 +0200 Subject: gnu: emacs-webpaste: Update to 3.2.1. * gnu/packages/emacs-xyz.scm (emacs-webpaste): Update to 3.2.1. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 9091fbd43d..1adbeea1d0 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -27932,7 +27932,7 @@ rules about where space should be left to separate words and parentheses.") (define-public emacs-webpaste (package (name "emacs-webpaste") - (version "3.2.0") + (version "3.2.1") (source (origin (method git-fetch) @@ -27942,7 +27942,7 @@ rules about where space should be left to separate words and parentheses.") (file-name (git-file-name name version)) (sha256 (base32 - "08545ihkzflw80rwklnxiswrpdrl8kr74xzxm5wsgrf36fkj9rn2")))) + "1d481pdnh7cnbyka7wn59czlci63zwfqms8n515svg92qm573ckd")))) (build-system emacs-build-system) (arguments `(#:tests? #t -- cgit 1.4.1 From 87e3a633c973c9a3ca4efd122b4bfd59a0c72e90 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 16:13:27 +0200 Subject: gnu: emacs-window-purpose: Update to 1.8. * gnu/packages/emacs-xyz.scm (emacs-window-purpose): Update to 1.8. --- gnu/packages/emacs-xyz.scm | 82 ++++++++++++++++++++++------------------------ 1 file changed, 40 insertions(+), 42 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 1adbeea1d0..130cc66564 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -8514,50 +8514,48 @@ possible, and falls back to moving the left or top border otherwise.") (license license:gpl3+)))) (define-public emacs-window-purpose - (let ((commit "f6421966761ad911fe8861aba2b110c5dd60d1ea") - (revision "1")) - (package - (name "emacs-window-purpose") - (version (git-version "1.7" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/bmag/emacs-purpose.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1p0y5gnrw7q65py2wjdf1hrdpiw5c2zbgvfbfmb13257jq5mga38")))) - (build-system emacs-build-system) - (propagated-inputs - `(("emacs-let-alist" ,emacs-let-alist) - ("emacs-imenu-list" ,emacs-imenu-list))) - (arguments - '(#:include - '("^[^/]+.el$" - "^[^/]+.el.in$" - "^dir$" - "^[^/]+.info$" - "^[^/]+.texi$" - "^[^/]+.texinfo$" - "^doc/dir$" - "^doc/[^/]+.info$" - "^doc/[^/]+.texi$" - "^doc/[^/]+.texinfo$" - "^layouts$") - #:exclude - '("^.dir-locals.el$" - "^test.el$" - "^tests.el$" - "^[^/]+-test.el$" - "^[^/]+-tests.el$"))) - (home-page "https://github.com/bmag/emacs-purpose") - (synopsis "Purpose-based window management for Emacs") - (description "Purpose is a package that introduces the concept of a + (package + (name "emacs-window-purpose") + (version "1.8") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bmag/emacs-purpose.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1bq0s56wj6ibyh625zfnisy8yniz72dpg4mcgq55azsbnd4fblqq")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-let-alist" ,emacs-let-alist) + ("emacs-imenu-list" ,emacs-imenu-list))) + (arguments + '(#:include + '("^[^/]+.el$" + "^[^/]+.el.in$" + "^dir$" + "^[^/]+.info$" + "^[^/]+.texi$" + "^[^/]+.texinfo$" + "^doc/dir$" + "^doc/[^/]+.info$" + "^doc/[^/]+.texi$" + "^doc/[^/]+.texinfo$" + "^layouts$") + #:exclude + '("^.dir-locals.el$" + "^test.el$" + "^tests.el$" + "^[^/]+-test.el$" + "^[^/]+-tests.el$"))) + (home-page "https://github.com/bmag/emacs-purpose") + (synopsis "Purpose-based window management for Emacs") + (description "Purpose is a package that introduces the concept of a \"purpose\" for windows and buffers, and then helps you maintain a robust window layout easily.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public emacs-iedit ;; Last release version was in 2016. -- cgit 1.4.1 From 0a7a2679054566e437e466f298307abf2cbd5e62 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 16:14:03 +0200 Subject: gnu: emacs-with-editor: Update to 3.0.4. * gnu/packages/emacs-xyz.scm (emacs-with-editor): Update to 3.0.4. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 130cc66564..4bd5c47a74 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -548,7 +548,7 @@ configuration files, such as .gitattributes, .gitignore, and .git/config.") (define-public emacs-with-editor (package (name "emacs-with-editor") - (version "3.0.2") + (version "3.0.4") (source (origin (method git-fetch) @@ -557,7 +557,7 @@ configuration files, such as .gitattributes, .gitignore, and .git/config.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0hw6i5r3adkm4988badi94825lywkrh3sddiff4z04kj1nj15d0k")))) + (base32 "1bmvkrfnjzrf0ch2mh75cv784mzs64i4f44l91xysapjqv46lfqn")))) (build-system emacs-build-system) (arguments `(#:phases -- cgit 1.4.1 From 555bc7a77f49314938a637005b711e6185ac38cd Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 16:14:38 +0200 Subject: gnu: emacs-with-simulated-input: Update to 3.0. * gnu/packages/emacs-xyz.scm (emacs-with-simulated-input): Update to 3.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 4bd5c47a74..0ee0797223 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -16480,7 +16480,7 @@ parallel to Gradle — its configuration is a program on its own.") (define-public emacs-with-simulated-input (package (name "emacs-with-simulated-input") - (version "2.4") + (version "3.0") (source (origin (method git-fetch) @@ -16490,7 +16490,7 @@ parallel to Gradle — its configuration is a program on its own.") (file-name (git-file-name name version)) (sha256 (base32 - "12d3mhvzj74qwc4rdcb236jbqnf5lam8pk78j92kwbwjk1jaz2cf")))) + "0n8h84whsh0aph8xhn9plprix9f6bysgvarz2anz7kwns19js6s4")))) (build-system emacs-build-system) (arguments ;; The test suite fails with error: "Spies can only be created in -- cgit 1.4.1 From b76db6e0ceafe8515c5eec23faf8b14a38a28b08 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 16:16:07 +0200 Subject: gnu: emacs-writegood-mode: Update to 2.0.4. * gnu/packages/emacs-xyz.scm (emacs-writegood-mode): Update to 2.0.4. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 0ee0797223..ca4179a693 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -11378,7 +11378,7 @@ later translated into the host format, e.g., LaTeX or HTML.") (define-public emacs-writegood-mode (package (name "emacs-writegood-mode") - (version "2.0.2") + (version "2.0.4") (home-page "https://github.com/bnbeckwith/writegood-mode") (source (origin (method git-fetch) @@ -11387,7 +11387,7 @@ later translated into the host format, e.g., LaTeX or HTML.") (commit (string-append "v" version)))) (sha256 (base32 - "1nnjn1r669hvvzfycllwap4w04m8rfsk4nzcg8057m1f263kj31b")) + "1nwngnddlkcvix7qx39fadab7hqzg8snb0k63kwpr8v57lyrm48z")) (file-name (string-append name "-checkout")))) (build-system emacs-build-system) (synopsis "Polish up poor writing on the fly") -- cgit 1.4.1 From 636d25cce083f88b52e2dd08e3c29b5a9ba57f15 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 16:37:55 +0200 Subject: gnu: links: Update to 2.23. * gnu/packages/web-browsers.scm (links): Update to 2.23. --- gnu/packages/web-browsers.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index a8e77f8c7e..214320d2a1 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -178,14 +178,14 @@ older or slower computers and embedded systems.") (define-public links (package (name "links") - (version "2.22") + (version "2.23") (source (origin (method url-fetch) (uri (string-append "http://links.twibright.com/download/" "links-" version ".tar.bz2")) (sha256 (base32 - "0k88qbmq0mf6zmk2v158c0rxvqbi7ysn58xyf4qqw7kz79mrhr03")))) + "0idcwryfbf6ds5x2fx1k21m459qz5mrz3hw4a6ziiz91yl1d4q36")))) (build-system gnu-build-system) (arguments `(#:phases -- cgit 1.4.1 From d5aa478854b46a3e45af149a5e9fcbe9c52c4d62 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 16:38:36 +0200 Subject: gnu: oil: Update to 0.8.11. * gnu/packages/shells.scm (oil): Update to 0.8.11. --- gnu/packages/shells.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm index 5c35b11333..48f72401b4 100644 --- a/gnu/packages/shells.scm +++ b/gnu/packages/shells.scm @@ -829,14 +829,14 @@ Shell (pdksh).") (define-public oil (package (name "oil") - (version "0.8.10") + (version "0.8.11") (source (origin (method url-fetch) (uri (string-append "https://www.oilshell.org/download/oil-" version ".tar.gz")) (sha256 - (base32 "03ixqspizvgj869b524c33pg9c6h64g04r4pjkxfp1fxvgca70db")))) + (base32 "12fhcqgv0sm3i9i4qa7yggjf2qsbjlmi6yblwxb735f86357ps8a")))) (build-system gnu-build-system) (arguments `(#:strip-binaries? #f ; strip breaks the binary -- cgit 1.4.1 From 34fe60e8b1233897f03fae63d33c94d45dfe40fc Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 16:38:49 +0200 Subject: gnu: httpd: Update to 2.4.48. * gnu/packages/web.scm (httpd): Update to 2.4.48. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 30a12098a0..41d815c0e5 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -248,14 +248,14 @@ (define-public httpd (package (name "httpd") - (version "2.4.47") + (version "2.4.48") (source (origin (method url-fetch) (uri (string-append "mirror://apache/httpd/httpd-" version ".tar.bz2")) (sha256 (base32 - "1jh31j4740wz463l1j49ir2lhh42x9z4byiq25m12y75r3dhdl13")))) + "0v4npxnvih5mlxx6dywwhhfs8xvgcckc0hxzwk3hi0g8nbkjdj0v")))) (build-system gnu-build-system) (native-inputs `(("pcre" ,pcre "bin"))) ;for 'pcre-config' (inputs `(("apr" ,apr) -- cgit 1.4.1 From 65161ebb1b310c0ad0e6f734ca813bc08e7baeb9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 16:41:03 +0200 Subject: gnu: svt-hevc: Update to 1.5.1. * gnu/packages/video.scm (svt-hevc): Update to 1.5.1. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 961094a80b..2eef76558a 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -286,7 +286,7 @@ video and audio streams from a DVD.") (define-public svt-hevc (package (name "svt-hevc") - (version "1.5.0") + (version "1.5.1") (source (origin (method git-fetch) @@ -296,7 +296,7 @@ video and audio streams from a DVD.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "038r3x3axil895vh2dq6223623ybrc45vn58vfmfb7cikz68sy23")))) + (base32 "0rac70p6rpvdx9v0bdd8nphgr7imdxb7nz0x77n3p7h3180zz9x0")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ; Test script is stand-alone -- cgit 1.4.1 From f0b20dc3a9429a321d19a183bf1c2a714483be05 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 17:18:51 +0200 Subject: gnu: remmina: Update to 1.4.17. * gnu/packages/vnc.scm (remmina): Update to 1.4.17. --- gnu/packages/vnc.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/vnc.scm b/gnu/packages/vnc.scm index 6ff3e38b0a..a28cb512ab 100644 --- a/gnu/packages/vnc.scm +++ b/gnu/packages/vnc.scm @@ -61,7 +61,7 @@ (define-public remmina (package (name "remmina") - (version "1.4.16") + (version "1.4.17") (source (origin (method git-fetch) @@ -71,7 +71,7 @@ (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "09sjsgvh13jnhs6mhj9icyka0ad3qlnkbzvg7djj9rajzaf1y048")))) + (base32 "0aww3j5g3770j8fcnc14j1g1g0452kj48jn4awxdj2yx7i58rc91")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; No target -- cgit 1.4.1 From 7aa9785aa6959ede719ec56a982d54b819bcf83d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 18:22:24 +0200 Subject: gnu: welle-io: Update to 2.3. * gnu/packages/radio.scm (welle-io): Update to 2.3. --- gnu/packages/radio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 8f9e180723..23a26d6a5e 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -1539,7 +1539,7 @@ receiver.") (define-public welle-io (package (name "welle-io") - (version "2.2") + (version "2.3") (source (origin (method git-fetch) @@ -1548,7 +1548,7 @@ receiver.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "04fpm6sc431dl9i5h53xpd6k85j22sv8aawl7b6wv2fzpfsd9fwa")))) + (base32 "1xl1lanw0xgmgks67dbfb2h52jxnrd1i2zik56v0q8dwsr7f0daw")))) (build-system qt-build-system) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit 1.4.1 From 95f104b161c870a4e868e6ffba538188318f7091 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 18:23:31 +0200 Subject: gnu: hamlib: Update to 4.2. * gnu/packages/radio.scm (hamlib): Update to 4.2. --- gnu/packages/radio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 23a26d6a5e..1145c12c87 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -853,7 +853,7 @@ you must extend 'udev-service-type' with this package. E.g.: (define-public hamlib (package (name "hamlib") - (version "4.1") + (version "4.2") (source (origin (method url-fetch) @@ -861,7 +861,7 @@ you must extend 'udev-service-type' with this package. E.g.: "https://github.com/Hamlib/Hamlib/releases/download/" version "/hamlib-" version ".tar.gz")) (sha256 - (base32 "0hi3nc1k55mxff05amdv5iwryaz6r3205l24q0bg7l84f53bkm5l")))) + (base32 "1m8gb20i8ga6ndnnw187ry1h4z8wx27v1hl7c610r6ky60pv4072")))) (build-system gnu-build-system) (native-inputs `(("doxygen" ,doxygen) -- cgit 1.4.1 From 949b376c8c08424d354a2a8e7888d5b3dc6fb202 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 18:49:39 +0200 Subject: gnu: Add emacs-literate-elisp. * gnu/packages/emacs-xyz.scm (emacs-literate-elisp): New variable. --- gnu/packages/emacs-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index ca4179a693..c3b3559f10 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -4489,6 +4489,27 @@ in Lisp modes.") (description "This package provides dynamic evaluation in Emacs.") (license license:gpl3+)))) +(define-public emacs-literate-elisp + (package + (name "emacs-literate-elisp") + (version "0.8") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jingtaozf/literate-elisp") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0i9468rh61l4xq918fgwk6li93lpm6zbn0lkpxr7pbvkgrl5xsr6")))) + (build-system emacs-build-system) + (home-page "https://github.com/jingtaozf/literate-elisp/tags") + (synopsis "Load Emacs Lisp code blocks from Org files") + (description + "Literate-Elisp is an Emacs lisp library to provide an easy way to use +literal programming in Emacs lisp. It extends the Emacs load mechanism so +Emacs can load Org files as Lisp source files directly.") + (license license:gpl3+))) + (define-public emacs-literate-calc-mode (let ((commit "a50e897a816cb5580ad6ec867eeaae212e0e4798") (revision "1")) -- cgit 1.4.1 From a208b5033e056346c983273e6740a0989f3cd6c3 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 18:53:19 +0200 Subject: gnu: emacs-chronometrist: Add missing propagated input. * gnu/packages/emacs-xyz.scm (emacs-chronometrist)[input]: Add emacs-literate-elisp. --- gnu/packages/emacs-xyz.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index c3b3559f10..f3da977351 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -2623,6 +2623,7 @@ Lock key.") (propagated-inputs `(("emacs-anaphora" ,emacs-anaphora) ("emacs-dash" ,emacs-dash) + ("emacs-literate-elisp" ,emacs-literate-elisp) ("emacs-s" ,emacs-s) ("emacs-ts" ,emacs-ts))) (home-page "https://github.com/contrapunctus-1/chronometrist") -- cgit 1.4.1 From ef8d95ceb8466327dedd2725e0147bf691e67ee0 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 19:15:01 +0200 Subject: gnu: emacs-ebib: Add missing propagated input. * gnu/packages/emacs-xyz.scm (emacs-ebib)[propagated input]: Add emacs-biblio. --- gnu/packages/emacs-xyz.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index f3da977351..a70c596f72 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -16642,7 +16642,8 @@ files to be expanded upon opening them.") (base32 "1xgpdw0sxl2c9dn6x6fk0rqpqlqxsjlj0vyag611blj600br7dqr")))) (build-system emacs-build-system) (propagated-inputs - `(("emacs-parsebib" ,emacs-parsebib))) + `(("emacs-biblio" ,emacs-biblio) + ("emacs-parsebib" ,emacs-parsebib))) (home-page "https://joostkremers.github.io/ebib/") (synopsis "BibTeX database manager for Emacs") (description -- cgit 1.4.1 From 7de36f7575330e9ede02728f601a468728e0d0ee Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 19:25:08 +0200 Subject: gnu: emacs-esxml: Limit packaged files. * gnu/packages/emacs-xyz.scm (emacs-esxml)[arguments]: Use full emacs. Only package two files. Remove unnecessary phases. --- gnu/packages/emacs-xyz.scm | 23 ++++------------------- 1 file changed, 4 insertions(+), 19 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a70c596f72..cf66dc67f8 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -15310,25 +15310,10 @@ Lisp.") "1xzxmgsg0j72sf1vjh9gjswz3c29js0kqhm7r3jrqrh3a5agdnml")))) (build-system emacs-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-sources - (lambda _ - ;; See: https://github.com/tali713/esxml/pull/28. - (substitute* "css-lite.el" - ((";;; main interface") - (string-append ";;; main interface\n" - "(require 'cl-lib)")) - (("mapcan") - "cl-mapcan") - (("',\\(cl-mapcan #'process-css-rule rules\\)") - "(cl-mapcan #'process-css-rule ',rules)")) - (substitute* "esxml-form.el" - ((",esxml-form-field-defn") - "#'esxml-form-field-defn")) - ;; See: https://github.com/tali713/esxml/issues/25 - (delete-file "esxpath.el") - #t))))) + `(#:emacs ,emacs ;need libxml + ;; XXX: Only the two following files are meant to be packaged. + ;; Byte-compiling the others Elisp files leads to build errors anyway. + #:include (list "esxml.el" "esxml-query.el"))) (propagated-inputs `(("emacs-kv" ,emacs-kv))) (home-page "https://github.com/tali713/esxml/") -- cgit 1.4.1 From 8415731203a8e4f8a3c874cd812e1a9a603a008c Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:05:46 +1000 Subject: gnu: libfm-qt: Update to 0.17.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (libfm-qt): Update to 0.17.1. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 20efba17b7..01d89079b8 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -973,14 +973,14 @@ for LXQt.") (define-public libfm-qt (package (name "libfm-qt") - (version "0.15.1") + (version "0.17.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "034kc8i571m31fksprih6iiykxj85j98fmm6nrkmlwql45kr6rvs")))) + (base32 "1991lm1gnw9s5wwn1yf3vba63bfmrrgsxc70h3nhdl9mh16qygxa")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no tests -- cgit 1.4.1 From 1ae280cd5e7ea58946ac526dde4c6ca846eaf023 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:05:47 +1000 Subject: gnu: lxqt-qtplugin: Update to 0.17.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-qtplugin): Update to 0.17.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 01d89079b8..6ca7b473dc 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -10,6 +10,7 @@ ;;; Copyright © 2019, 2020 Reza Alizadeh Majd ;;; Copyright © 2020 Fakhri Sajadi ;;; Copyright © 2020 André Batista +;;; Copyright © 2021 Brendan Tildesley ;;; ;;; This file is part of GNU Guix. ;;; @@ -735,14 +736,14 @@ when laptop batteries are low on power.") (define-public lxqt-qtplugin (package (name "lxqt-qtplugin") - (version "0.15.1") + (version "0.17.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "17kmpm3nn07xyxz21f86y3hqi6s0jvqyhsc703zy0463sc58vvys")))) + (base32 "14c6abxfg3vda333wrvb5lk45c45hnb66jclbs3vsmrjxdb13vv5")))) (build-system cmake-build-system) (inputs `(("libdbusmenu-qt" ,libdbusmenu-qt) -- cgit 1.4.1 From 64f28a62b20af3d73aa81cd4b5974c744bef1f16 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:05:48 +1000 Subject: gnu: lxqt-build-tools: Update to 0.9.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-build-tools): Update to 0.9.0. [propagated-inputs]: Add perl. dependent projects require it via the CMake files. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 6ca7b473dc..b7c001868f 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -128,7 +128,7 @@ to statistics about the system on which it's run.") (define-public lxqt-build-tools (package (name "lxqt-build-tools") - (version "0.7.0") + (version "0.9.0") (source (origin (method url-fetch) @@ -136,7 +136,7 @@ to statistics about the system on which it's run.") "/download/" version "/lxqt-build-tools-" version ".tar.xz")) (sha256 - (base32 "147vdkc25mrlr0fy785yzwhm4gwjxa5xl3n3hljz4c97m531kzl5")))) + (base32 "0kayad5l72h8n90zkf3hy8fxy72n4b1mrkjglpa9dj0cdj6qg0lp")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; no tests @@ -151,6 +151,9 @@ to statistics about the system on which it's run.") ("glib" ,glib))) (inputs `(("qtbase" ,qtbase))) + (propagated-inputs + ;; Dependent projects require Perl via the CMake files. + `(("perl" ,perl))) (synopsis "LXQt Build tools") (description "Lxqt-build-tools is providing several tools needed to build LXQt -- cgit 1.4.1 From c4df64d3ba231e6f3b814a187b8760b2ce959108 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:05:49 +1000 Subject: gnu: libqtxdg: Update to 3.7.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (libqtxdg): Update to 3.7.1. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index b7c001868f..3280b01f67 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -164,7 +164,7 @@ itself as well as other components maintained by the LXQt project.") (define-public libqtxdg (package (name "libqtxdg") - (version "3.5.0") + (version "3.7.1") (source (origin (method url-fetch) @@ -172,7 +172,7 @@ itself as well as other components maintained by the LXQt project.") "https://github.com/lxqt/libqtxdg/releases/download/" version "/libqtxdg-" version ".tar.xz")) (sha256 - (base32 "0g2mwipgl8737jhgqymjixvk745svh2rlini3qr92lrg60v9paa1")))) + (base32 "16wav2b948c837cpbvdr6hs1zifwrpdk3yjvbzzp2l1hndvbwz27")))) (build-system cmake-build-system) (arguments '(#:configure-flags -- cgit 1.4.1 From 9e2341947b902e21554b6619e573d8efcb4984b0 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:05:50 +1000 Subject: gnu: liblxqt: Update to 0.17.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (liblxqt): Update to 0.17.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 3280b01f67..e7c62d12b5 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -202,7 +202,7 @@ in Qt.") (define-public liblxqt (package (name "liblxqt") - (version "0.15.1") + (version "0.17.0") (source (origin (method url-fetch) @@ -210,7 +210,7 @@ in Qt.") "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "0mg62gypjpmpjd3lr7rrvzmkkhli1vf5pri47hg76byz84vng4a9")))) + (base32 "0ay3j6zdgffw3mzaq3wdq96la7fnn2dw52ij6987slv31563nknl")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; no tests -- cgit 1.4.1 From 7cd88666d0b76ffca54ade6e2f1e7b62504e8e08 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:05:51 +1000 Subject: gnu: libsysstat: Update to 0.4.5. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (libsysstat): Update to 0.4.5. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index e7c62d12b5..2c9d92a51d 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -248,14 +248,14 @@ components of the LXQt desktop environment.") (define-public libsysstat (package (name "libsysstat") - (version "0.4.3") + (version "0.4.5") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1s5s7skzy3sh4rlnfy7r0cg3r1scvp35ldd28bhnqjya99m7ip37")))) + (base32 "1ljy5ggvqvpm3k6kfy03dn47ygr9lzi8hmqws4dcqfc9sx86b6zi")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no tests (inputs -- cgit 1.4.1 From cfd40e64b999f8562fb0e6a9b13b7fa35edaa26d Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:05:52 +1000 Subject: gnu: lxqt-about: Update to 0.17.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-about): Update to 0.17.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 2c9d92a51d..9eed23edd5 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -274,14 +274,14 @@ and memory usage or network traffic.") (define-public lxqt-about (package (name "lxqt-about") - (version "0.15.0") + (version "0.17.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "0p24z1vykyp8dkhwaxxi4hw5150yv9a2ncc55vbwx4c6bmmibmsh")))) + (base32 "04riqf2xgbcnq67l5zb0dfnnmc4a2zljx8zfn3jlvxirnd73l0zm")))) (build-system cmake-build-system) (inputs `(("kwindowsystem" ,kwindowsystem) -- cgit 1.4.1 From a5fe52001042970d9b7d063d5a218484ab7fa7c5 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:05:53 +1000 Subject: gnu: lxqt-admin: Update to 0.17.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-admin): Update to 0.17.0. [arguments]: Patch another Polkit file install path. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 9eed23edd5..a2cbc3fc95 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -317,14 +317,14 @@ LXQt and the system it's running on.") (define-public lxqt-admin (package (name "lxqt-admin") - (version "0.15.0") + (version "0.17.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1zal37hyzqimwsymmi3w15n1iq78g53754s8abc9ylkzc236xpfc")))) + (base32 "07fkn3zmpfxjzzsv1hyv50sx0359n10lxjil35qn266nz165wj43")))) (build-system cmake-build-system) (inputs `(("kwindowsystem" ,kwindowsystem) @@ -342,7 +342,8 @@ LXQt and the system it's running on.") (modify-phases %standard-phases (add-after 'unpack 'patch-source (lambda _ - (substitute* "lxqt-admin-user/CMakeLists.txt" + (substitute* '("lxqt-admin-user/CMakeLists.txt" + "lxqt-admin-time/CMakeLists.txt") (("DESTINATION \"\\$\\{POLKITQT-1_POLICY_FILES_INSTALL_DIR\\}") "DESTINATION \"share/polkit-1/actions")) #t)) -- cgit 1.4.1 From e84f3a75f8d2f258f877f18385085fd8b63dd704 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:05:54 +1000 Subject: gnu: lxqt-config: Update to 0.17.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-config): Update to 0.17.1. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index a2cbc3fc95..24418a8f4a 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -364,14 +364,14 @@ the operating system LXQt is running on.") (define-public lxqt-config (package (name "lxqt-config") - (version "0.15.0") + (version "0.17.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "18fagd6ynmx74qw0pjkkg2n3v6s18n6lcsbj7lvfd4lkbcfnzqpb")))) + (base32 "0nr43d6fyc5zg4b3iwpca2cy58ry8q0rahrk6ixm7wrvmaiwkh93")))) (build-system cmake-build-system) (inputs `(("eudev" ,eudev) -- cgit 1.4.1 From c10b29b473e1568464099073f77f0d507b538281 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:05:55 +1000 Subject: gnu: lxqt-globalkeys: Update to 0.17.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-globalkeys): Update to 0.17.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 24418a8f4a..dee81c700a 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -433,7 +433,7 @@ configuration of both LXQt and the underlying operating system.") (define-public lxqt-globalkeys (package (name "lxqt-globalkeys") - (version "0.15.0") + (version "0.17.0") (source (origin (method url-fetch) @@ -441,7 +441,7 @@ configuration of both LXQt and the underlying operating system.") "releases/download/" version "/" "lxqt-globalkeys-" version ".tar.xz")) (sha256 - (base32 "1wfvpvy32p60j7xibfa30skzxx2187qrsqxm1npabj1y5bva2m6f")))) + (base32 "0pnyqiqhaawrnyvw3ljp850d911abaalnl4rgvl2xyzybvlhki4h")))) (build-system cmake-build-system) (inputs `(("kwindowsystem" ,kwindowsystem) -- cgit 1.4.1 From f4a88fe79f4c5073f1e52f8222ad2d09fd27f195 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:05:56 +1000 Subject: gnu: lxqt-notificationd: Update to 0.17.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-notificationd): Update to 0.17.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index dee81c700a..9b93df34d2 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -482,14 +482,14 @@ as a whole and are not limited to distinct applications.") (define-public lxqt-notificationd (package (name "lxqt-notificationd") - (version "0.15.0") + (version "0.17.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "01fva6q2vb0aframxgm0jslvb3z0dcwmhz0yr239bskvdwpn885w")))) + (base32 "1dyal7brmfnydfgb6lpxnqww8fj5gzixs7s3wf5nn2ihsz1wm4nk")))) (build-system cmake-build-system) (inputs `(("kwindowsystem" ,kwindowsystem) -- cgit 1.4.1 From af56f2e5d4472798ddd0b885914d0842e9cc8e35 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:05:58 +1000 Subject: gnu: lxqt-policykit: Update to 0.17.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-policykit): Update to 0.17.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 9b93df34d2..931ccd9a3d 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -642,14 +642,14 @@ of other programs.") (define-public lxqt-policykit (package (name "lxqt-policykit") - (version "0.15.0") + (version "0.17.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "0kzc9mxl47bz6mifmk4xi9sxh7jl31d55j7cq8vijqg3w1yb5rp2")))) + (base32 "119bjhx208g7wxmr8r0ajb3wl6vagq1aks6zz07df4bgjs3nnpli")))) (build-system cmake-build-system) (inputs `(("kwindowsystem" ,kwindowsystem) -- cgit 1.4.1 From d0133d59eb8d262bfe77a5b40c5149fb9d46cbcc Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:05:59 +1000 Subject: gnu: lxqt-powermanagement: Update to 0.17.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-powermanagement): Update to 0.17.1. [inputs]: Add lxqt-globalkeys. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 931ccd9a3d..0db6786ffa 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -691,20 +691,21 @@ LXQt.") (define-public lxqt-powermanagement (package (name "lxqt-powermanagement") - (version "0.15.0") + (version "0.17.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1kal7w6ngs9yrg309p4wacmabpynsrysmbpfkpphg158z548wwl0")))) + (base32 "00njx8a8cs0zzpz798qc9j16k7i4y0ydy1xmmcq9yv0wawh4gqck")))) (build-system cmake-build-system) (inputs `(("kidletime" ,kidletime) ("kwindowsystem" ,kwindowsystem) ("liblxqt" ,liblxqt) ("libqtxdg" ,libqtxdg) + ("lxqt-globalkeys" ,lxqt-globalkeys) ("qtbase" ,qtbase) ("qtsvg" ,qtsvg) ("qtx11extras" ,qtx11extras) -- cgit 1.4.1 From 9987e7a2313d52f622ffcf6df578a8db7c224854 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:00 +1000 Subject: gnu: lxqt-runner: Update to 0.17.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-runner): Update to 0.17.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 0db6786ffa..f201b426dc 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -779,14 +779,14 @@ Qt with LXQt.") (define-public lxqt-runner (package (name "lxqt-runner") - (version "0.15.0") + (version "0.17.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "02xxpflhh6a8qpnjhl5mrl07ikzl5x21mf0rj8nmm0v28rpkqjk1")))) + (base32 "0n53jbvkmp4vgi21a720gsvi407m4ybqk8xrpnm5f48yjr88r9i4")))) (build-system cmake-build-system) (inputs `(("kwindowsystem" ,kwindowsystem) -- cgit 1.4.1 From 78604a1b9cb700cb818a747d1d583d677dd84e6e Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:01 +1000 Subject: gnu: lxqt-session: Update to 0.17.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-session): Update to 0.17.1. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index f201b426dc..50b9c755a1 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -828,20 +828,21 @@ allows for launching applications or shutting down the system.") (define-public lxqt-session (package (name "lxqt-session") - (version "0.15.0") + (version "0.17.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "17y6l1l2m2hzxlzvr7wbixnldbr7waky97vj6lx72r81l45wqkz4")))) + (base32 "0iwwfyngpbhs2dwvbw0cci0bf3qbqcpjjw7h5vm46nimvgp8q1fr")))) (build-system cmake-build-system) (inputs `(("eudev" ,eudev) ("kwindowsystem" ,kwindowsystem) ("liblxqt" ,liblxqt) ("libqtxdg" ,libqtxdg) + ("procps" ,procps) ("qtbase" ,qtbase) ("qtsvg" ,qtsvg) ("qtx11extras" ,qtx11extras) -- cgit 1.4.1 From e84201476e4df68cc5f976328bf6c0b95557c98f Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:05:57 +1000 Subject: gnu: lxqt-panel: Update to 0.17.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-panel): Update to 0.17.1. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 50b9c755a1..ad76dd339d 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -567,14 +567,14 @@ of other programs.") (define-public lxqt-panel (package (name "lxqt-panel") - (version "0.15.1") + (version "0.17.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1b40l9p31nz96q38vwgd1zj142xcwqnjwljsird4nnzs2smjn1c6")))) + (base32 "1k2cfs1mhad486kh93vbxma3jpjksp4hzjv1xmp1g5alb5dgnc0q")))) (build-system cmake-build-system) (inputs `(("alsa-lib" ,alsa-lib) -- cgit 1.4.1 From d71c5ecfd5d8ffc21e05e40d675f7b5253bb42cd Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:02 +1000 Subject: gnu: lxqt-sudo: Update to 0.17.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-sudo): Update to 0.17.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index ad76dd339d..21e705d50b 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -900,14 +900,14 @@ for the LXQt desktop environment.") (define-public lxqt-sudo (package (name "lxqt-sudo") - (version "0.15.0") + (version "0.17.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1v4gzmld3zqi3y9pdy3hb8lq81jwbgi4ia00lbzccg8cm0m8n55w")))) + (base32 "02s38m0ywp0gjkjczvrc4r1ignshbajlj084xd61d3rcm7vahhic")))) (build-system cmake-build-system) (inputs `(("kwindowsystem" ,kwindowsystem) -- cgit 1.4.1 From 4979d4e5110ba702f634b19a5ff5d77576dfa9ae Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:03 +1000 Subject: gnu: lxqt-themes: Update to 0.17.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-themes): Update to 0.17.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 21e705d50b..a52a986682 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -942,14 +942,14 @@ permissions of other users including root.") (define-public lxqt-themes (package (name "lxqt-themes") - (version "0.15.0") + (version "0.17.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1dzv60q1dhi666ajh218smkp3ybh5vl2mxyvlbyc9zwvhgx3f0d1")))) + (base32 "0kmvcz6rxghxxgb0m264zbvycc1zjma8mr4cpwg5kyrzb47rdw9z")))) (build-system cmake-build-system) (native-inputs `(("lxqt-build-tools" ,lxqt-build-tools))) -- cgit 1.4.1 From 8878369e453dfd52d8ca9df2f7bb6fbd326d8b58 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:04 +1000 Subject: gnu: pcmanfm-qt: Update to 0.17.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (pcmanfm-qt): Update to 0.17.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index a52a986682..b01c3a7fdb 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -1013,14 +1013,14 @@ components to build desktop file managers which belongs to LXDE.") (define-public pcmanfm-qt (package (name "pcmanfm-qt") - (version "0.15.1") + (version "0.17.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1izc60hrc16sv2ig9psr3br9iq8nln6a2ycfspzycgpk8rh0f6jd")))) + (base32 "1axs7dnh2z08ygy28iipfbgfck15k2i2pwlf0v8d8axjrmavzb3l")))) (build-system cmake-build-system) (inputs `(("libfm-qt" ,libfm-qt) -- cgit 1.4.1 From 528a3c48eb4a7d70cad68c29e955658dba761d9a Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:05 +1000 Subject: gnu: lximage-qt: Update to 0.17.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lximage-qt): Update to 0.17.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index b01c3a7fdb..5a90e12c77 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -1090,14 +1090,14 @@ manager Compton.") (define-public lximage-qt (package (name "lximage-qt") - (version "0.15.0") + (version "0.17.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "02iyymb8ywlzvv69lga5a86b7kh4v78zw6qzq5kcnjp1rpj2rjrk")))) + (base32 "0g6hs41xfw2ghhwpj0rqr2ciri0x9v984689yrnmnvah88zlya1f")))) (build-system cmake-build-system) (inputs `(("libexif" ,libexif) -- cgit 1.4.1 From aff495c8eb3953fe718cb15d3ff612aa306bba74 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:06 +1000 Subject: gnu: obconf-qt: Update to 0.16.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (obconf-qt): Update to 0.16.1. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 5a90e12c77..b0fd8885dc 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -1120,14 +1120,14 @@ image viewer.") (define-public obconf-qt (package (name "obconf-qt") - (version "0.15.0") + (version "0.16.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1vcv2y54hgxcf76cr775632kajmvz3v4x1q3r6p1lzs9s7lmrh6q")))) + (base32 "0hlbivdbiw7wjhwrp8qfmq50ks19v0q21m3pyjj0k2na7nv9d3a5")))) (build-system cmake-build-system) (inputs `(("imlib2" ,imlib2) -- cgit 1.4.1 From 50b98fec89c14d6122dd161931155f8aa9a84e9f Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:07 +1000 Subject: gnu: pavucontrol-qt: Update to 0.17.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (pavucontrol-qt): Update to 0.17.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index b0fd8885dc..ab7af74eb6 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -1155,14 +1155,14 @@ window manager OpenBox.") (define-public pavucontrol-qt (package (name "pavucontrol-qt") - (version "0.15.0") + (version "0.17.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "15wknwmb4640r5fm4wiq6xa70qa2djay2806wyvajh11xjmqy566")))) + (base32 "0w51dpjayav78lmhw966fz3gvypkmv64xgsd7x5rqs8am39lq9vc")))) (build-system cmake-build-system) (inputs `(("glib" ,glib) -- cgit 1.4.1 From 4ff16c5dce6e3bc3e9e075bcc028da29d232b291 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:08 +1000 Subject: gnu: qtermwidget: Update to 0.17.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (qtermwidget): Update to 0.17.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index ab7af74eb6..8ae3315fdf 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -1215,14 +1215,14 @@ processes currently in existence, much like code{top} or code{ps}.") (define-public qtermwidget (package (name "qtermwidget") - (version "0.15.0") + (version "0.17.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1vn3bbc99py0ak7z9s6p71n9cacpckz57a1p97iwb0p23g4zgjkf")))) + (base32 "10lv475qj0x3c3vl4yhjyr6y10qj5pq8n5pal5k24f6pf7xv412f")))) (build-system cmake-build-system) (inputs `(("qtbase" ,qtbase) -- cgit 1.4.1 From 680f3a321369159bbb6b587f4408ababeb12072f Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:09 +1000 Subject: gnu: qterminal: Update to 0.17.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (qterminal): Update to 0.17.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 8ae3315fdf..39f930e4dc 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -1240,14 +1240,14 @@ processes currently in existence, much like code{top} or code{ps}.") (define-public qterminal (package (name "qterminal") - (version "0.15.0") + (version "0.17.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "0r7xmwjpak47ayj7cj37bwrdlv1mx5nhqpccb5pbn2fh8slp8zsm")))) + (base32 "0rfv7a6ncm8fs8aicinh9l29w4636gxzcqz735jmch2r41v9i1d9")))) (build-system cmake-build-system) (inputs `(("qtbase" ,qtbase) -- cgit 1.4.1 From 76f4af8eb4d4347e948610cbbc332f1051ae4a39 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:10 +1000 Subject: gnu: screengrab: Update to 2.2.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (screengrab): Update to 2.2.0. [native-inputs]: Add perl. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 39f930e4dc..dc08db674f 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -1267,14 +1267,14 @@ QTermWidget.") (define-public screengrab (package (name "screengrab") - (version "2.0.1") + (version "2.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/screengrab/releases/download/" version "/screengrab-" version ".tar.xz")) (sha256 - (base32 "14znjw3d3gw02fsmhrjcj86l173m2ypl1x8hhba9ld23icr1gqwf")))) + (base32 "0cilzw7rz5m2klzpax7rrs5rr6whfda2svwzsn2jvmrirmh5by7r")))) (build-system cmake-build-system) (inputs `(("kwindowsystem" ,kwindowsystem) @@ -1284,6 +1284,7 @@ QTermWidget.") ("qtx11extras" ,qtx11extras))) (native-inputs `(("pkg-config" ,pkg-config) + ("perl" ,perl) ("qttools" ,qttools))) (arguments '(#:tests? #f)) ; no tests -- cgit 1.4.1 From 50ea35ba25ebcfc2719cd12b461dfe5d49f110e4 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:11 +1000 Subject: gnu: lxqt-archiver: Update to 0.4.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-archiver): Update to 0.4.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index dc08db674f..2016913546 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -1298,14 +1298,14 @@ easily publishing them on internet image hosting services.") (define-public lxqt-archiver (package (name "lxqt-archiver") - (version "0.2.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1i725zaah0wv18j5fchg6isbh4b601filx549cq2hkzf2sylh9ff")))) + (base32 "0fzgq7cyr7hx8qmq84xfgbsdx04mc1r7vzq5mz79j7bp2ysh134z")))) (build-system cmake-build-system) (inputs `(("glib" ,glib) -- cgit 1.4.1 From 223b40b7c9c929686a17b139122128ac44c62fe5 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:12 +1000 Subject: gnu: compton-conf: Update to 0.16.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (compton-conf): Update to 0.16.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 2016913546..ce0c1859d2 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -1055,14 +1055,14 @@ LXDE.") (define-public compton-conf (package (name "compton-conf") - (version "0.15.0") + (version "0.16.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1ii1bans7wdafm9rmxvsdqp3ad4cj0pa8kf92plbmbm3nycpf1q9")))) + (base32 "0haarzhndjp0wndfhcdy6zl2whpdn3w0qzr3rr137kfqibc58lvx")))) (build-system cmake-build-system) (inputs `(("libconfig" ,libconfig) -- cgit 1.4.1 From 811a02770e857651a58fcc57c1ef76297e9eea37 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:13 +1000 Subject: gnu: qps: Update to 2.3.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (qps): Update to 2.3.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index ce0c1859d2..ca9eef42a1 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -1185,14 +1185,14 @@ window manager OpenBox.") (define-public qps (package (name "qps") - (version "2.1.0") + (version "2.3.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "0yym1bpglz8vha28x7k21fxx1vlsq19m3fyhk2cq3pwq3nqijwp7")))) + (base32 "0zg0czrh3dlbnl5smxamhkdbj1g0szm47w1c0fwpaplgc1vv5lfq")))) (build-system cmake-build-system) (inputs `(("kwindowsystem" ,kwindowsystem) -- cgit 1.4.1 From 73c8bb7cd6ffa32e4462f933f2f21088506bc8f0 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:14 +1000 Subject: gnu: lxqt-openssh-askpass: Update to 0.17.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-openssh-askpass): Update to 0.17.0. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index ca9eef42a1..0b815622d3 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -528,14 +528,14 @@ according to the Desktop Notifications Specification.") (define-public lxqt-openssh-askpass (package (name "lxqt-openssh-askpass") - (version "0.15.0") + (version "0.17.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1h8nhj4ig8419kfdqjsig16ayf2byrzgrk698aiym544n5ayjwak")))) + (base32 "0gdcy8c21sbfrlfz9c3zqw4dvdwf309flkjgqanwwl9i8hr26chr")))) (build-system cmake-build-system) (inputs `(("kwindowsystem" ,kwindowsystem) -- cgit 1.4.1 From 3e294125c0c9ab789faa33fad53ea83c37774cb2 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:15 +1000 Subject: gnu: lxqt-connman-applet: Update to 0.15-db1618d5. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-connman-applet): Update to 0.15-db1618d5 (translation updates). Untabify. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 0b815622d3..b5a549a7fc 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -1329,7 +1329,7 @@ like @command{tar} and @command{zip}.") (define-public lxqt-connman-applet ;; since the main developers didn't release any version yet, their ;; latest commit on `master` branch at the moment used for this version. - (let ((commit "8a6cc14371a2f18f963e6a2996446082bb60f17d") + (let ((commit "db1618d58fd3439142c4e44b24cba0dbb68b7141") (revision "0")) (package (name "lxqt-connman-applet") @@ -1341,7 +1341,8 @@ like @command{tar} and @command{zip}.") (url (string-append "https://github.com/lxqt/" name)) (commit commit))) (file-name (git-file-name name version)) - (sha256 (base32 "0br4bxfrl8k7lq84aq4grznlk8xzzjgkmd19bf9mwjr0a87gg72v")))) + (sha256 + (base32 "087641idpg7n8yhh5biis4wv52ayw3rddirwqb34bf5fwj664pw9")))) (build-system cmake-build-system) (inputs `(("kwindowsystem" ,kwindowsystem) @@ -1365,13 +1366,13 @@ like @command{tar} and @command{zip}.") "/share/lxqt/translations")) (("\\$\\{LXQT_ETC_XDG_DIR\\}") "etc/xdg")) #t)) - (add-after 'unpack 'remove-definitions - (lambda _ - (substitute* "CMakeLists.txt" - (("include\\(LXQtCompilerSettings NO_POLICY_SCOPE\\)") - "include(LXQtCompilerSettings NO_POLICY_SCOPE) + (add-after 'unpack 'remove-definitions + (lambda _ + (substitute* "CMakeLists.txt" + (("include\\(LXQtCompilerSettings NO_POLICY_SCOPE\\)") + "include(LXQtCompilerSettings NO_POLICY_SCOPE) remove_definitions(-DQT_NO_CAST_TO_ASCII -DQT_NO_CAST_FROM_ASCII)")) - #t))))) + #t))))) (home-page "https://github.com/lxqt/lxqt-connman-applet") (synopsis "System-tray applet for connman") (description "This package provides a Qt-based system-tray applet for -- cgit 1.4.1 From c03908fef0bbb27450ea19d5993e36c309d8a186 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:16 +1000 Subject: gnu: lxqt: Use the projects version number. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt): Use the projects version number. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index b5a549a7fc..849ed98339 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -1385,7 +1385,7 @@ desktop.") (define-public lxqt (package (name "lxqt") - (version (package-version lxqt-session)) + (version "17.0") (source #f) (build-system trivial-build-system) (arguments '(#:builder (begin (mkdir %output) #t))) -- cgit 1.4.1 From 20eea7b9040f11cd36fd4e76f68b54d2bc051b0e Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:17 +1000 Subject: gnu: lxqt: Use picom instead of compton. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt): [inputs]: Use picom instead of compton. Remove deprecated compton-conf. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 849ed98339..fcccf669e4 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -1416,8 +1416,7 @@ desktop.") ("lxqt-themes" ,lxqt-themes) ("pcmanfm-qt" ,pcmanfm-qt) ;; Extra - ("compton" ,compton) - ("compton-conf" ,compton-conf) + ("picom" ,picom) ("font-dejavu" ,font-dejavu) ("lximage-qt" ,lximage-qt) ("obconf-qt" ,obconf-qt) -- cgit 1.4.1 From 6d5ff521937cb1794a0b7c0437b2e7167a7e4aa2 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:18 +1000 Subject: gnu: lxqt-config: Move libkscreen to propagated-inputs. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (lxqt-config): Move libkscreen to propagated-inputs. Kscreen is a runtime dependency. lxqt-config-monitor will not open without it available. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index fcccf669e4..c0a948db3c 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -376,7 +376,6 @@ the operating system LXQt is running on.") (inputs `(("eudev" ,eudev) ("kwindowsystem" ,kwindowsystem) - ("libkscreen" ,libkscreen) ("liblxqt" ,liblxqt) ("libqtxdg" ,libqtxdg) ("libxcursor" ,libxcursor) @@ -392,6 +391,10 @@ the operating system LXQt is running on.") `(("pkg-config" ,pkg-config) ("lxqt-build-tools" ,lxqt-build-tools) ("qttools" ,qttools))) + ;; XXX: This is a workaround so libkscreen can find the backends as we + ;; dont have a way specify them. We may want to patch like Nix does. + (propagated-inputs + `(("libkscreen" ,libkscreen))) (arguments '(#:tests? #f ; no tests #:phases -- cgit 1.4.1 From f8adff1ea237b09322b9e046a0fe3cd1c43fe590 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 17 May 2021 00:06:19 +1000 Subject: gnu: Update lxqt home-page for all lxqt packages. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm: Replace all lxqt.github.io with lxqt-project.org, where it redirects to. Signed-off-by: Ludovic Courtès --- gnu/packages/lxqt.scm | 58 +++++++++++++++++++++++++-------------------------- 1 file changed, 29 insertions(+), 29 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index c0a948db3c..b4cdcaac0f 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -158,7 +158,7 @@ to statistics about the system on which it's run.") (description "Lxqt-build-tools is providing several tools needed to build LXQt itself as well as other components maintained by the LXQt project.") - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (license license:lgpl2.1+))) (define-public libqtxdg @@ -239,7 +239,7 @@ in Qt.") (native-inputs `(("lxqt-build-tools" ,lxqt-build-tools) ("qttools" ,qttools))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "Core utility library for all LXQt components") (description "liblxqt provides the basic libraries shared by the components of the LXQt desktop environment.") @@ -262,7 +262,7 @@ components of the LXQt desktop environment.") `(("qtbase" ,qtbase))) (native-inputs `(("lxqt-build-tools" ,lxqt-build-tools))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "Library used to query system info and statistics") (description "libsysstat is a library to query system information like CPU and memory usage or network traffic.") @@ -308,7 +308,7 @@ and memory usage or network traffic.") (string-append (assoc-ref outputs "out") "/share/lxqt/translations"))) #t))))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "Provides information about LXQt and the system") (description "lxqt-about is a dialogue window providing information about LXQt and the system it's running on.") @@ -355,7 +355,7 @@ LXQt and the system it's running on.") (string-append (assoc-ref outputs "out") "/share/lxqt/translations"))) #t))))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "LXQt system administration tool") (description "lxqt-admin is providing two GUI tools to adjust settings of the operating system LXQt is running on.") @@ -427,7 +427,7 @@ the operating system LXQt is running on.") (string-append (assoc-ref outputs "out") "/share/lxqt/translations"))) #t))))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "Tools to configure LXQt and the underlying operating system") (description "lxqt-config is providing several tools involved in the configuration of both LXQt and the underlying operating system.") @@ -475,7 +475,7 @@ configuration of both LXQt and the underlying operating system.") (string-append (assoc-ref outputs "out") "/share/lxqt/translations"))) #t))))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "Daemon used to register global keyboard shortcuts") (description "lxqt-globalkeys is providing tools to set global keyboard shortcuts in LXQt sessions, that is shortcuts which apply to the LXQt session @@ -522,7 +522,7 @@ as a whole and are not limited to distinct applications.") (string-append (assoc-ref outputs "out") "/share/lxqt/translations"))) #t))))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "The LXQt notification daemon") (description "lxqt-notificationd is LXQt's implementation of a daemon according to the Desktop Notifications Specification.") @@ -561,7 +561,7 @@ according to the Desktop Notifications Specification.") (string-append (assoc-ref outputs "out") "/share/lxqt/translations"))) #t))))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "GUI to query passwords on behalf of SSH agents") (description "lxqt-openssh-askpass is a GUI to query credentials on behalf of other programs.") @@ -637,7 +637,7 @@ of other programs.") (("/usr/share/X11/xkb/rules/evdev.xml") (string-append xkb "/share/X11/xkb/rules/evdev.xml"))) #t)))))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "The LXQt desktop panel") (description "lxqt-panel represents the taskbar of LXQt.") (license license:lgpl2.1+))) @@ -685,7 +685,7 @@ of other programs.") (string-append (assoc-ref outputs "out") "/share/lxqt/translations"))) #t))))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "The LXQt PolicyKit agent") (description "lxqt-policykit is the polkit authentication agent of LXQt.") @@ -734,7 +734,7 @@ LXQt.") (string-append (assoc-ref outputs "out") "/share/lxqt/translations"))) #t))))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "Power management module for LXQt") (description "lxqt-powermanagement is providing tools to monitor power management events and optionally trigger actions like e. g. shut down a system @@ -773,7 +773,7 @@ when laptop batteries are low on power.") (("DESTINATION \"\\$\\{QT_PLUGINS_DIR\\}") "DESTINATION \"lib/qt5/plugins")) #t))))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "LXQt Qt platform integration plugin") (description "lxqt-qtplugin is providing a library libqtlxqt to integrate Qt with LXQt.") @@ -822,7 +822,7 @@ Qt with LXQt.") (string-append (assoc-ref outputs "out") "/share/lxqt/translations"))) #t))))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "Tool used to launch programs quickly by typing their names") (description "lxqt-runner provides a GUI that comes up on the desktop and allows for launching applications or shutting down the system.") @@ -894,7 +894,7 @@ allows for launching applications or shutting down the system.") `("XDG_CONFIG_DIRS" ":" suffix ("/run/current-system/profile/share" "/run/current-system/profile/share/pcmanfm-qt"))) #t)))))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "Session manager for LXQt") (description "lxqt-session provides the standard session manager for the LXQt desktop environment.") @@ -935,7 +935,7 @@ for the LXQt desktop environment.") (string-append (assoc-ref outputs "out") "/share/lxqt/translations"))) #t))))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "GUI frontend for sudo/su") (description "lxqt-sudo is a graphical front-end of commands sudo and su respectively. As such it enables regular users to launch applications with @@ -969,7 +969,7 @@ permissions of other users including root.") (("DESTINATION \"\\$\\{LXQT_SHARE_DIR\\}") "DESTINATION \"share/lxqt")) #t))))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "Themes, graphics and icons for LXQt") (description "This package comprises a number of graphic files and themes for LXQt.") @@ -1007,7 +1007,7 @@ for LXQt.") `(("pkg-config" ,pkg-config) ("lxqt-build-tools" ,lxqt-build-tools) ("qttools" ,qttools))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "Qt binding for libfm") (description "libfm-qt is the Qt port of libfm, a library providing components to build desktop file managers which belongs to LXDE.") @@ -1046,7 +1046,7 @@ components to build desktop file managers which belongs to LXDE.") (("@LXQT_SHARE_DIR@") "/run/current-system/profile/share/lxqt" )) #t))))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "File manager and desktop icon manager") (description "PCManFM-Qt is the Qt port of PCManFM, the file manager of LXDE.") @@ -1084,7 +1084,7 @@ LXDE.") (("DESTINATION \"\\$\\{LXQT_ETC_XDG_DIR\\}") "DESTINATION \"etc/xdg")) #t))))) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "GUI configuration tool for compton X composite manager") (description "@code{compton-conf} is a configuration tool for X composite manager Compton.") @@ -1114,7 +1114,7 @@ manager Compton.") ("qttools" ,qttools))) (arguments '(#:tests? #f)) ; no tests - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "The image viewer and screenshot tool for lxqt") (description "LXImage-Qt is the Qt port of LXImage, a simple and fast image viewer.") @@ -1149,7 +1149,7 @@ image viewer.") ("qttools" ,qttools))) (arguments '(#:tests? #f)) ; no tests - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "Openbox configuration tool") (description "ObConf-Qt is a Qt port of ObConf, a configuration editor for window manager OpenBox.") @@ -1179,7 +1179,7 @@ window manager OpenBox.") ("qttools" ,qttools))) (arguments '(#:tests? #f)) ; no tests - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "Pulseaudio mixer in Qt") (description "@code{pavucontrol-qt} is the Qt port of volume control @code{pavucontrol} of sound server @code{PulseAudio}.") @@ -1209,7 +1209,7 @@ window manager OpenBox.") ("qttools" ,qttools))) (arguments '(#:tests? #f)) ; no tests - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "Qt-based visual process status monitor") (description "@code{qps} is a monitor that displays the status of the processes currently in existence, much like code{top} or code{ps}.") @@ -1235,7 +1235,7 @@ processes currently in existence, much like code{top} or code{ps}.") ("qttools" ,qttools))) (arguments '(#:tests? #f)) ; no tests - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "The terminal widget for QTerminal") (description "QTermWidget is a terminal emulator widget for Qt 5.") (license license:gpl2+))) @@ -1261,7 +1261,7 @@ processes currently in existence, much like code{top} or code{ps}.") ("qttools" ,qttools))) (arguments '(#:tests? #f)) ; no tests - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "Lightweight Qt-based terminal emulator") (description "QTerminal is a lightweight Qt terminal emulator based on QTermWidget.") @@ -1291,7 +1291,7 @@ QTermWidget.") ("qttools" ,qttools))) (arguments '(#:tests? #f)) ; no tests - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "Crossplatform tool for fast making screenshots") (description "ScreenGrab is a program for fast creating screenshots, and easily publishing them on internet image hosting services.") @@ -1322,7 +1322,7 @@ easily publishing them on internet image hosting services.") ("qttools" ,qttools))) (arguments '(#:tests? #f)) - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (synopsis "Simple & lightweight desktop-agnostic Qt file archiver") (description "This package provides a Qt graphical interface to archiving programs @@ -1430,5 +1430,5 @@ desktop.") ("qterminal" ,qterminal))) (synopsis "The Lightweight Qt Desktop Environment") (description "LXQt is a lightweight Qt desktop environment.") - (home-page "https://lxqt.github.io") + (home-page "https://lxqt-project.org") (license license:gpl2+))) -- cgit 1.4.1 From 395e20ed0803995244b238dd002edd37bdc4cd00 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Sat, 29 May 2021 14:01:56 +0530 Subject: gnu: Register gnu/services/ci.scm and gnu/tests/ci.scm. This is a follow-up to commit eda4bb4f16f74436b0caf1c584888c89b3c4c69b. * gnu/local.mk (GNU_SYSTEM_MODULES): Add gnu/services/ci.scm and gnu/tests/ci.scm. --- gnu/local.mk | 3 +++ 1 file changed, 3 insertions(+) (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index cf13d672bd..0c0a6b924a 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -41,6 +41,7 @@ # Copyright © 2020 Vinicius Monego # Copyright © 2021 Björn Höfling # Copyright © 2021 Philip McGrath +# Copyright © 2021 Arun Isaac # # This file is part of GNU Guix. # @@ -599,6 +600,7 @@ GNU_SYSTEM_MODULES = \ %D%/services/base.scm \ %D%/services/certbot.scm \ %D%/services/cgit.scm \ + %D%/services/ci.scm \ %D%/services/configuration.scm \ %D%/services/cuirass.scm \ %D%/services/cups.scm \ @@ -690,6 +692,7 @@ GNU_SYSTEM_MODULES = \ %D%/tests.scm \ %D%/tests/audio.scm \ %D%/tests/base.scm \ + %D%/tests/ci.scm \ %D%/tests/cups.scm \ %D%/tests/databases.scm \ %D%/tests/desktop.scm \ -- cgit 1.4.1 From c094e574f2b78b2f090aa740c1284418c16b2fcd Mon Sep 17 00:00:00 2001 From: raingloom Date: Fri, 28 May 2021 03:59:16 +0200 Subject: gnu: Break up import loop between (gnu packages racket) and (gnu packages chez). MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/racket.scm: Remove (gnu packages chez) import. Signed-off-by: Ludovic Courtès --- gnu/packages/racket.scm | 2 -- 1 file changed, 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/racket.scm b/gnu/packages/racket.scm index be33270b30..2d606071fe 100644 --- a/gnu/packages/racket.scm +++ b/gnu/packages/racket.scm @@ -32,8 +32,6 @@ #:use-module (ice-9 match) #:use-module (gnu packages) #:use-module (gnu packages bash) - #:use-module ((gnu packages chez) - #:select (chez-scheme)) #:use-module (gnu packages compression) #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) -- cgit 1.4.1 From 036f9980c4d5db180716dadc88382b39d6fdc3cf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 29 May 2021 22:17:53 +0200 Subject: gnu: guile-studio: Update to 0.1.1. * gnu/packages/guile-xyz.scm (guile-studio): Update to 0.1.1. --- gnu/packages/guile-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index be3dacba33..4c7c089505 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -2744,11 +2744,11 @@ The picture values can directly be displayed in Geiser.") guile-picture-language)) (define-public guile-studio - (let ((commit "93622e788e727d3275291f999f7e570de6a5bb35") + (let ((commit "dd0ad42e51feafebda7cc29afe7c8bc7a182a842") (revision "1")) (package (name "guile-studio") - (version (git-version "0.1.0" revision commit)) + (version (git-version "0.1.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -2757,7 +2757,7 @@ The picture values can directly be displayed in Geiser.") (file-name (git-file-name name version)) (sha256 (base32 - "0n6y0bcmkx50m8rccz7a6h4yxmwq54pf2bfzpd5ndz2bsiwiq13l")))) + "1cpqilly8dqmai1qsgjxy99zs34sfz95zwxhzx979wryqb69vi0q")))) (build-system gnu-build-system) (arguments `(#:modules -- cgit 1.4.1 From c63623305af2b13361aa519ba44c29fac71a1fc3 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 28 May 2021 13:16:56 -0400 Subject: gnu: linux-libre: Update to 5.12.8. * gnu/packages/linux.scm (linux-libre-5.12-version): Update to 5.12.8. (linux-libre-5.12-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index f127e36e36..a1ed6877d8 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -356,7 +356,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernels. That is, the most recently released major ;; versions that are still supported upstream. -(define-public linux-libre-5.12-version "5.12.7") +(define-public linux-libre-5.12-version "5.12.8") (define deblob-scripts-5.12 (linux-libre-deblob-scripts linux-libre-5.12-version @@ -364,7 +364,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1qp25fd4wgjyk7dzdq9yirm1z5w68sd1p3wv8lch8259i51gwjnf"))) (define-public linux-libre-5.12-pristine-source (let ((version linux-libre-5.12-version) - (hash (base32 "0ircrclggrbmm80vz7irhg73qvhjddsmf7zclw5cqnnmm3qfj8jk"))) + (hash (base32 "134g8d5zvbzdqxy7z6a527dqcmiq4ixf7s05rnnsc4qcajpbcimd"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.12))) -- cgit 1.4.1 From a6a22f710f2bbfcb5db7ca8cd1fbb347fa7d1b1d Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 28 May 2021 13:17:14 -0400 Subject: gnu: linux-libre 5.10: Update to 5.10.41. * gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.41. (linux-libre-5.10-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a1ed6877d8..4929967908 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -372,7 +372,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; -(define-public linux-libre-5.10-version "5.10.40") +(define-public linux-libre-5.10-version "5.10.41") (define deblob-scripts-5.10 (linux-libre-deblob-scripts linux-libre-5.10-version @@ -380,7 +380,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0hh27ccqimagr3aij7ygwikxw66y63sqwd0xlf49bhpjd090r9a7"))) (define-public linux-libre-5.10-pristine-source (let ((version linux-libre-5.10-version) - (hash (base32 "091g9g29m4vh66bxihiylyprb3cxr8cy4m494klb2lkirlx8103l"))) + (hash (base32 "0wb739q7dha8nxkd72x42k4in5nw633yw065ppwc8rq7x2fpa17n"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.10))) -- cgit 1.4.1 From 570b4c81357007ecc7173f5c01c51c9600224912 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 28 May 2021 13:17:28 -0400 Subject: gnu: linux-libre 5.4: Update to 5.4.123. * gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.123. (linux-libre-5.4-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 4929967908..615a2523f9 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -385,7 +385,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.10))) -(define-public linux-libre-5.4-version "5.4.122") +(define-public linux-libre-5.4-version "5.4.123") (define deblob-scripts-5.4 (linux-libre-deblob-scripts linux-libre-5.4-version @@ -393,7 +393,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1xghbbnaisjd0k1klbyn1p7r6r4x5a1bpmkm56a3gh2zvw4s7mj8"))) (define-public linux-libre-5.4-pristine-source (let ((version linux-libre-5.4-version) - (hash (base32 "00g6s3ymriwddshy5sd458b1wfvw2ynxv6dr63ziykwfq50jlr9p"))) + (hash (base32 "1pi223dls52piw65s3v4ml23wdyy73xpbdvp511187b6zgzk7zlf"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.4))) -- cgit 1.4.1 From 18562b7708f27f213957ae41cb36954244f7264a Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 22:56:09 +0200 Subject: gnu: emacs-org-generate: Disable tests to let the package build. * gnu/packages/emacs-xyz.scm (emacs-org-generate)[propagated-inputs]: Add with-simulated-inputs for tests... [arguments]<#:tests?>: ... yet disable them for now as there seems to be an issue with Cort library. --- gnu/packages/emacs-xyz.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index cf66dc67f8..14498f1c6e 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -27196,11 +27196,14 @@ opening Org Ref's @code{cite:} links.") (base32 "0z2frp5mn3lp2xskwanw2rncrwa50x3aphy87vfxmhx4fqlqrzy8")))) (inputs - `(("emacs-cort" ,emacs-cort))) ;tests suite + `(("emacs-cort" ,emacs-cort) + ("emacs-with-simulated-input" ,emacs-with-simulated-input))) (propagated-inputs `(("emacs-mustache" ,emacs-mustache))) (arguments - `(#:tests? #t + ;; FIXME: Tests fail with "Wrong type argument: sequencep, :equal". It + ;; seems to be an issue with Cort library. + `(#:tests? #f #:test-command '("emacs" "--batch" "--quick" "--directory=." "--load=org-generate-tests.el" "--funcall=cort-test-run"))) -- cgit 1.4.1 From dd083bd05a141dbc391b0027bdb88465e0735815 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 29 May 2021 23:03:38 +0200 Subject: gnu: emacs-evil-magit: Update to 0.4.2-5.98c076f. * gnu/packages/emacs-xyz.scm (emacs-evil-magit): Update to 0.4.2-5.98c076f. --- gnu/packages/emacs-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 14498f1c6e..2bd75c0dde 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -19461,8 +19461,8 @@ Org-mode file, and citations of Zotero items in Pandoc Markdown files.") (license license:gpl3+))) (define-public emacs-evil-magit - (let ((commit "253c644807013fe92429acdef418748794b8f254") - (revision "4")) + (let ((commit "98c076fbeb6d2d7d71e02dc204ba3ad5d577abda") + (revision "5")) (package (name "emacs-evil-magit") (version (git-version "0.4.2" revision commit)) @@ -19475,7 +19475,7 @@ Org-mode file, and citations of Zotero items in Pandoc Markdown files.") (file-name (git-file-name name version)) (sha256 (base32 - "08mh7phxsdb9w4dfs0pmr4l4fdzzr2rm88z2s8karfi5j5ik2ag5")))) + "0b4iplxh3rmy8jadhf05pgksv1798d68d1jrhfry93jca8x9crxs")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-evil" ,emacs-evil) -- cgit 1.4.1 From 055d0fa3249966fbf9d1e96056d444d7fbf8d605 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 29 May 2021 23:14:12 +0200 Subject: gnu: Add guile-drmaa. * gnu/packages/guile-xyz.scm (guile-drmaa): New variable. --- gnu/packages/guile-xyz.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 4c7c089505..6db5134344 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -4569,6 +4569,39 @@ including parsing and code generation.") "Guile Shapefile is a Guile library for reading shapefiles.") (license license:expat))) +(define-public guile-drmaa + (package + (name "guile-drmaa") + (version "0.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.elephly.net/software/guile-drmaa.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1m2x62n3x5hi5vnsvv2zgqhgpzrfq7r5095fzzjd1aaybi9i9igg")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("pkg-config" ,pkg-config) + ("texinfo" ,texinfo) + ("sed" ,sed))) + (inputs + `(("guile" ,guile-3.0))) + (propagated-inputs + `(("guile-bytestructures" ,guile-bytestructures) + ("nyacc" ,nyacc))) + (home-page "https://git.elephly.net/software/guile-drmaa.git") + (synopsis "Guile bindings to DRMAA") + (description "This project provides Guile bindings to the DRMAA library +version 1. DRMAA is a resource management library implemented by HPC cluster +schedulers.") + (license license:gpl3+))) + (define-public guile-libyaml (let ((commit "f5d33a6880e96571d3cb079ed7755ffc156cac46") (revision "1")) -- cgit 1.4.1 From d7d6c9e4e697c33634c89628d10995d0f070db96 Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Sat, 29 May 2021 21:17:41 -0700 Subject: gnu: bootloader: Fix install-allwinner64-u-boot. This fixes boot breakage introduced in commit: a65c935e29766940148d52b8116634b1e1cbcba6 Multiple files were still needed, but the filenames changed. * gnu/bootloader/u-boot.scm (install-allwinner64-u-boot): Update to use both SPL and u-boot files with new filenames. --- gnu/bootloader/u-boot.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/bootloader/u-boot.scm b/gnu/bootloader/u-boot.scm index 122c7c9861..6cad33b741 100644 --- a/gnu/bootloader/u-boot.scm +++ b/gnu/bootloader/u-boot.scm @@ -73,9 +73,12 @@ (define install-allwinner64-u-boot #~(lambda (bootloader root-index image) - (let ((spl (string-append bootloader "/libexec/u-boot-sunxi-with-spl.fit.itb"))) + (let ((spl (string-append bootloader "/libexec/u-boot-sunxi-with-spl.bin")) + (u-boot (string-append bootloader "/libexec/u-boot-sunxi-with-spl.fit.itb"))) (write-file-on-device spl (stat:size (stat spl)) - image (* 8 1024))))) + image (* 8 1024)) + (write-file-on-device u-boot (stat:size (stat u-boot)) + image (* 40 1024))))) (define install-imx-u-boot #~(lambda (bootloader root-index image) -- cgit 1.4.1 From b5069d8eaa09d20ed622b284f4004b155fc11ef8 Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Mon, 10 May 2021 04:27:43 +0000 Subject: gnu: linux-libre@5.12: Apply patch to fix eDP panel on Pinebook Pro. * gnu/packages/linux.scm (linux-libre-5.12-source): Add Pinebook Pro LCD patch. (linux-libre-5.10-pristine-source): Fix whitespace and add comment. --- gnu/packages/linux.scm | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 615a2523f9..b803426b74 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -481,14 +481,18 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (define-public linux-libre-5.12-source (source-with-patches linux-libre-5.12-pristine-source (list %boot-logo-patch - %linux-libre-arm-export-__sync_icache_dcache-patch))) + %linux-libre-arm-export-__sync_icache_dcache-patch + ;; Pinebook Pro patch to fix LCD display + (search-patch + "linux-libre-arm64-generic-pinebook-lcd.patch")))) (define-public linux-libre-5.10-source (source-with-patches linux-libre-5.10-pristine-source (list %boot-logo-patch %linux-libre-arm-export-__sync_icache_dcache-patch - (search-patch - "linux-libre-arm64-generic-pinebook-lcd.patch")))) + ;; Pinebook Pro patch to fix LCD display + (search-patch + "linux-libre-arm64-generic-pinebook-lcd.patch")))) (define-public linux-libre-5.4-source (source-with-patches linux-libre-5.4-pristine-source -- cgit 1.4.1 From fd90a36869d24557b2d456f8fb8f3a487c75045f Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Sun, 30 May 2021 11:12:19 +0200 Subject: gnu: cuirass: Update to 1.0.0-24.f0be14a. * gnu/packages/ci.scm (cuirass): Update to 1.0.0-24.f0be14a. --- gnu/packages/ci.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm index 588f52ae56..0f8d1d3e8f 100644 --- a/gnu/packages/ci.scm +++ b/gnu/packages/ci.scm @@ -73,8 +73,8 @@ (file-name (string-append name "-" version "-checkout"))))))) (define-public cuirass - (let ((commit "58e3551d6dcc3cf4a9d072d6c56531ae3b6e7bbe") - (revision "23")) + (let ((commit "f0be14a95ae05253063672585e0fb246e3e5383a") + (revision "24")) (package (name "cuirass") (version (git-version "1.0.0" revision commit)) @@ -87,7 +87,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0m2w0258m9mb1gq1522z4mhinhs3xgbmdas4aaqnf50hsnxmh7h5")))) + "04x7kal63r3f50nyd2a0s1xw966xcxwpgmanhlqh20rg4nxl1pkq")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build utils) -- cgit 1.4.1 From 8774e1b73709b24fa52b71293ec7f99b825e2af0 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Sun, 30 May 2021 11:32:39 +0200 Subject: gnu: cuirass: Update to 1.0.0-25.2120276. * gnu/packages/ci.scm (cuirass): Update to 1.0.0-25.2120276. --- gnu/packages/ci.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm index 0f8d1d3e8f..0a5f3afbd2 100644 --- a/gnu/packages/ci.scm +++ b/gnu/packages/ci.scm @@ -73,8 +73,8 @@ (file-name (string-append name "-" version "-checkout"))))))) (define-public cuirass - (let ((commit "f0be14a95ae05253063672585e0fb246e3e5383a") - (revision "24")) + (let ((commit "21202760c0d15c99b69ef235ff129ab9cb478186") + (revision "25")) (package (name "cuirass") (version (git-version "1.0.0" revision commit)) @@ -87,7 +87,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "04x7kal63r3f50nyd2a0s1xw966xcxwpgmanhlqh20rg4nxl1pkq")))) + "1bzzycz7jmmrph730p8d3q2h76ab6i8j72wblm3w0szf8vimcqfk")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build utils) -- cgit 1.4.1 From 4562c60d984f135b7bdc45b92732f584862d6859 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 20:23:58 +0200 Subject: gnu: rlwrap: Update to 0.45.1. * gnu/packages/readline.scm (rlwrap): Update to 0.45.1. [source]: Use GIT-FETCH and GIT-FILE-NAME. [native-inputs]: Add automake & autoconf. --- gnu/packages/readline.scm | 26 +++++++++++++++----------- 1 file changed, 15 insertions(+), 11 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/readline.scm b/gnu/packages/readline.scm index 8a36883347..3cca1aefe7 100644 --- a/gnu/packages/readline.scm +++ b/gnu/packages/readline.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2012, 2013, 2014, 2020 Ludovic Courtès ;;; Copyright © 2016, 2019 Efraim Flashner ;;; Copyright © 2016 Jan Nieuwenhuizen -;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2018, 2021 Tobias Geerinckx-Rice ;;; Copyright © 2019 Marius Bakke ;;; ;;; This file is part of GNU Guix. @@ -23,10 +23,12 @@ (define-module (gnu packages readline) #:use-module (guix licenses) #:use-module (gnu packages) + #:use-module (gnu packages autotools) #:use-module (gnu packages ncurses) #:use-module (gnu packages perl) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix build-system gnu) #:use-module (guix utils) #:use-module (ice-9 format)) @@ -144,19 +146,21 @@ comfortable for anyone.") (define-public rlwrap (package (name "rlwrap") - (version "0.43") + (version "0.45.1") (source - (origin - (method url-fetch) - (uri (string-append "https://github.com/hanslub42/rlwrap/releases/" - "download/v" version "/" - name "-" version ".tar.gz")) - (sha256 - (base32 - "0bzb7ylk2770iv59v2d0gypb21y2xn87m299s9rqm6rdi2vx11lf")))) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hanslub42/rlwrap") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0shf59mkql584a0p449psnbr26bfik5pizg4vsa75g4gbi6mn4r7")))) (build-system gnu-build-system) (native-inputs - `(("perl" ,perl))) + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("perl" ,perl))) (inputs `(("readline" ,readline))) (synopsis "Wrapper to allow the editing of keyboard commands") -- cgit 1.4.1 From efd524e084f7ce111da1e05e107b1e01b718a45a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 20:24:44 +0200 Subject: gnu: rlwrap: Fix single-quotation in Texinfo. * gnu/packages/readline.scm (rlwrap)[description]: Fix mark-up. --- gnu/packages/readline.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/readline.scm b/gnu/packages/readline.scm index 3cca1aefe7..d8d333e587 100644 --- a/gnu/packages/readline.scm +++ b/gnu/packages/readline.scm @@ -169,6 +169,6 @@ comfortable for anyone.") readline library to allow the editing of keyboard input for any command. You should consider rlwrap especially when you need user-defined completion (by way of completion word lists) and persistent history, or if you want to program -'special effects' using the filter mechanism.") +`special effects' using the filter mechanism.") (home-page "https://github.com/hanslub42/rlwrap") (license gpl2+))) -- cgit 1.4.1 From fc71a45afdb4e7ee45d1c952c56c3b83cafaac1e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 20:24:55 +0200 Subject: gnu: python-cookiecutter: Update to 1.7.3. * gnu/packages/python-xyz.scm (python-cookiecutter): Update to 1.7.3. --- gnu/packages/python-xyz.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d978942402..e4cc0009c5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -12850,14 +12850,13 @@ designed to work across multiple versions of Python.") (define-public python-cookiecutter (package (name "python-cookiecutter") - (version "1.7.2") + (version "1.7.3") (source (origin (method url-fetch) (uri (pypi-uri "cookiecutter" version)) (sha256 - (base32 - "1b2xa5dypk1vf8aq599fd8zw4y0pwvq3hgl7ia8aiv8gg3ab5dpg")))) + (base32 "0mx49whhwcxmvcak27zr7p7ndzkn3w7psfd7fzh3n91fi1r4v6kb")))) (build-system python-build-system) (native-inputs `(("python-freezegun" ,python-freezegun) -- cgit 1.4.1 From 2a600ae5ff92f6164020d0cec51190f28fdc904c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 23:22:15 +0200 Subject: gnu: python-fastjsonschema: Update to 2.15.1. * gnu/packages/python-xyz.scm (python-fastjsonschema): Update to 2.15.1. --- gnu/packages/python-xyz.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e4cc0009c5..b3ed73f04a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10788,14 +10788,13 @@ JSON Reference and JSON Pointer.") (define-public python-fastjsonschema (package (name "python-fastjsonschema") - (version "2.15.0") + (version "2.15.1") (source (origin (method url-fetch) (uri (pypi-uri "fastjsonschema" version)) (sha256 - (base32 - "0xknp399gpdjf08lrq2yvv66s7nsc51fgbm6vph7vyyg1ckbmv71")))) + (base32 "1ln2j60jzyn6p8i8ljygfgrji58hc23452g7nllkcjdk4p93c7v7")))) (build-system python-build-system) (arguments `(#:tests? #f ; Fail with a strange backtrace ending in importlib. -- cgit 1.4.1 From cc142c91cf8bda1eb4de8b26b6ecfd0dbc7c9ee6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 23:36:20 +0200 Subject: gnu: net-snmp: Update to 5.9.1. * gnu/packages/networking.scm (net-snmp): Update to 5.9.1. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index f65c8a7f13..7286e513f7 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -3190,14 +3190,14 @@ Features: (define-public net-snmp (package (name "net-snmp") - (version "5.9") + (version "5.9.1") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/net-snmp/net-snmp/" version "/net-snmp-" version ".tar.gz")) (sha256 (base32 - "0wb0vyafpspw3mcifkjjmf17r1r80kjvslycscb8nvaxz1k3lc04")) + "0gwcyi9qk707jgfsgmdr9w2w3r892fnqaam9v7zxpkg69njd8zzb")) (modules '((guix build utils))) (snippet '(begin -- cgit 1.4.1 From 3573e73840a59e4168cf744b86442b181b30c243 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 23:36:59 +0200 Subject: gnu: net-snmp: Omit static library. * gnu/packages/networking.scm (net-snmp)[arguments]: Add "--disable-static" configure flag. --- gnu/packages/networking.scm | 1 + gnu/packages/python.scm | 4 ++-- gnu/packages/xdisorg.scm | 4 ++-- 3 files changed, 5 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 7286e513f7..945123e600 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -3214,6 +3214,7 @@ Features: (list (string-append "LDFLAGS=-Wl,-rpath=" (assoc-ref %outputs "out") "/lib") + "--disable-static" "--with-logfile=/var/log/snmpd.log" (string-append "--with-openssl=" (assoc-ref %build-inputs "openssl"))) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index ce424bdeb0..e694321e17 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -651,7 +651,7 @@ To function properly, this package should not be installed together with the (define-public micropython (package (name "micropython") - (version "1.14") + (version "1.15") (source (origin (method url-fetch) @@ -659,7 +659,7 @@ To function properly, this package should not be installed together with the "releases/download/v" version "/micropython-" version ".tar.xz")) (sha256 - (base32 "0k6ri3rxxnnmvcbi7z7x59r21f4vj9dcf9j64jhj1cgazmb62c4p")) + (base32 "04sfrfcljhfps340l4wh5ffwkhw1ydraday8nv92nv7gmnrj1l2j")) (modules '((guix build utils))) (snippet '(begin diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index bf4b062973..5573e2afb5 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -1235,7 +1235,7 @@ Escape key when Left Control is pressed and released on its own.") (define-public libwacom (package (name "libwacom") - (version "1.7") + (version "1.10") (source (origin (method url-fetch) (uri (string-append @@ -1243,7 +1243,7 @@ Escape key when Left Control is pressed and released on its own.") "libwacom-" version "/libwacom-" version ".tar.bz2")) (sha256 (base32 - "0797gc055dgg2jfqijy9823bd83jwr4wb2z9id992qlcr0xmz1rw")))) + "14aj4ss1chxxgaprs9sfriia2ch9wj9rqay0ndkzk1m7jx2qrjgn")))) (build-system glib-or-gtk-build-system) (arguments `(#:configure-flags '("--disable-static"))) -- cgit 1.4.1 From 237b744d23254c28123f6bf48b6e5e9e5c33438a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 29 May 2021 23:41:35 +0200 Subject: gnu: python-hupper: Update to 1.10.3. * gnu/packages/python-web.scm (python-hupper): Update to 1.10.3. --- gnu/packages/python-web.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 4468a9b8cd..f20f1c1f55 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -14,7 +14,7 @@ ;;; Copyright © 2015 Cyril Roelandt ;;; Copyright © 2015, 2016, 2017, 2019 Leo Famulari ;;; Copyright © 2016, 2019 Hartmut Goebel -;;; Copyright © 2016, 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice +;;; Copyright © 2016–2021 Tobias Geerinckx-Rice ;;; Copyright © 2015, 2017 Ben Woodcroft ;;; Copyright © 2015, 2016 Christopher Allan Webber ;;; Copyright © 2017 Adriano Peluso @@ -5498,13 +5498,13 @@ according to the standard set by PasteDeploy ") (define-public python-hupper (package (name "python-hupper") - (version "1.10.2") + (version "1.10.3") (source (origin (method url-fetch) (uri (pypi-uri "hupper" version)) (sha256 (base32 - "0am0p6g5cz6xmcaf04xq8q6dzdd9qz0phj6gcmpsckf2mcyza61q")))) + "1nbc648d110jx6ziji980cdmzsd14p8fqrcarsdvr1vm5jvm2vyd")))) (build-system python-build-system) (arguments '(#:test-target "pytest")) (native-inputs -- cgit 1.4.1 From ae303853d447018a98d0ec7663ccde969d87302d Mon Sep 17 00:00:00 2001 From: Rovanion Luckey Date: Fri, 28 May 2021 17:19:56 +0200 Subject: gnu: Add lingot. * gnu/packages/music.scm (lingot): New public variable. Signed-off-by: Tobias Geerinckx-Rice --- gnu/packages/music.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index fb15a6ea84..ed64d70a0b 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -38,6 +38,7 @@ ;;; Copyright © 2021 Brendan Tildesley ;;; Copyright © 2021 Bonface Munyoki Kilyungi ;;; Copyright © 2021 Frank Pursel +;;; Copyright © 2021 Rovanion Luckey ;;; ;;; This file is part of GNU Guix. ;;; @@ -1340,6 +1341,47 @@ Sega Master System/Mark III, Sega Genesis/Mega Drive, BBC Micro ;; demo and player directories are under the Expat license license:expat)))) +(define-public lingot + (package + (name "lingot") + (version "1.1.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ibancg/lingot") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "04lcjzfhddbyskxr2068z609y6x0s2gjx1wl78w0dkxdi459zrn9")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("cunit" ,cunit) + ("glib" ,glib "bin") ; for glib-compile-resources + ("intltool" ,intltool) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (inputs + `(("alsa-lib" ,alsa-lib) + ("fftw" ,fftw) + ("gtk+" ,gtk+) + ("jack" ,jack-2) + ("json-c" ,json-c) + ("pulseaudio" ,pulseaudio))) + (home-page "http://lingot.nongnu.org/") + (synopsis "Accurate & configurable musical instrument tuner") + (description + "LINGOT is a musical instrument tuner. It's accurate, easy to use, and +highly configurable. Originally conceived to tune electric guitars, it can now +be used to tune other instruments. + +It looks like an analogue tuner, with a gauge indicating the relative shift to a +certain note, determined automatically as the closest note to the estimated +frequency.") + (license license:gpl2+))) + (define-public ninjas2 (package (name "ninjas2") -- cgit 1.4.1 From c00b1760f605255719a525e52c268b222a1f5184 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 30 May 2021 11:51:30 +0200 Subject: gnu: vapoursynth: Wrap with own PYTHONPATH. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This fixes, e.g., ‘vspipe -v’ in a pure environment. * gnu/packages/video.scm (vapoursynth)[arguments]: Add a 'wrap phase. Reported by maddo of #guix. --- gnu/packages/video.scm | 12 ++++++++++++ 1 file changed, 12 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 2eef76558a..5975004049 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2817,6 +2817,18 @@ capabilities.") (base32 "1krfdzc2x2vxv4nq9kiv1c09hgj525qn120ah91fw2ikq8ldvmx4")))) (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'install 'wrap + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (site (string-append out "/lib/python" + ,(version-major+minor + (package-version python)) + "/site-packages"))) + (wrap-program (string-append out "/bin/vspipe") + `("PYTHONPATH" ":" = (,site))))))))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) -- cgit 1.4.1 From 0f6902ea79963a2c5d931414103de978a86f9dfd Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 09:46:34 +0300 Subject: gnu: julia-jllwrappers: Move to (gnu packages julia-jll). * gnu/packages/julia-xyz.scm (julia-jlwrappers): Move to ... * gnu/packages/julia-jll.scm: ... here. * gnu/local.mk (GNU_SYSTEM_MODULES): Register julia-jll.scm --- gnu/local.mk | 1 + gnu/packages/julia-jll.scm | 70 ++++++++++++++++++++++++++++++++++++++++++++++ gnu/packages/julia-xyz.scm | 44 +---------------------------- 3 files changed, 72 insertions(+), 43 deletions(-) create mode 100644 gnu/packages/julia-jll.scm (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 0c0a6b924a..a5820b5827 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -308,6 +308,7 @@ GNU_SYSTEM_MODULES = \ %D%/packages/jrnl.scm \ %D%/packages/jose.scm \ %D%/packages/julia.scm \ + %D%/packages/julia-jll.scm \ %D%/packages/julia-xyz.scm \ %D%/packages/jupyter.scm \ %D%/packages/kawa.scm \ diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm new file mode 100644 index 0000000000..1b63c06312 --- /dev/null +++ b/gnu/packages/julia-jll.scm @@ -0,0 +1,70 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2021 Nicolò Balzarotti +;;; Copyright © 2021 Efraim Flashner +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu packages julia-jll) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix git-download) + #:use-module (guix utils) + #:use-module (guix build-system julia) + #:use-module (gnu packages) + #:use-module (gnu packages julia)) + +(define-public julia-jllwrappers + (package + (name "julia-jllwrappers") + (version "1.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaPackaging/JLLWrappers.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0v7xhsv9z16d657yp47vgc86ggc01i1wigqh3n0d7i1s84z7xa0h")))) + (arguments + ;; Wants to download stuff + '(#:tests? #f + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'custom-override-path + (lambda* (#:key inputs #:allow-other-keys) + ;; Make @generate_wrapper_header take an optional argument that + ;; guix packagers can pass to override the default "override" + ;; binary path. This won't be needed when something like + ;; https://github.com/JuliaPackaging/JLLWrappers.jl/pull/27 + ;; will be merged. + (substitute* "src/wrapper_generators.jl" + (("generate_wrapper_header.*") + "generate_wrapper_header(src_name, override_path = nothing)\n") + (("pkg_dir = .*" all) + (string-append + all "\n" "override = something(override_path," + "joinpath(dirname(pkg_dir), \"override\"))\n")) + (("@static if isdir.*") "@static if isdir($override)\n") + (("return joinpath.*") "return $override\n")) + #t))))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaPackaging/JLLWrappers.jl") + (synopsis "Julia macros used by JLL packages") + (description "This package contains Julia macros that enable JLL packages +to generate themselves. It is not intended to be used by users, but rather is +used in autogenerated packages via @code{BinaryBuilder.jl}.") + (license license:expat))) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 551f016929..b8ba5bf93f 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -27,6 +27,7 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) + #:use-module (gnu packages julia-jll) #:use-module (gnu packages maths) #:use-module (gnu packages tls) #:use-module (gnu packages web)) @@ -1077,49 +1078,6 @@ external IRs. It can be used with Julia metaprogramming tools such as Cassette.") (license license:expat))) -(define-public julia-jllwrappers - (package - (name "julia-jllwrappers") - (version "1.3.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/JuliaPackaging/JLLWrappers.jl") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0v7xhsv9z16d657yp47vgc86ggc01i1wigqh3n0d7i1s84z7xa0h")))) - (arguments - ;; Wants to download stuff - '(#:tests? #f - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'custom-override-path - (lambda* (#:key inputs #:allow-other-keys) - ;; Make @generate_wrapper_header take an optional argument that - ;; guix packagers can pass to override the default "override" - ;; binary path. This won't be needed when something like - ;; https://github.com/JuliaPackaging/JLLWrappers.jl/pull/27 - ;; will be merged. - (substitute* "src/wrapper_generators.jl" - (("generate_wrapper_header.*") - "generate_wrapper_header(src_name, override_path = nothing)\n") - (("pkg_dir = .*" all) - (string-append - all "\n" "override = something(override_path," - "joinpath(dirname(pkg_dir), \"override\"))\n")) - (("@static if isdir.*") "@static if isdir($override)\n") - (("return joinpath.*") "return $override\n")) - #t))))) - (build-system julia-build-system) - (home-page "https://github.com/JuliaPackaging/JLLWrappers.jl") - (synopsis "Julia macros used by JLL packages") - (description "This package contains Julia macros that enable JLL packages -to generate themselves. It is not intended to be used by users, but rather is -used in autogenerated packages via @code{BinaryBuilder.jl}.") - (license license:expat))) - (define-public julia-jpegturbo-jll (package (name "julia-jpegturbo-jll") -- cgit 1.4.1 From e5ff6dc3f390c190552c7d3e71aa490dc8c5434b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 09:55:07 +0300 Subject: gnu: julia-compilersupportlibraries-jll: Move to (gnu packages julia-jll). * gnu/packages/julia-xyz.scm (julia-compilersupportlibraries-jll): Move to ... * gnu/packages/julia-jll.scm: ... here. --- gnu/packages/julia-jll.scm | 47 ++++++++++++++++++++++++++++++++++++++++++++++ gnu/packages/julia-xyz.scm | 45 -------------------------------------------- 2 files changed, 47 insertions(+), 45 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 1b63c06312..8b6ef39c43 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2021 Nicolò Balzarotti +;;; Copyright © 2021 Simon Tournier ;;; Copyright © 2021 Efraim Flashner ;;; ;;; This file is part of GNU Guix. @@ -24,8 +25,54 @@ #:use-module (guix utils) #:use-module (guix build-system julia) #:use-module (gnu packages) + #:use-module (gnu packages gcc) #:use-module (gnu packages julia)) +;;; TODO: Remove this autogenerated source package +;;; and build it from realse source using + +(define-public julia-compilersupportlibraries-jll + (package + (name "julia-compilersupportlibraries-jll") + (version "0.4.0+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/CompilerSupportLibraries_jll.jl") + (commit (string-append "CompilerSupportLibraries-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "03j6xdvps259mhdzpjqf41l65w2l9sahvxg4wrp34hcf69wkrzpy")))) + (build-system julia-build-system) + (arguments + `(#:tests? #f ; no runtests.jl + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"CompilerSupportLibraries\", \"" + (assoc-ref inputs "gfortran:lib") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$")) + #t))))) + (inputs ;required by artifacts + `(("gfortran:lib" ,gfortran "lib"))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/CompilerSupportLibraries_jll.jl") + (synopsis "Internal wrappers") + (description "This package provides compiler support for libraries. It is +an autogenerated source package constructed using @code{BinaryBuilder.jl}. The +originating @code{build_tarballs.jl} script can be found on the community +build tree Yggdrasil.") + (license license:expat))) + (define-public julia-jllwrappers (package (name "julia-jllwrappers") diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index b8ba5bf93f..35f7bd8d3f 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -24,7 +24,6 @@ #:use-module (guix git-download) #:use-module (guix build-system julia) #:use-module (gnu packages compression) - #:use-module (gnu packages gcc) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages julia-jll) @@ -405,50 +404,6 @@ provides a macro that lets you use the latest syntax in a backwards-compatible way.") (license license:expat))) -;;; TODO: Remove this autogenerated source package -;;; and build it from realse source using -(define-public julia-compilersupportlibraries-jll - (package - (name "julia-compilersupportlibraries-jll") - (version "0.4.0+1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/JuliaBinaryWrappers/CompilerSupportLibraries_jll.jl") - (commit (string-append "CompilerSupportLibraries-v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "03j6xdvps259mhdzpjqf41l65w2l9sahvxg4wrp34hcf69wkrzpy")))) - (build-system julia-build-system) - (arguments - `(#:tests? #f ; no runtests.jl - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'override-binary-path - (lambda* (#:key inputs #:allow-other-keys) - (map - (lambda (wrapper) - (substitute* wrapper - (("generate_wrapper_header.*") - (string-append - "generate_wrapper_header(\"CompilerSupportLibraries\", \"" - (assoc-ref inputs "gfortran:lib") "\")\n")))) - ;; There's a Julia file for each platform, override them all - (find-files "src/wrappers/" "\\.jl$")) - #t))))) - (inputs ;required by artifacts - `(("gfortran:lib" ,gfortran "lib"))) - (propagated-inputs - `(("julia-jllwrappers" ,julia-jllwrappers))) - (home-page "https://github.com/JuliaBinaryWrappers/CompilerSupportLibraries_jll.jl") - (synopsis "Internal wrappers") - (description "This package provides compiler support for libraries. It is -an autogenerated source package constructed using @code{BinaryBuilder.jl}. The -originating @code{build_tarballs.jl} script can be found on the community -build tree Yggdrasil.") - (license license:expat))) - (define-public julia-constructionbase (package (name "julia-constructionbase") -- cgit 1.4.1 From cc54d4b6e2addd437aea70dd47632191cfb98645 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 10:10:29 +0300 Subject: gnu: julia-gumbo-jll: Move to (gnu packages julia-jll). * gnu/packages/julia-xyz.scm (julia-gumbo-jll): Move to ... * gnu/packages/julia-jll.scm: ... here. --- gnu/packages/julia-jll.scm | 42 +++++++++++++++++++++++++++++++++++++++++- gnu/packages/julia-xyz.scm | 42 +----------------------------------------- 2 files changed, 42 insertions(+), 42 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 8b6ef39c43..062e504034 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -26,7 +26,8 @@ #:use-module (guix build-system julia) #:use-module (gnu packages) #:use-module (gnu packages gcc) - #:use-module (gnu packages julia)) + #:use-module (gnu packages julia) + #:use-module (gnu packages web)) ;;; TODO: Remove this autogenerated source package ;;; and build it from realse source using @@ -73,6 +74,45 @@ originating @code{build_tarballs.jl} script can be found on the community build tree Yggdrasil.") (license license:expat))) +(define-public julia-gumbo-jll + (package + (name "julia-gumbo-jll") + (version "0.10.1+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Gumbo_jll.jl") + (commit (string-append "Gumbo-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "00a182x5hfpjzyvrxdn8wh4h67q899p5dzqp19a5s22si4g41k76")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (let ((gumbo (string-append (assoc-ref inputs "gumbo-parser")))) + (for-each + (lambda (wrapper) + (substitute* wrapper + (("(const libgumbo = )\"(.*)\"" all const libname) + (string-append const "\"" gumbo "/lib/" libname "\"\n")) + (("(global artifact_dir =).*" all m) + (string-append m " \"" gumbo "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$")))))))) + (inputs + `(("gumbo-parser" ,gumbo-parser))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/Gumbo_jll.jl") + (synopsis "Gumbo HTML parsing library wrappers") + (description "This package provides a wrapper for Gumbo HTML parsing library.") + (license license:expat))) + (define-public julia-jllwrappers (package (name "julia-jllwrappers") diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 35f7bd8d3f..49439ae0a2 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -28,8 +28,7 @@ #:use-module (gnu packages imagemagick) #:use-module (gnu packages julia-jll) #:use-module (gnu packages maths) - #:use-module (gnu packages tls) - #:use-module (gnu packages web)) + #:use-module (gnu packages tls)) (define-public julia-abstractffts (package @@ -762,45 +761,6 @@ differentiation (AD).") library for parsing HTML.") (license license:expat))) -(define-public julia-gumbo-jll - (package - (name "julia-gumbo-jll") - (version "0.10.1+1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/JuliaBinaryWrappers/Gumbo_jll.jl") - (commit (string-append "Gumbo-v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "00a182x5hfpjzyvrxdn8wh4h67q899p5dzqp19a5s22si4g41k76")))) - (build-system julia-build-system) - (arguments - '(#:tests? #f ; no runtests - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'override-binary-path - (lambda* (#:key inputs #:allow-other-keys) - (let ((gumbo (string-append (assoc-ref inputs "gumbo-parser")))) - (for-each - (lambda (wrapper) - (substitute* wrapper - (("(const libgumbo = )\"(.*)\"" all const libname) - (string-append const "\"" gumbo "/lib/" libname "\"\n")) - (("(global artifact_dir =).*" all m) - (string-append m " \"" gumbo "\"")))) - ;; There's a Julia file for each platform, override them all - (find-files "src/wrappers/" "\\.jl$")))))))) - (inputs - `(("gumbo-parser" ,gumbo-parser))) - (propagated-inputs - `(("julia-jllwrappers" ,julia-jllwrappers))) - (home-page "https://github.com/JuliaBinaryWrappers/Gumbo_jll.jl") - (synopsis "Gumbo HTML parsing library wrappers") - (description "This package provides a wrapper for Gumbo HTML parsing library.") - (license license:expat))) - (define-public julia-http (package (name "julia-http") -- cgit 1.4.1 From f0e0b9a55ac39da37bd0c75d7df6528118eba8cd Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 10:25:28 +0300 Subject: gnu: julia-jpegturbo-jll: Move to (gnu packages julia-jll). * gnu/packages/julia-xyz.scm (julia-jpegturbo-jll): Move to ... * gnu/packages/julia-jll.scm: ... here. --- gnu/packages/julia-jll.scm | 38 ++++++++++++++++++++++++++++++++++++++ gnu/packages/julia-xyz.scm | 37 ------------------------------------- 2 files changed, 38 insertions(+), 37 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 062e504034..0357ead64b 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -26,6 +26,7 @@ #:use-module (guix build-system julia) #:use-module (gnu packages) #:use-module (gnu packages gcc) + #:use-module (gnu packages image) #:use-module (gnu packages julia) #:use-module (gnu packages web)) @@ -155,3 +156,40 @@ build tree Yggdrasil.") to generate themselves. It is not intended to be used by users, but rather is used in autogenerated packages via @code{BinaryBuilder.jl}.") (license license:expat))) + +(define-public julia-jpegturbo-jll + (package + (name "julia-jpegturbo-jll") + (version "2.0.1+2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/JpegTurbo_jll.jl") + (commit (string-append "JpegTurbo-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1xp1x0hrj337bgwwffwpyq7xg031j2a38fim29lixqa0a0y80x6y")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"JpegTurbo\"") + (string-append "\"" (assoc-ref inputs "libjpeg-turbo") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libjpeg-turbo" ,libjpeg-turbo))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/JpegTurbo_jll.jl") + (synopsis "Libjpeg-turbo library wrappers") + (description "This package provides a wrapper for the libjpeg-turbo library.") + (license license:expat))) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 49439ae0a2..2a49cf5d6a 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -993,43 +993,6 @@ external IRs. It can be used with Julia metaprogramming tools such as Cassette.") (license license:expat))) -(define-public julia-jpegturbo-jll - (package - (name "julia-jpegturbo-jll") - (version "2.0.1+2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/JuliaBinaryWrappers/JpegTurbo_jll.jl") - (commit (string-append "JpegTurbo-v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1xp1x0hrj337bgwwffwpyq7xg031j2a38fim29lixqa0a0y80x6y")))) - (build-system julia-build-system) - (arguments - '(#:tests? #f ; no runtests - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'override-binary-path - (lambda* (#:key inputs #:allow-other-keys) - (map - (lambda (wrapper) - (substitute* wrapper - (("artifact\"JpegTurbo\"") - (string-append "\"" (assoc-ref inputs "libjpeg-turbo") "\"")))) - ;; There's a Julia file for each platform, override them all - (find-files "src/wrappers/" "\\.jl$"))))))) - (inputs - `(("libjpeg-turbo" ,libjpeg-turbo))) - (propagated-inputs - `(("julia-jllwrappers" ,julia-jllwrappers))) - (home-page "https://github.com/JuliaBinaryWrappers/JpegTurbo_jll.jl") - (synopsis "Libjpeg-turbo library wrappers") - (description "This package provides a wrapper for the libjpeg-turbo library.") - (license license:expat))) - (define-public julia-json (package (name "julia-json") -- cgit 1.4.1 From e2496a814f8ac4b62b91e05fc9899b9bb85b3ac4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 10:29:27 +0300 Subject: gnu: julia-mbedtls-jll: Move to (gnu packages julia-jll). * gnu/packages/julia-xyz.scm (julia-mbedtls-jll): Move to ... * gnu/packages/julia-jll.scm: ... here. --- gnu/packages/julia-jll.scm | 41 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/julia-xyz.scm | 43 +------------------------------------------ 2 files changed, 42 insertions(+), 42 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 0357ead64b..77216864d7 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -28,6 +28,7 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages image) #:use-module (gnu packages julia) + #:use-module (gnu packages tls) #:use-module (gnu packages web)) ;;; TODO: Remove this autogenerated source package @@ -193,3 +194,43 @@ used in autogenerated packages via @code{BinaryBuilder.jl}.") (synopsis "Libjpeg-turbo library wrappers") (description "This package provides a wrapper for the libjpeg-turbo library.") (license license:expat))) + +(define-public julia-mbedtls-jll + (package + (name "julia-mbedtls-jll") + ;; version 2.25.0+0 is not compatible with current mbedtls 2.23.0, + ;; upgrade this when mbedtls is updated in guix + (version "2.24.0+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/MbedTLS_jll.jl") + (commit (string-append "MbedTLS-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0kk9dlxdh7yms21npgrdfmjbj8q8ng6kdhrzw3jr2d7rp696kp99")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; No runtests.jl + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"MbedTLS\", \"" + (assoc-ref inputs "mbedtls-apache") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$")) + #t))))) + (inputs `(("mbedtls-apache" ,mbedtls-apache))) + (propagated-inputs `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/MbedTLS_jll.jl") + (synopsis "Apache's mbed TLS binary wrappers") + (description "This Julia module provides @code{mbed TLS} libraries and +wrappers.") + (license license:expat))) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 2a49cf5d6a..397e5e597e 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -27,8 +27,7 @@ #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages julia-jll) - #:use-module (gnu packages maths) - #:use-module (gnu packages tls)) + #:use-module (gnu packages maths)) (define-public julia-abstractffts (package @@ -1147,46 +1146,6 @@ that let you do deep transformations of code.") TLS} and cryptography C library for Julia.") (license license:expat))) -(define-public julia-mbedtls-jll - (package - (name "julia-mbedtls-jll") - ;; version 2.25.0+0 is not compatible with current mbedtls 2.23.0, - ;; upgrade this when mbedtls is updated in guix - (version "2.24.0+1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/JuliaBinaryWrappers/MbedTLS_jll.jl") - (commit (string-append "MbedTLS-v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0kk9dlxdh7yms21npgrdfmjbj8q8ng6kdhrzw3jr2d7rp696kp99")))) - (build-system julia-build-system) - (arguments - '(#:tests? #f ; No runtests.jl - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'override-binary-path - (lambda* (#:key inputs #:allow-other-keys) - (map - (lambda (wrapper) - (substitute* wrapper - (("generate_wrapper_header.*") - (string-append - "generate_wrapper_header(\"MbedTLS\", \"" - (assoc-ref inputs "mbedtls-apache") "\")\n")))) - ;; There's a Julia file for each platform, override them all - (find-files "src/wrappers/" "\\.jl$")) - #t))))) - (inputs `(("mbedtls-apache" ,mbedtls-apache))) - (propagated-inputs `(("julia-jllwrappers" ,julia-jllwrappers))) - (home-page "https://github.com/JuliaBinaryWrappers/MbedTLS_jll.jl") - (synopsis "Apache's mbed TLS binary wrappers") - (description "This Julia module provides @code{mbed TLS} libraries and -wrappers.") - (license license:expat))) - (define-public julia-msgpack (package (name "julia-msgpack") -- cgit 1.4.1 From 0083404175a8da57ab165d4517ad743990b27edc Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 10:32:47 +0300 Subject: gnu: julia-openspecfun-jll: Move to (gnu packages julia-jll). * gnu/packages/julia-xyz.scm (julia-openspecfun-jll): Move to ... * gnu/packages/julia-jll.scm: ... here. --- gnu/packages/julia-jll.scm | 45 ++++++++++++++++++++++++++++++++++++++++++ gnu/packages/julia-xyz.scm | 49 +--------------------------------------------- 2 files changed, 46 insertions(+), 48 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 77216864d7..a403829ff2 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -28,6 +28,7 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages image) #:use-module (gnu packages julia) + #:use-module (gnu packages maths) #:use-module (gnu packages tls) #:use-module (gnu packages web)) @@ -234,3 +235,47 @@ used in autogenerated packages via @code{BinaryBuilder.jl}.") (description "This Julia module provides @code{mbed TLS} libraries and wrappers.") (license license:expat))) + +(define-public julia-openspecfun-jll + (let ((commit "6c505cce3bdcd9cd2b15b4f9362ec3a42c4da71c")) + (package + (name "julia-openspecfun-jll") + (version "0.5.3+4") ;tag not created upstream + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/OpenSpecFun_jll.jl") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0bl2gcgndsbiwhwy8fl070cjm1fyf9kxj6gkikgirmzgjl29iakn")))) + (build-system julia-build-system) + (arguments + `(#:tests? #f ; no runtests.jl + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"OpenSpecFun\", \"" + (assoc-ref inputs "openspecfun") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$")) + #t))))) + (inputs + `(("openspecfun" ,openspecfun))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-compilersupportlibraries-jll" ,julia-compilersupportlibraries-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/OpenSpecFun_jll.jl") + (synopsis "Internal wrappers") + (description "This package provides a wrapper for OpenSpecFun. It is an +autogenerated source package constructed using @code{BinaryBuilder.jl}. The +originating @code{build_tarballs.jl} script can be found on the community +build tree Yggdrasil.") + (license license:expat)))) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 397e5e597e..86cb2933f7 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -26,8 +26,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) - #:use-module (gnu packages julia-jll) - #:use-module (gnu packages maths)) + #:use-module (gnu packages julia-jll)) (define-public julia-abstractffts (package @@ -1233,52 +1232,6 @@ have arbitrary indices, similar to those found in some other programming languages like Fortran.") (license license:expat))) -;;; TODO: Remove this autogenerated source package -;;; and build it from realse source using -(define-public julia-openspecfun-jll -(let ((commit "6c505cce3bdcd9cd2b15b4f9362ec3a42c4da71c")) - (package - (name "julia-openspecfun-jll") - (version "0.5.3+4") ;tag not created upstream - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/JuliaBinaryWrappers/OpenSpecFun_jll.jl") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0bl2gcgndsbiwhwy8fl070cjm1fyf9kxj6gkikgirmzgjl29iakn")))) - (build-system julia-build-system) - (arguments - `(#:tests? #f ; no runtests.jl - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'override-binary-path - (lambda* (#:key inputs #:allow-other-keys) - (map - (lambda (wrapper) - (substitute* wrapper - (("generate_wrapper_header.*") - (string-append - "generate_wrapper_header(\"OpenSpecFun\", \"" - (assoc-ref inputs "openspecfun") "\")\n")))) - ;; There's a Julia file for each platform, override them all - (find-files "src/wrappers/" "\\.jl$")) - #t))))) - (inputs - `(("openspecfun" ,openspecfun))) - (propagated-inputs - `(("julia-jllwrappers" ,julia-jllwrappers) - ("julia-compilersupportlibraries-jll" ,julia-compilersupportlibraries-jll))) - (home-page "https://github.com/JuliaBinaryWrappers/OpenSpecFun_jll.jl") - (synopsis "Internal wrappers") - (description "This package provides a wrapper for OpenSpecFun. It is an -autogenerated source package constructed using @code{BinaryBuilder.jl}. The -originating @code{build_tarballs.jl} script can be found on the community -build tree Yggdrasil.") - (license license:expat)))) - (define-public julia-parameters (package (name "julia-parameters") -- cgit 1.4.1 From fda20c75216c8459165107460b8ed6cc7cb5f292 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 10:35:31 +0300 Subject: gnu: julia-zlib-jll: Move to (gnu packages julia-jll). * gnu/packages/julia-xyz.scm (julia-zlib-jll): Move to ... * gnu/packages/julia-jll.scm: ... here. --- gnu/packages/julia-jll.scm | 39 +++++++++++++++++++++++++++++++++++++++ gnu/packages/julia-xyz.scm | 39 --------------------------------------- 2 files changed, 39 insertions(+), 39 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index a403829ff2..9d6d692f8a 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -25,6 +25,7 @@ #:use-module (guix utils) #:use-module (guix build-system julia) #:use-module (gnu packages) + #:use-module (gnu packages compression) #:use-module (gnu packages gcc) #:use-module (gnu packages image) #:use-module (gnu packages julia) @@ -279,3 +280,41 @@ autogenerated source package constructed using @code{BinaryBuilder.jl}. The originating @code{build_tarballs.jl} script can be found on the community build tree Yggdrasil.") (license license:expat)))) + +(define-public julia-zlib-jll + (package + (name "julia-zlib-jll") + (version "1.2.12+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Zlib_jll.jl") + (commit (string-append "Zlib-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "05ih0haqapkzr40swvq63cafnqlc4yp6yfa1wvdyq8v3n4kxhfqa")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Zlib\", \"" + (assoc-ref inputs "zlib") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/Zlib_jll.jl") + (synopsis "Zlib library wrappers") + (description "This package provides a wrapper for Zlib.") + (license license:expat))) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 86cb2933f7..3eabf7a5ad 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1772,45 +1772,6 @@ useful in order to support @code{VersionNumber} comparisons applied to archives in Julia.") (license license:expat))) -(define-public julia-zlib-jll - (package - (name "julia-zlib-jll") - (version "1.2.12+1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/JuliaBinaryWrappers/Zlib_jll.jl") - (commit (string-append "Zlib-v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "05ih0haqapkzr40swvq63cafnqlc4yp6yfa1wvdyq8v3n4kxhfqa")))) - (build-system julia-build-system) - (arguments - '(#:tests? #f ; no runtests - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'override-binary-path - (lambda* (#:key inputs #:allow-other-keys) - (map - (lambda (wrapper) - (substitute* wrapper - (("generate_wrapper_header.*") - (string-append - "generate_wrapper_header(\"Zlib\", \"" - (assoc-ref inputs "zlib") "\")\n")))) - ;; There's a Julia file for each platform, override them all - (find-files "src/wrappers/" "\\.jl$"))))))) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("julia-jllwrappers" ,julia-jllwrappers))) - (home-page "https://github.com/JuliaBinaryWrappers/Zlib_jll.jl") - (synopsis "Zlib library wrappers") - (description "This package provides a wrapper for Zlib.") - (license license:expat))) - (define-public julia-zstd-jll (package (name "julia-zstd-jll") -- cgit 1.4.1 From 4a1d456a99948b75be078146b44b6e89880b9bc4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 10:36:55 +0300 Subject: gnu: julia-zstd-jll: Move to (gnu packages julia-jll). * gnu/packages/julia-xyz.scm (julia-zstd-jll): Move to ... * gnu/packages/julia-jll.scm: ... here. --- gnu/packages/julia-jll.scm | 38 ++++++++++++++++++++++++++++++++++++++ gnu/packages/julia-xyz.scm | 40 ---------------------------------------- 2 files changed, 38 insertions(+), 40 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 9d6d692f8a..15a1808df2 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -318,3 +318,41 @@ build tree Yggdrasil.") (synopsis "Zlib library wrappers") (description "This package provides a wrapper for Zlib.") (license license:expat))) + +(define-public julia-zstd-jll + (package + (name "julia-zstd-jll") + (version "1.5.0+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Zstd_jll.jl") + (commit (string-append "Zstd-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "15g5wsvga4p9bjmx97xqwqdnfzfbwfl6c4a9iaphcncwgcrnw6y6")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Zstd\", \"" + (assoc-ref inputs "zstd:lib") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("zstd:lib" ,zstd "lib"))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/Zstd_jll.jl") + (synopsis "Zstd library wrappers") + (description "This package provides a wrapper for the zstd library.") + (license license:expat))) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 3eabf7a5ad..3b73b4352b 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -23,7 +23,6 @@ #:use-module (guix packages) #:use-module (guix git-download) #:use-module (guix build-system julia) - #:use-module (gnu packages compression) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages julia-jll)) @@ -1772,45 +1771,6 @@ useful in order to support @code{VersionNumber} comparisons applied to archives in Julia.") (license license:expat))) -(define-public julia-zstd-jll - (package - (name "julia-zstd-jll") - (version "1.5.0+0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/JuliaBinaryWrappers/Zstd_jll.jl") - (commit (string-append "Zstd-v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "15g5wsvga4p9bjmx97xqwqdnfzfbwfl6c4a9iaphcncwgcrnw6y6")))) - (build-system julia-build-system) - (arguments - '(#:tests? #f ; no runtests - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'override-binary-path - (lambda* (#:key inputs #:allow-other-keys) - (map - (lambda (wrapper) - (substitute* wrapper - (("generate_wrapper_header.*") - (string-append - "generate_wrapper_header(\"Zstd\", \"" - (assoc-ref inputs "zstd:lib") "\")\n")))) - ;; There's a Julia file for each platform, override them all - (find-files "src/wrappers/" "\\.jl$"))))))) - (inputs - `(("zstd:lib" ,zstd "lib"))) - (propagated-inputs - `(("julia-jllwrappers" ,julia-jllwrappers))) - (home-page "https://github.com/JuliaBinaryWrappers/Zstd_jll.jl") - (synopsis "Zstd library wrappers") - (description "This package provides a wrapper for the zstd library.") - (license license:expat))) - (define-public julia-zygoterules (package (name "julia-zygoterules") -- cgit 1.4.1 From 8ca2dc09b7cf06e12bb43e41ac9dc852f495c1b4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 10:39:07 +0300 Subject: gnu: julia-libpng-jll: Move to (gnu packages julia-jll). * gnu/packages/julia-xyz.scm (julia-libpng-jll): Move to ... * gnu/packages/julia-jll.scm: ... here. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ gnu/packages/julia-xyz.scm | 38 -------------------------------------- 2 files changed, 37 insertions(+), 38 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 15a1808df2..c5fbf930ce 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -197,6 +197,43 @@ used in autogenerated packages via @code{BinaryBuilder.jl}.") (description "This package provides a wrapper for the libjpeg-turbo library.") (license license:expat))) +(define-public julia-libpng-jll + (package + (name "julia-libpng-jll") + (version "1.6.37+5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/LibPNG_jll.jl") + (commit (string-append "libpng-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "10azxv26j8r193dg9i9x7ajm3frhwbhj8zzi40fj59fxm81xz6dx")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"libpng\"") + (string-append "\"" (assoc-ref inputs "libpng") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libpng" ,libpng))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-zlib-jll" ,julia-zlib-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/LibPNG_jll.jl") + (synopsis "Libpng library wrappers") + (description "This package provides a wrapper for the libpng library.") + (license license:expat))) + (define-public julia-mbedtls-jll (package (name "julia-mbedtls-jll") diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 3b73b4352b..659b490425 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1015,44 +1015,6 @@ Cassette.") and printing JSON documents.") (license license:expat))) -(define-public julia-libpng-jll - (package - (name "julia-libpng-jll") - (version "1.6.37+5") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/JuliaBinaryWrappers/LibPNG_jll.jl") - (commit (string-append "libpng-v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "10azxv26j8r193dg9i9x7ajm3frhwbhj8zzi40fj59fxm81xz6dx")))) - (build-system julia-build-system) - (arguments - '(#:tests? #f ; no runtests - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'override-binary-path - (lambda* (#:key inputs #:allow-other-keys) - (map - (lambda (wrapper) - (substitute* wrapper - (("artifact\"libpng\"") - (string-append "\"" (assoc-ref inputs "libpng") "\"")))) - ;; There's a Julia file for each platform, override them all - (find-files "src/wrappers/" "\\.jl$"))))))) - (inputs - `(("libpng" ,libpng))) - (propagated-inputs - `(("julia-jllwrappers" ,julia-jllwrappers) - ("julia-zlib-jll" ,julia-zlib-jll))) - (home-page "https://github.com/JuliaBinaryWrappers/LibPNG_jll.jl") - (synopsis "Libpng library wrappers") - (description "This package provides a wrapper for the libpng library.") - (license license:expat))) - (define-public julia-libtiff-jll (package (name "julia-libtiff-jll") -- cgit 1.4.1 From da12e8f7c79aa3821678721c168965325bd83c5b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 10:40:52 +0300 Subject: gnu: julia-libtiff-jll: Move to (gnu packages julia-jll). * gnu/packages/julia-xyz.scm (julia-libtiff-jll): Move to ... * gnu/packages/julia-jll.scm: ... here. --- gnu/packages/julia-jll.scm | 39 +++++++++++++++++++++++++++++++++++++++ gnu/packages/julia-xyz.scm | 41 ----------------------------------------- 2 files changed, 39 insertions(+), 41 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index c5fbf930ce..e8d382afea 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -234,6 +234,45 @@ used in autogenerated packages via @code{BinaryBuilder.jl}.") (description "This package provides a wrapper for the libpng library.") (license license:expat))) +(define-public julia-libtiff-jll + (package + (name "julia-libtiff-jll") + (version "4.1.0+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Libtiff_jll.jl") + (commit (string-append "Libtiff-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "07zzhmwmh2g4645ghv76z40hza2ghlb7sw15b1pii7f9kfcsgf45")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Libtiff\"") + (string-append "\"" (assoc-ref inputs "libtiff") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libtiff" ,libtiff))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-jpegturbo-jll" ,julia-jpegturbo-jll) + ("julia-zlib-jll" ,julia-zlib-jll) + ("julia-zstd-jll" ,julia-zstd-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Libtiff_jll.jl") + (synopsis "Libtiff library wrappers") + (description "This package provides a wrapper for libtiff") + (license license:expat))) + (define-public julia-mbedtls-jll (package (name "julia-mbedtls-jll") diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 659b490425..2fe172b6d3 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -23,7 +23,6 @@ #:use-module (guix packages) #:use-module (guix git-download) #:use-module (guix build-system julia) - #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages julia-jll)) @@ -1015,46 +1014,6 @@ Cassette.") and printing JSON documents.") (license license:expat))) -(define-public julia-libtiff-jll - (package - (name "julia-libtiff-jll") - (version "4.1.0+1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/JuliaBinaryWrappers/Libtiff_jll.jl") - (commit (string-append "Libtiff-v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "07zzhmwmh2g4645ghv76z40hza2ghlb7sw15b1pii7f9kfcsgf45")))) - (build-system julia-build-system) - (arguments - '(#:tests? #f ; no runtests - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'override-binary-path - (lambda* (#:key inputs #:allow-other-keys) - (map - (lambda (wrapper) - (substitute* wrapper - (("artifact\"Libtiff\"") - (string-append "\"" (assoc-ref inputs "libtiff") "\"")))) - ;; There's a Julia file for each platform, override them all - (find-files "src/wrappers/" "\\.jl$"))))))) - (inputs - `(("libtiff" ,libtiff))) - (propagated-inputs - `(("julia-jllwrappers" ,julia-jllwrappers) - ("julia-jpegturbo-jll" ,julia-jpegturbo-jll) - ("julia-zlib-jll" ,julia-zlib-jll) - ("julia-zstd-jll" ,julia-zstd-jll))) - (home-page "https://github.com/JuliaBinaryWrappers/Libtiff_jll.jl") - (synopsis "Libtiff library wrappers") - (description "This package provides a wrapper for libtiff") - (license license:expat))) - (define-public julia-macrotools (package (name "julia-macrotools") -- cgit 1.4.1 From 191c345d3ea78beae0b4a2ad4e26cd2f51222cb4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 10:42:24 +0300 Subject: gnu: julia-imagemagick-jll: Move to (gnu packages julia-jll). * gnu/packages/julia-xyz.scm (julia-imagemagick-jll): Move to ... * gnu/packages/julia-jll.scm: ... here. --- gnu/packages/julia-jll.scm | 44 ++++++++++++++++++++++++++++++++++++++++++++ gnu/packages/julia-xyz.scm | 44 -------------------------------------------- 2 files changed, 44 insertions(+), 44 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index e8d382afea..7fcc11957a 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -28,6 +28,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages gcc) #:use-module (gnu packages image) + #:use-module (gnu packages imagemagick) #:use-module (gnu packages julia) #:use-module (gnu packages maths) #:use-module (gnu packages tls) @@ -117,6 +118,49 @@ build tree Yggdrasil.") (description "This package provides a wrapper for Gumbo HTML parsing library.") (license license:expat))) +(define-public julia-imagemagick-jll + (package + (name "julia-imagemagick-jll") + (version "6.9.10-12+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/ImageMagick_jll.jl") + (commit (string-append "ImageMagick-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1a0vnnjl52yqi7jgpr0dmx5ah5nlpylv5hc8aw2l89b9f36ff8jg")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + ;; Make sure we match the current library. + (("libMagickWand-6.Q16.so.6") "libMagickWand-6.Q16.so.7") + (("artifact\"ImageMagick\"") + (string-append "\"" (assoc-ref inputs "imagemagick") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-jpegturbo-jll" ,julia-jpegturbo-jll) + ("julia-libpng-jll" ,julia-libpng-jll) + ("julia-libtiff-jll" ,julia-libtiff-jll) + ("julia-zlib-jll" ,julia-zlib-jll))) + (inputs + `(("imagemagick" ,imagemagick))) + (home-page "https://github.com/JuliaBinaryWrappers/ImageMagick_jll.jl") + (synopsis "Imagemagick library wrappers") + (description "This package provides a wrapper for Imagemagick.") + (license license:expat))) + (define-public julia-jllwrappers (package (name "julia-jllwrappers") diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 2fe172b6d3..ff207456c3 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -23,7 +23,6 @@ #:use-module (guix packages) #:use-module (guix git-download) #:use-module (guix build-system julia) - #:use-module (gnu packages imagemagick) #:use-module (gnu packages julia-jll)) (define-public julia-abstractffts @@ -835,49 +834,6 @@ implementing both a client and a server.") conditional ifelse. It is similar to @code{Core.ifelse} but it is extendable.") (license license:expat))) -(define-public julia-imagemagick-jll - (package - (name "julia-imagemagick-jll") - (version "6.9.10-12+3") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/JuliaBinaryWrappers/ImageMagick_jll.jl") - (commit (string-append "ImageMagick-v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1a0vnnjl52yqi7jgpr0dmx5ah5nlpylv5hc8aw2l89b9f36ff8jg")))) - (build-system julia-build-system) - (arguments - '(#:tests? #f ; no runtests - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'override-binary-path - (lambda* (#:key inputs #:allow-other-keys) - (map - (lambda (wrapper) - (substitute* wrapper - ;; Make sure we match the current library. - (("libMagickWand-6.Q16.so.6") "libMagickWand-6.Q16.so.7") - (("artifact\"ImageMagick\"") - (string-append "\"" (assoc-ref inputs "imagemagick") "\"")))) - ;; There's a Julia file for each platform, override them all - (find-files "src/wrappers/" "\\.jl$"))))))) - (propagated-inputs - `(("julia-jllwrappers" ,julia-jllwrappers) - ("julia-jpegturbo-jll" ,julia-jpegturbo-jll) - ("julia-libpng-jll" ,julia-libpng-jll) - ("julia-libtiff-jll" ,julia-libtiff-jll) - ("julia-zlib-jll" ,julia-zlib-jll))) - (inputs - `(("imagemagick" ,imagemagick))) - (home-page "https://github.com/JuliaBinaryWrappers/ImageMagick_jll.jl") - (synopsis "Imagemagick library wrappers") - (description "This package provides a wrapper for Imagemagick.") - (license license:expat))) - (define-public julia-indexing (package (name "julia-indexing") -- cgit 1.4.1 From 4073aeae4635019f5d792338ef9fd3c8fe37b29b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 10:44:29 +0300 Subject: gnu: Add julia-x264-jll. * gnu/packages/julia-jll.scm (julia-x264-jll): New variable. --- gnu/packages/julia-jll.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 7fcc11957a..319b8fd882 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -32,6 +32,7 @@ #:use-module (gnu packages julia) #:use-module (gnu packages maths) #:use-module (gnu packages tls) + #:use-module (gnu packages video) #:use-module (gnu packages web)) ;;; TODO: Remove this autogenerated source package @@ -401,6 +402,47 @@ originating @code{build_tarballs.jl} script can be found on the community build tree Yggdrasil.") (license license:expat)))) +(define-public julia-x264-jll + (package + (name "julia-x264-jll") + (version "2020.7.14+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/x264_jll.jl") + (commit (string-append "x264-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "131srmmcwhp9f2x4dq3dw4pzv2z0428mdrb923yzzlm7a89nf28p")))) + (build-system julia-build-system) + (arguments + `(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (let ((libx264 (assoc-ref inputs "libx264"))) + (map + (lambda (wrapper) + (substitute* wrapper + ;; Make sure we match the current library. + (("libx264.so.157") + (string-append "libx264.so." + ,(version-major (package-version libx264)))) + (("artifact\"x264\"") + (string-append "\"" libx264 "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$")))))))) + (inputs + `(("libx264" ,libx264))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/x264_jll.jl") + (synopsis "x264 library wrappers") + (description "This package provides a wrapper for the x264 video library.") + (license license:expat))) + (define-public julia-zlib-jll (package (name "julia-zlib-jll") -- cgit 1.4.1 From 76cdb2b821ba6bcce36a0c712bf8c90f84f08dd0 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 10:48:06 +0300 Subject: gnu: Add julia-bzip2-jll. * gnu/packages/julia-jll.scm (julia-bzip2-jll): New variable. --- gnu/packages/julia-jll.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 319b8fd882..05f5d2a811 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -38,6 +38,46 @@ ;;; TODO: Remove this autogenerated source package ;;; and build it from realse source using +(define-public julia-bzip2-jll + (package + (name "julia-bzip2-jll") + (version "1.0.7+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Bzip2_jll.jl") + (commit (string-append "Bzip2-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "188ngx4axdqr55ahv2xssl3cf699l1sxi41j336m9sw8plf4hhk8")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; No runtests.jl + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Bzip2\", \"" + (assoc-ref inputs "bzip2") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$")) + #t))))) + (inputs + `(("bzip2" ,bzip2))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/Bzip2_jll.jl") + (synopsis "Bzip2 binary wrappers") + (description "This Julia module provides a wrapper for the @code{Bzip2} +compression program.") + (license license:expat))) + (define-public julia-compilersupportlibraries-jll (package (name "julia-compilersupportlibraries-jll") -- cgit 1.4.1 From a1b7d59ca61f687804bc5958e1fa08fda27d43c5 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 10:50:21 +0300 Subject: gnu: Add julia-fribidi-jll. * gnu/packages/julia-jll.scm (julia-fribidi-jll): New variable. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 05f5d2a811..fc3e5ab723 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -26,6 +26,7 @@ #:use-module (guix build-system julia) #:use-module (gnu packages) #:use-module (gnu packages compression) + #:use-module (gnu packages fribidi) #:use-module (gnu packages gcc) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) @@ -120,6 +121,42 @@ originating @code{build_tarballs.jl} script can be found on the community build tree Yggdrasil.") (license license:expat))) +(define-public julia-fribidi-jll + (package + (name "julia-fribidi-jll") + (version "1.0.5+5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/FriBidi_jll.jl") + (commit (string-append "FriBidi-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1nmaqhsnm51hyvnbr9riqfp3f636xyxn2ybych598xpkhhjqldwh")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"FriBidi\"") + (string-append "\"" (assoc-ref inputs "fribidi") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("fribidi" ,fribidi))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/FriBidi_jll.jl") + (synopsis "Fribidi library wrappers") + (description "This package provides a wrapper for the fribidi library.") + (license license:expat))) + (define-public julia-gumbo-jll (package (name "julia-gumbo-jll") -- cgit 1.4.1 From 741aab4c424732d2c052d873a660f94c676e9f92 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 10:53:06 +0300 Subject: gnu: Add julia-freetype2-jll. * gnu/packages/julia-jll.scm (julia-freetype2-jll): New variable. --- gnu/packages/julia-jll.scm | 43 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index fc3e5ab723..26df3eec79 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -26,6 +26,7 @@ #:use-module (guix build-system julia) #:use-module (gnu packages) #:use-module (gnu packages compression) + #:use-module (gnu packages fontutils) #:use-module (gnu packages fribidi) #:use-module (gnu packages gcc) #:use-module (gnu packages image) @@ -121,6 +122,48 @@ originating @code{build_tarballs.jl} script can be found on the community build tree Yggdrasil.") (license license:expat))) +(define-public julia-freetype2-jll + (package + (name "julia-freetype2-jll") + (version "2.10.4+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/FreeType2_jll.jl") + (commit (string-append "FreeType2-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "03lgmb59lipc3bi7z22j4a53bbjmcwkf0xzpwan889p1ix3ry1lr")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; No runtests.jl + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"FreeType2\", \"" + (assoc-ref inputs "freetype") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$")) + #t))))) + (inputs + `(("freetype" ,freetype))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-bzip2-jll" ,julia-bzip2-jll) + ("julia-zlib-jll" ,julia-zlib-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/FreeType2_jll.jl") + (synopsis "Freetype2 binary wrappers") + (description "This Julia module provides a wrapper for the freetype font +rendering library.") + (license license:expat))) + (define-public julia-fribidi-jll (package (name "julia-fribidi-jll") -- cgit 1.4.1 From 6e07d698d2e395bdb085ccc3806739854c235946 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 10:56:05 +0300 Subject: gnu: Add julia-libfdk-aac-jll. * gnu/packages/julia-jll.scm (julia-libfdk-aac-jll): New variable. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 26df3eec79..2fbad4f138 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -25,6 +25,7 @@ #:use-module (guix utils) #:use-module (guix build-system julia) #:use-module (gnu packages) + #:use-module (gnu packages audio) #:use-module (gnu packages compression) #:use-module (gnu packages fontutils) #:use-module (gnu packages fribidi) @@ -362,6 +363,42 @@ used in autogenerated packages via @code{BinaryBuilder.jl}.") (description "This package provides a wrapper for the libjpeg-turbo library.") (license license:expat))) +(define-public julia-libfdk-aac-jll + (package + (name "julia-libfdk-aac-jll") + (version "0.1.6+2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/libfdk_aac_jll.jl") + (commit (string-append "libfdk_aac-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0jinb205dn1yfvl0mx7dsah4xj3r8vc3ig8yl72langjc7vrwdn0")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"libfdk_aac\"") + (string-append "\"" (assoc-ref inputs "libfdk") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libfdk" ,libfdk))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/libfdk_aac_jll.jl") + (synopsis "FDK library wrappers") + (description "This package provides a wrapper for the libfdk audio library.") + (license license:expat))) + (define-public julia-libpng-jll (package (name "julia-libpng-jll") -- cgit 1.4.1 From d3f8731b63bca5fc39ef9973d7b928fae1977e9b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 10:57:56 +0300 Subject: gnu: Add julia-lame-jll. * gnu/packages/julia-jll.scm (julia-lame-jll): New variable. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 2fbad4f138..ec3253cb14 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -34,6 +34,7 @@ #:use-module (gnu packages imagemagick) #:use-module (gnu packages julia) #:use-module (gnu packages maths) + #:use-module (gnu packages mp3) #:use-module (gnu packages tls) #:use-module (gnu packages video) #:use-module (gnu packages web)) @@ -363,6 +364,42 @@ used in autogenerated packages via @code{BinaryBuilder.jl}.") (description "This package provides a wrapper for the libjpeg-turbo library.") (license license:expat))) +(define-public julia-lame-jll + (package + (name "julia-lame-jll") + (version "3.100.0+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/LAME_jll.jl") + (commit (string-append "LAME-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1ck14hwrapcn5wiazf4m2brkqmlpiqpyr0468p467418av837y1c")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"LAME\"") + (string-append "\"" (assoc-ref inputs "lame") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("lame" ,lame))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/LAME_jll.jl") + (synopsis "Lame library wrappers") + (description "This package provides a wrapper for the lame audio encoder.") + (license license:expat))) + (define-public julia-libfdk-aac-jll (package (name "julia-libfdk-aac-jll") -- cgit 1.4.1 From 75ea06d8db27fb58fcf7a673af367b8805598d52 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 11:00:20 +0300 Subject: gnu: Add julia-ogg-jll. * gnu/packages/julia-jll.scm (julia-ogg-jll): New variable. --- gnu/packages/julia-jll.scm | 39 ++++++++++++++++++++++++++++++++++++++- 1 file changed, 38 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index ec3253cb14..1cf9b7deff 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -37,7 +37,8 @@ #:use-module (gnu packages mp3) #:use-module (gnu packages tls) #:use-module (gnu packages video) - #:use-module (gnu packages web)) + #:use-module (gnu packages web) + #:use-module (gnu packages xiph)) ;;; TODO: Remove this autogenerated source package ;;; and build it from realse source using @@ -552,6 +553,42 @@ used in autogenerated packages via @code{BinaryBuilder.jl}.") wrappers.") (license license:expat))) +(define-public julia-ogg-jll + (package + (name "julia-ogg-jll") + (version "1.3.4+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Ogg_jll.jl") + (commit (string-append "Ogg-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0p27wgy48gfw8g0hzlvcxrp0346nqnyxa88pydm87ll3sfx9b4ww")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Ogg\"") + (string-append "\"" (assoc-ref inputs "libogg") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libogg" ,libogg))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/Ogg_jll.jl") + (synopsis "Libogg library wrappers") + (description "This package provides a wrapper for the libogg library.") + (license license:expat))) + (define-public julia-openspecfun-jll (let ((commit "6c505cce3bdcd9cd2b15b4f9362ec3a42c4da71c")) (package -- cgit 1.4.1 From 92e817ea15c08654f8961d75fbd879266c3c9dad Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 11:02:30 +0300 Subject: gnu: Add julia-libvorbis-jll. * gnu/packages/julia-jll.scm (julia-libvorbis-jll): New variable. --- gnu/packages/julia-jll.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 1cf9b7deff..9e542fbf47 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -513,6 +513,44 @@ used in autogenerated packages via @code{BinaryBuilder.jl}.") (description "This package provides a wrapper for libtiff") (license license:expat))) +(define-public julia-libvorbis-jll + (package + (name "julia-libvorbis-jll") + (version "1.3.6+4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/libvorbis_jll.jl") + (commit (string-append "libvorbis-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1zmwhpjy6gr865psjn600g6ickskp4sq34qf1qg8ji6x4v09pzrh")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"libvorbis\"") + (string-append "\"" (assoc-ref inputs "libvorbis") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libvorbis" ,libvorbis))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-ogg-jll" ,julia-ogg-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/libvorbis_jll.jl") + (synopsis "Libvorbis library wrappers") + (description + "This package provides a wrapper for the libvorbis audio library.") + (license license:expat))) + (define-public julia-mbedtls-jll (package (name "julia-mbedtls-jll") -- cgit 1.4.1 From 5cd1372745bb993654ca089cf0f75185de0eb2ec Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 11:09:27 +0300 Subject: gnu: Add julia-x265-jll. * gnu/packages/julia-jll.scm (julia-x265-jll): New variable. --- gnu/packages/julia-jll.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 9e542fbf47..40d1d2bfb6 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -712,6 +712,42 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the x264 video library.") (license license:expat))) +(define-public julia-x265-jll + (package + (name "julia-x265-jll") + (version "3.0.0+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/x265_jll.jl") + (commit (string-append "x265-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "082jgjlc2zm9rzg8p7l9nd4hlg17ziwp2b8rrcpicpb6fxb7sjh4")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"x265\"") + (string-append "\"" (assoc-ref inputs "x265") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("x265" ,x265))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/x265_jll.jl") + (synopsis "x265 library wrappers") + (description "This package provides a wrapper for the x265 video library.") + (license license:expat))) + (define-public julia-zlib-jll (package (name "julia-zlib-jll") -- cgit 1.4.1 From a18d0aac7ae02cff87aeda0ea0db24c854084910 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 11:15:23 +0300 Subject: gnu: Add julia-openssl-jll. * gnu/packages/julia-jll.scm (julia-openssl-jll): New variable. --- gnu/packages/julia-jll.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 40d1d2bfb6..acdfb926c7 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -671,6 +671,42 @@ originating @code{build_tarballs.jl} script can be found on the community build tree Yggdrasil.") (license license:expat)))) +(define-public julia-openssl-jll + (package + (name "julia-openssl-jll") + (version "1.1.1+2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/OpenSSL_jll.jl") + (commit (string-append "OpenSSL-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0qly9pjhah95jdgvckkj615yfbsavvsygpfq9sqz4716q4zv0d5z")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"OpenSSL\"") + (string-append "\"" (assoc-ref inputs "openssl") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("openssl" ,openssl))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/OpenSSL_jll.jl") + (synopsis "Openssl library wrappers") + (description "This package provides a wrapper for the openssl library.") + (license license:expat))) + (define-public julia-x264-jll (package (name "julia-x264-jll") -- cgit 1.4.1 From afff06e4cee2c4a40ddf8d3c072643b359e600d7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 11:16:23 +0300 Subject: gnu: Add julia-opus-jll. * gnu/packages/julia-jll.scm (julia-opus-jll): New variable. --- gnu/packages/julia-jll.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index acdfb926c7..904597a506 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -707,6 +707,42 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the openssl library.") (license license:expat))) +(define-public julia-opus-jll + (package + (name "julia-opus-jll") + (version "1.3.1+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Opus_jll.jl") + (commit (string-append "Opus-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1zm0rnr3pi83bzza1azlrv8l7l0mjpykc3qz4b5p9zcdzf7aw4vn")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Opus\"") + (string-append "\"" (assoc-ref inputs "opus") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("opus" ,opus))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/Opus_jll.jl") + (synopsis "Opus library wrappers") + (description "This package provides a wrapper for the opus audio library.") + (license license:expat))) + (define-public julia-x264-jll (package (name "julia-x264-jll") -- cgit 1.4.1 From f711bb110b1ba1f25d73ecccaa4cfd27e555e2c7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 11:17:26 +0300 Subject: gnu: Add julia-libass-jll. * gnu/packages/julia-jll.scm (julia-libass-jll): New variable. --- gnu/packages/julia-jll.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 904597a506..5f4d0351cb 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -401,6 +401,46 @@ used in autogenerated packages via @code{BinaryBuilder.jl}.") (description "This package provides a wrapper for the lame audio encoder.") (license license:expat))) +(define-public julia-libass-jll + (package + (name "julia-libass-jll") + (version "0.14.0+2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/libass_jll.jl") + (commit (string-append "libass-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "05nvis5ifmaq1g0c98hcpnl0ky22qgp64d4lb6g6r4yrrn6kqlsc")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"libass\"") + (string-append "\"" (assoc-ref inputs "libass") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libass" ,libass))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-bzip2-jll" ,julia-bzip2-jll) + ("julia-freetype2-jll" ,julia-freetype2-jll) + ("julia-fribidi-jll" ,julia-fribidi-jll) + ("julia-zlib-jll" ,julia-zlib-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/libass_jll.jl") + (synopsis "Libass library wrappers") + (description "This package provides a wrapper for libass.") + (license license:expat))) + (define-public julia-libfdk-aac-jll (package (name "julia-libfdk-aac-jll") -- cgit 1.4.1 From 94963f09bf5a67e88e89cc682c31af7116827776 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 11:18:19 +0300 Subject: gnu: Add julia-ffmpeg-jll. * gnu/packages/julia-jll.scm (julia-ffmpeg-jll): New variable. --- gnu/packages/julia-jll.scm | 49 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 5f4d0351cb..6d0549207f 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -125,6 +125,55 @@ originating @code{build_tarballs.jl} script can be found on the community build tree Yggdrasil.") (license license:expat))) +(define-public julia-ffmpeg-jll + (package + (name "julia-ffmpeg-jll") + (version "4.3.1+2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/FFMPEG_jll.jl") + (commit (string-append "FFMPEG-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1f8pq9nxiiqay9qcsly1wkfpyz9nbxakf78ryi2c7g8p5v80k6d3")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"FFMPEG\"") + (string-append "\"" (assoc-ref inputs "ffmpeg") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("ffmpeg" ,ffmpeg))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-bzip2-jll" ,julia-bzip2-jll) + ("julia-freetype2-jll" ,julia-freetype2-jll) + ("julia-fribidi-jll" ,julia-fribidi-jll) + ("julia-lame-jll" ,julia-lame-jll) + ("julia-libass-jll" ,julia-libass-jll) + ("julia-libfdk-aac-jll" ,julia-libfdk-aac-jll) + ("julia-libvorbis-jll" ,julia-libvorbis-jll) + ("julia-openssl-jll" ,julia-openssl-jll) + ("julia-opus-jll" ,julia-opus-jll) + ("julia-ogg-jll" ,julia-ogg-jll) + ("julia-x264-jll" ,julia-x264-jll) + ("julia-x265-jll" ,julia-x265-jll) + ("julia-zlib-jll" ,julia-zlib-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/FFMPEG_jll.jl") + (synopsis "ffmpeg library wrappers") + (description "This package provides a wrapper for ffmpeg.") + (license license:expat))) + (define-public julia-freetype2-jll (package (name "julia-freetype2-jll") -- cgit 1.4.1 From 0c1b3444e1924c0998820f83ed6f4bea23eb36c7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 11:20:48 +0300 Subject: gnu: Add julia-ffmpeg. * gnu/packages/julia-xyz.scm (julia-ffmpeg): New variable. --- gnu/packages/julia-xyz.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index ff207456c3..60e518e251 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -596,6 +596,30 @@ stressing the robustness of differentiation tools.") (description "This package provides various examples.") (license license:expat)))) +(define-public julia-ffmpeg + (package + (name "julia-ffmpeg") + (version "0.4.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaIO/FFMPEG.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1kwqixwhnnxs59xsw2k44xxnkx5fn4y49g58l5snfbszycxq7lls")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-ffmpeg-jll" ,julia-ffmpeg-jll) + ("julia-x264-jll" ,julia-x264-jll))) + (home-page "https://github.com/JuliaIO/FFMPEG.jl") + (synopsis "Julia Package for ffmpeg") + (description "This package is made to be included into packages that just +need the ffmpeg binaries + executables, and don't want the overhead of +@code{VideoIO.jl}.") + (license license:expat))) + (define-public julia-fillarrays (package (name "julia-fillarrays") -- cgit 1.4.1 From b3ffbab8f84056fe714b53885811bcfc1711c579 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 11:25:20 +0300 Subject: gnu: Add julia-libiconv-jll. * gnu/packages/julia-jll.scm (julia-libiconv-jll): New variable. --- gnu/packages/julia-jll.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 6d0549207f..2b2ed8a87b 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -26,6 +26,7 @@ #:use-module (guix build-system julia) #:use-module (gnu packages) #:use-module (gnu packages audio) + #:use-module (gnu packages base) #:use-module (gnu packages compression) #:use-module (gnu packages fontutils) #:use-module (gnu packages fribidi) @@ -526,6 +527,44 @@ used in autogenerated packages via @code{BinaryBuilder.jl}.") (description "This package provides a wrapper for the libfdk audio library.") (license license:expat))) +(define-public julia-libiconv-jll + (package + (name "julia-libiconv-jll") + (version "1.16.1+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Libiconv_jll.jl") + (commit (string-append "Libiconv-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "185f2460ypig1klgi8rdb0s2c8l4hxdbmsz9ihj7bdydl964s2hh")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Libiconv\", \"" + (assoc-ref inputs "libiconv") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libiconv" ,libiconv))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/Libiconv_jll.jl") + (synopsis "Libiconv library wrappers") + (description "This package provides a wrapper for the libiconv library.") + (license license:expat))) + (define-public julia-libpng-jll (package (name "julia-libpng-jll") -- cgit 1.4.1 From 09b63f2cd8031f762530d8d7423440327244c595 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 11:26:42 +0300 Subject: gnu: Add julia-libffi-jll. * gnu/packages/julia-jll.scm (julia-libffi-jll): New variable. --- gnu/packages/julia-jll.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 2b2ed8a87b..07578820eb 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -34,6 +34,7 @@ #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages julia) + #:use-module (gnu packages libffi) #:use-module (gnu packages maths) #:use-module (gnu packages mp3) #:use-module (gnu packages tls) @@ -527,6 +528,43 @@ used in autogenerated packages via @code{BinaryBuilder.jl}.") (description "This package provides a wrapper for the libfdk audio library.") (license license:expat))) +(define-public julia-libffi-jll + (package + (name "julia-libffi-jll") + (version "3.3.0+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Libffi_jll.jl") + (commit (string-append "Libffi-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "008ajchli77airvibdgqw7gvmhk9w63qrv94f88iz1ixxyrycnm0")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("lib64") "lib") + (("artifact\"Libffi\"") + (string-append "\"" (assoc-ref inputs "libffi") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libffi" ,libffi))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/Libffi_jll.jl") + (synopsis "Libffi library wrappers") + (description "This package provides a wrapper for the libffi library.") + (license license:expat))) + (define-public julia-libiconv-jll (package (name "julia-libiconv-jll") -- cgit 1.4.1 From 7180dcdfb1c31b9cff8932995902b17e3c62bce9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 11:28:19 +0300 Subject: gnu: Add julia-xml2-jll. * gnu/packages/julia-jll.scm (julia-xml2-jll): New variable. --- gnu/packages/julia-jll.scm | 43 ++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 42 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 07578820eb..96f9b1b84a 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -40,7 +40,8 @@ #:use-module (gnu packages tls) #:use-module (gnu packages video) #:use-module (gnu packages web) - #:use-module (gnu packages xiph)) + #:use-module (gnu packages xiph) + #:use-module (gnu packages xml)) ;;; TODO: Remove this autogenerated source package ;;; and build it from realse source using @@ -986,6 +987,46 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the x265 video library.") (license license:expat))) +(define-public julia-xml2-jll + (package + (name "julia-xml2-jll") + (version "2.9.12+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/XML2_jll.jl") + (commit (string-append "XML2-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1g6wf5r5v2qx6cwv05kd9amcsmv65vkajk43m9r1c35jqs9m8fnm")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"XML2\", \"" + (assoc-ref inputs "libxml2") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxml2" ,libxml2))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-libiconv-jll" ,julia-libiconv-jll) + ("julia-zlib-jll" ,julia-zlib-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/XML2_jll.jl") + (synopsis "XML2 library wrappers") + (description "This package provides a wrapper for the libxml2 library.") + (license license:expat))) + (define-public julia-zlib-jll (package (name "julia-zlib-jll") -- cgit 1.4.1 From ceb7936ff524565db5f307e3ed725e07d718a77c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 11:29:34 +0300 Subject: gnu: Add julia-gettext-jll. * gnu/packages/julia-jll.scm (julia-gettext-jll): New variable. --- gnu/packages/julia-jll.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 96f9b1b84a..658acc4563 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -31,6 +31,7 @@ #:use-module (gnu packages fontutils) #:use-module (gnu packages fribidi) #:use-module (gnu packages gcc) + #:use-module (gnu packages gettext) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages julia) @@ -255,6 +256,47 @@ rendering library.") (description "This package provides a wrapper for the fribidi library.") (license license:expat))) +(define-public julia-gettext-jll + (package + (name "julia-gettext-jll") + (version "0.21.0+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Gettext_jll.jl") + (commit (string-append "Gettext-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ghwkwv970q6j9ggkl0zlyrflhx8rd39y5i2zkc6p26084kyrxmf")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Gettext\", \"" + (assoc-ref inputs "gettext") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("gettext" ,gettext-minimal))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-compilersupportlibraries-jll" ,julia-compilersupportlibraries-jll) + ("julia-libiconv-jll" ,julia-libiconv-jll) + ("julia-xml2-jll" ,julia-xml2-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Gettext_jll.jl") + (synopsis "Gettext library wrappers") + (description "This package provides a wrapper for the gettext library.") + (license license:expat))) + (define-public julia-gumbo-jll (package (name "julia-gumbo-jll") -- cgit 1.4.1 From 088e1a50900f3aaa77c12c7ff5eb6e5f938b01c1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 11:31:15 +0300 Subject: gnu: Add julia-pcre-jll. * gnu/packages/julia-jll.scm (julia-pcre-jll): New variable. --- gnu/packages/julia-jll.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 658acc4563..637fd267dc 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -38,6 +38,7 @@ #:use-module (gnu packages libffi) #:use-module (gnu packages maths) #:use-module (gnu packages mp3) + #:use-module (gnu packages pcre) #:use-module (gnu packages tls) #:use-module (gnu packages video) #:use-module (gnu packages web) @@ -952,6 +953,44 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the opus audio library.") (license license:expat))) +(define-public julia-pcre-jll + (package + (name "julia-pcre-jll") + (version "8.44.0+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/PCRE_jll.jl") + (commit (string-append "PCRE-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0fcn8m16vy92v9dj437hzlknq9zl6sw6rckmr5gmh07sf0n3wszs")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"PCRE\", \"" + (assoc-ref inputs "pcre") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("pcre" ,pcre))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/PCRE_jll.jl") + (synopsis "PCRE library wrappers") + (description "This package provides a wrapper for the pcre library.") + (license license:expat))) + (define-public julia-x264-jll (package (name "julia-x264-jll") -- cgit 1.4.1 From 5f7fb563095168280df0313c3ee5e8f941a35bc9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 11:59:59 +0300 Subject: gnu: Add julia-libmount-jll. * gnu/packages/julia-jll.scm (julia-libmount-jll): New variable. --- gnu/packages/julia-jll.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 637fd267dc..7c6316e683 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -36,6 +36,7 @@ #:use-module (gnu packages imagemagick) #:use-module (gnu packages julia) #:use-module (gnu packages libffi) + #:use-module (gnu packages linux) #:use-module (gnu packages maths) #:use-module (gnu packages mp3) #:use-module (gnu packages pcre) @@ -647,6 +648,45 @@ used in autogenerated packages via @code{BinaryBuilder.jl}.") (description "This package provides a wrapper for the libiconv library.") (license license:expat))) +(define-public julia-libmount-jll + (package + (name "julia-libmount-jll") + (version "2.35.0+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Libmount_jll.jl") + (commit (string-append "Libmount-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "04i4vm5rshz8nfmnxqx8rm3b9jd7b1xdiriac1bpsx3n0qf4pw89")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Libmount\", \"" + (assoc-ref inputs "util-linux") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("util-linux" ,util-linux "lib"))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/Libmount_jll.jl") + (synopsis "Libmount library wrappers") + (description "This package provides a wrapper for the libmount library +from util-linux.") + (license license:expat))) + (define-public julia-libpng-jll (package (name "julia-libpng-jll") -- cgit 1.4.1 From b729895ae2f9e0d5e30b35310a49fd92813b8a6e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:02:03 +0300 Subject: gnu: Add julia-glib-jll. * gnu/packages/julia-jll.scm (julia-glib-jll): New variable. --- gnu/packages/julia-jll.scm | 45 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 7c6316e683..203bc9cef7 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -32,6 +32,7 @@ #:use-module (gnu packages fribidi) #:use-module (gnu packages gcc) #:use-module (gnu packages gettext) + #:use-module (gnu packages glib) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages julia) @@ -299,6 +300,50 @@ rendering library.") (description "This package provides a wrapper for the gettext library.") (license license:expat))) +(define-public julia-glib-jll + (package + (name "julia-glib-jll") + (version "2.68.1+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Glib_jll.jl") + (commit (string-append "Glib-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0l0fm5m4rznljkig7k4cxpi4skm7j4nc6lqx5xr0sb0wfzbr2llv")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Glib\", \"" + (assoc-ref inputs "glib") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("glib" ,glib))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-gettext-jll" ,julia-gettext-jll) + ("julia-libffi-jll" ,julia-libffi-jll) + ("julia-libiconv-jll" ,julia-libiconv-jll) + ("julia-libmount-jll" ,julia-libmount-jll) + ("julia-pcre-jll" ,julia-pcre-jll) + ("julia-zlib-jll" ,julia-zlib-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Glib_jll.jl") + (synopsis "Glib library wrappers") + (description "This package provides a wrapper for the glib library.") + (license license:expat))) + (define-public julia-gumbo-jll (package (name "julia-gumbo-jll") -- cgit 1.4.1 From a4dbdbaccfd5eda4ef0992b5f8ed4cae8f575cef Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:06:44 +0300 Subject: gnu: Add julia-pixman-jll. * gnu/packages/julia-jll.scm (julia-pixman-jll): New variable. --- gnu/packages/julia-jll.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 203bc9cef7..2210778065 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -44,6 +44,7 @@ #:use-module (gnu packages tls) #:use-module (gnu packages video) #:use-module (gnu packages web) + #:use-module (gnu packages xdisorg) #:use-module (gnu packages xiph) #:use-module (gnu packages xml)) @@ -1076,6 +1077,44 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the pcre library.") (license license:expat))) +(define-public julia-pixman-jll + (package + (name "julia-pixman-jll") + (version "0.40.1+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Pixman_jll.jl") + (commit (string-append "Pixman-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ahawpgsiccmpa7gyxny7hq058igqvpza7ybqa44vl2nynnry2g7")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Pixman\", \"" + (assoc-ref inputs "pixman") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("pixman" ,pixman))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/Pixman_jll.jl") + (synopsis "Pixman library wrappers") + (description "This package provides a wrapper for the pixman library.") + (license license:expat))) + (define-public julia-x264-jll (package (name "julia-x264-jll") -- cgit 1.4.1 From e2ee6686efe11a439bb5c09a5d3543e78f4579f1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:08:04 +0300 Subject: gnu: Add julia-libuuid-jll. * gnu/packages/julia-jll.scm (julia-libuuid-jll): New variable. --- gnu/packages/julia-jll.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 2210778065..651d15599b 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -809,6 +809,44 @@ from util-linux.") (description "This package provides a wrapper for libtiff") (license license:expat))) +(define-public julia-libuuid-jll + (package + (name "julia-libuuid-jll") + (version "2.36.0+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Libuuid_jll.jl") + (commit (string-append "Libuuid-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0iz1qrrpl8sp336m1f884sdgwbdlkp9sm371cwcfq4iriaihbmbs")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Libuuid\", \"" + (assoc-ref inputs "util-linux") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("util-linux" ,util-linux "lib"))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/Libmount_jll.jl") + (synopsis "Libuuid library wrappers") + (description "This package provides a wrapper for the libuuid library from util-linux.") + (license license:expat))) + (define-public julia-libvorbis-jll (package (name "julia-libvorbis-jll") -- cgit 1.4.1 From 3d12f59d1f8437f17914d2ae0cb6b46f3b2dedae Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:08:48 +0300 Subject: gnu: Add julia-expat-jll. * gnu/packages/julia-jll.scm (julia-expat-jll): New variable. --- gnu/packages/julia-jll.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 651d15599b..c10d371769 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -133,6 +133,44 @@ originating @code{build_tarballs.jl} script can be found on the community build tree Yggdrasil.") (license license:expat))) +(define-public julia-expat-jll + (package + (name "julia-expat-jll") + (version "2.2.10+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Expat_jll.jl") + (commit (string-append "Expat-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0lkhkh0067lns35njpc1bqbx6653r99lrjcbgrihlln9a7k9qj1s")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Expat\", \"" + (assoc-ref inputs "expat") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("expat" ,expat))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/Expat_jll.jl") + (synopsis "Expat library wrappers") + (description "This package provides a wrapper for the expat library.") + (license license:expat))) + (define-public julia-ffmpeg-jll (package (name "julia-ffmpeg-jll") -- cgit 1.4.1 From 154f0a9b1439f2a18f6daf0b27a993da38c088e1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:10:26 +0300 Subject: gnu: Add julia-xorg-libxau-jll. * gnu/packages/julia-jll.scm (julia-xorg-libxau-jll): New variable. --- gnu/packages/julia-jll.scm | 39 ++++++++++++++++++++++++++++++++++++++- 1 file changed, 38 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index c10d371769..e528c42342 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -46,7 +46,8 @@ #:use-module (gnu packages web) #:use-module (gnu packages xdisorg) #:use-module (gnu packages xiph) - #:use-module (gnu packages xml)) + #:use-module (gnu packages xml) + #:use-module (gnu packages xorg)) ;;; TODO: Remove this autogenerated source package ;;; and build it from realse source using @@ -1308,6 +1309,42 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the libxml2 library.") (license license:expat))) +(define-public julia-xorg-libxau-jll + (package + (name "julia-xorg-libxau-jll") + (version "1.0.9+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libXau_jll.jl") + (commit (string-append "Xorg_libXau-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1bc59hzg4jgdy0lwykp6avxsb87fq9j79c30yxprwjvxq8xm3p8z")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_libXau\"") + (string-append "\"" (assoc-ref inputs "libxau") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxau" ,libxau))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libXau_jll.jl") + (synopsis "Libxau library wrappers") + (description "This package provides a wrapper for the libxau library.") + (license license:expat))) + (define-public julia-zlib-jll (package (name "julia-zlib-jll") -- cgit 1.4.1 From 71b0d280f7c1dcd6afa735314c970f44b465f6a4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:11:17 +0300 Subject: gnu: Add julia-xorg-libxdmcp-jll. * gnu/packages/julia-jll.scm (julia-xorg-libxdmcp-jll): New variable. --- gnu/packages/julia-jll.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index e528c42342..6d8230b85b 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -1345,6 +1345,42 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the libxau library.") (license license:expat))) +(define-public julia-xorg-libxdmcp-jll + (package + (name "julia-xorg-libxdmcp-jll") + (version "1.1.3+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libXdmcp_jll.jl") + (commit (string-append "Xorg_libXdmcp-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1ghw8c7ibkm2hv4h38qyhbxfmyizxszqv6fv8qzlb5031dmshnap")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_libXdmcp\"") + (string-append "\"" (assoc-ref inputs "libxdmcp") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxdmcp" ,libxdmcp))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libXdmcp_jll.jl") + (synopsis "Libxdmcp library wrappers") + (description "This package provides a wrapper for the libxdmcp library.") + (license license:expat))) + (define-public julia-zlib-jll (package (name "julia-zlib-jll") -- cgit 1.4.1 From cf4a0c1f67003146057597363f06bb0056687e0f Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:12:50 +0300 Subject: gnu: Add julia-libgpg-error-jll. * gnu/packages/julia-jll.scm (julia-libgpg-error-jll): New variable. --- gnu/packages/julia-jll.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 6d8230b85b..87cd840b9e 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -33,6 +33,7 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages gettext) #:use-module (gnu packages glib) + #:use-module (gnu packages gnupg) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages julia) @@ -695,6 +696,44 @@ used in autogenerated packages via @code{BinaryBuilder.jl}.") (description "This package provides a wrapper for the libffi library.") (license license:expat))) +(define-public julia-libgpg-error-jll + (package + (name "julia-libgpg-error-jll") + (version "1.42.0+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Libgpg_error_jll.jl") + (commit (string-append "Libgpg_error-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0jmsn0mhn6b35b5awbrlpjjszknsplr62li574fkgwfxlfixb8iy")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Libgpg_error\", \"" + (assoc-ref inputs "libgpg-error") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libgpg-error" ,libgpg-error))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/Libgpg_error_jll.jl") + (synopsis "libgpg-error library wrappers") + (description "This package provides a wrapper for the libgpg-error library.") + (license license:expat))) + (define-public julia-libiconv-jll (package (name "julia-libiconv-jll") -- cgit 1.4.1 From 2ee28bfc9f43df97913c5e54fe1206b92ef6662b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:15:00 +0300 Subject: gnu: Add julia-libgcrypt-jll. * gnu/packages/julia-jll.scm (julia-libgcrypt-jll): New variable. --- gnu/packages/julia-jll.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 87cd840b9e..73214cb652 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -696,6 +696,45 @@ used in autogenerated packages via @code{BinaryBuilder.jl}.") (description "This package provides a wrapper for the libffi library.") (license license:expat))) +(define-public julia-libgcrypt-jll + (package + (name "julia-libgcrypt-jll") + (version "1.8.7+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Libgcrypt_jll.jl") + (commit (string-append "Libgcrypt-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "06fsdwrfw3f4cdbg1ssswznvj8ar3w5w4vxxag1hacs14pxlm5gi")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Libgcrypt\", \"" + (assoc-ref inputs "libgcrypt") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libgcrypt" ,libgcrypt))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-libgpg-error-jll" ,julia-libgpg-error-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Libgcrypt_jll.jl") + (synopsis "libgcrypt library wrappers") + (description "This package provides a wrapper for the libgcrypt library.") + (license license:expat))) + (define-public julia-libgpg-error-jll (package (name "julia-libgpg-error-jll") -- cgit 1.4.1 From 6e795958ebbf2edcb4e0838b36a34613f863a3b6 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:16:09 +0300 Subject: gnu: Add julia-xorg-xtrans-jll. * gnu/packages/julia-jll.scm (julia-xorg-xtrans-jll): New variable. --- gnu/packages/julia-jll.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 73214cb652..cf54e14097 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -1459,6 +1459,42 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the libxdmcp library.") (license license:expat))) +(define-public julia-xorg-xtrans-jll + (package + (name "julia-xorg-xtrans-jll") + (version "1.4.0+2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_xtrans_jll.jl") + (commit (string-append "Xorg_xtrans-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "16rzkgc7l1j57l43v5ffrak164bdff7h1amm0y3mcnwjqmkig9dn")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_xtrans\"") + (string-append "\"" (assoc-ref inputs "xtrans") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("xtrans" ,xtrans))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_xtrans_jll.jl") + (synopsis "xtrans library wrappers") + (description "This package provides a wrapper for the xtrans library.") + (license license:expat))) + (define-public julia-zlib-jll (package (name "julia-zlib-jll") -- cgit 1.4.1 From f57a0f49925c53d6094722654ac29f4477517a89 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:17:10 +0300 Subject: gnu: Add julia-lzo-jll. * gnu/packages/julia-jll.scm (julia-lzo-jll): New variable. --- gnu/packages/julia-jll.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index cf54e14097..8f26a49244 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -1002,6 +1002,44 @@ from util-linux.") "This package provides a wrapper for the libvorbis audio library.") (license license:expat))) +(define-public julia-lzo-jll + (package + (name "julia-lzo-jll") + (version "2.10.1+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/LZO_jll.jl") + (commit (string-append "LZO-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1gy57znz3b6pk902vgdzlrwrxib0bcfl0zr1prinfbr9vfmiv1h0")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"LZO\", \"" + (assoc-ref inputs "lzo") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("lzo" ,lzo))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/LZO_jll.jl") + (synopsis "LZO library wrappers") + (description "This package provides a wrapper for the lzo library.") + (license license:expat))) + (define-public julia-mbedtls-jll (package (name "julia-mbedtls-jll") -- cgit 1.4.1 From 8a2e54cb6f0a96de22ae7dc4897bbbb86ed3bb87 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:21:56 +0300 Subject: gnu: Add julia-xslt-jll. * gnu/packages/julia-jll.scm (julia-xslt-jll): New variable. --- gnu/packages/julia-jll.scm | 43 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 8f26a49244..df9bf509ef 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -1533,6 +1533,49 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the xtrans library.") (license license:expat))) +(define-public julia-xslt-jll + (package + (name "julia-xslt-jll") + (version "1.1.34+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/XSLT_jll.jl") + (commit (string-append "XSLT-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0wjkfnrgpd7c6i4ga5xzsqqmfrxcdkr1kjsxmd9bff8cqvyknnhq")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"XSLT\", \"" + (assoc-ref inputs "libxslt") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxslt" ,libxslt))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-libgcrypt-jll" ,julia-libgcrypt-jll) + ("julia-libgpg-error-jll" ,julia-libgpg-error-jll) + ("julia-libiconv-jll" ,julia-libiconv-jll) + ("julia-xml2-jll" ,julia-xml2-jll) + ("julia-zlib-jll" ,julia-zlib-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/XSLT_jll.jl") + (synopsis "Xslt library wrappers") + (description "This package provides a wrapper for the libxslt library.") + (license license:expat))) + (define-public julia-zlib-jll (package (name "julia-zlib-jll") -- cgit 1.4.1 From f5cf7099825e4ed6c81192109abea75b096a7fee Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:22:43 +0300 Subject: gnu: Add julia-xorg-libpthread-stubs-jll. * gnu/packages/julia-jll.scm (julia-xorg-libpthread-stubs-jll): New variable. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index df9bf509ef..cd90eb23dc 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -1425,6 +1425,43 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the libxml2 library.") (license license:expat))) +(define-public julia-xorg-libpthread-stubs-jll + (package + (name "julia-xorg-libpthread-stubs-jll") + (version "0.1.0+2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libpthread_stubs_jll.jl") + (commit (string-append "Xorg_libpthread_stubs-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "161f4111xsb8xq4zs59jw95s94xfn1yxpii0p0dhn3yqgligggvx")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_libpthread_stubs\"") + (string-append "\"" (assoc-ref inputs "libpthread-stubs") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libpthread-stubs" ,libpthread-stubs))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xslt-jll" ,julia-xslt-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libpthread_stubs_jll.jl") + (synopsis "Libpthread-stubs library wrappers") + (description "This package provides a wrapper for the libpthread-stubs library.") + (license license:expat))) + (define-public julia-xorg-libxau-jll (package (name "julia-xorg-libxau-jll") -- cgit 1.4.1 From 6b10ebc98a086dcab861950411627929342d696e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:24:06 +0300 Subject: gnu: Add julia-xorg-libxcb-jll. * gnu/packages/julia-jll.scm (julia-xorg-libxcb-jll): New variable. --- gnu/packages/julia-jll.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index cd90eb23dc..933867a447 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -1498,6 +1498,46 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the libxau library.") (license license:expat))) +(define-public julia-xorg-libxcb-jll + (package + (name "julia-xorg-libxcb-jll") + (version "1.13.0+2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libxcb_jll.jl") + (commit (string-append "Xorg_libxcb-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "109m4r4v6ww31rq0klyqd3rf3j1yiycvld82d514d040w5027ssk")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_libxcb\"") + (string-append "\"" (assoc-ref inputs "libxcb") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxcb" ,libxcb))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libxau-jll" ,julia-xorg-libxau-jll) + ("julia-xorg-libpthread-stubs-jll" ,julia-xorg-libpthread-stubs-jll) + ("julia-xorg-libxdmcp-jll" ,julia-xorg-libxdmcp-jll) + ("julia-xslt-jll" ,julia-xslt-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libxcb_jll.jl") + (synopsis "Libxcb library wrappers") + (description "This package provides a wrapper for the libxcb library.") + (license license:expat))) + (define-public julia-xorg-libxdmcp-jll (package (name "julia-xorg-libxdmcp-jll") -- cgit 1.4.1 From 2b93e8cd66bf4f1e296528e62e866468a941f8ad Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:25:00 +0300 Subject: gnu: Add julia-xorg-libx11-jll. * gnu/packages/julia-jll.scm (julia-xorg-libx11-jll): New variable. --- gnu/packages/julia-jll.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 933867a447..33e7740298 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -1462,6 +1462,44 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the libpthread-stubs library.") (license license:expat))) +(define-public julia-xorg-libx11-jll + (package + (name "julia-xorg-libx11-jll") + (version "1.6.9+2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libX11_jll.jl") + (commit (string-append "Xorg_libX11-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1fw2dmmw04jmyss43g66q80w3j7wshmxgjccir1hh4c5d8x2zs39")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_libX11\"") + (string-append "\"" (assoc-ref inputs "libx11") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libx11" ,libx11))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libxcb-jll" ,julia-xorg-libxcb-jll) + ("julia-xorg-xtrans-jll" ,julia-xorg-xtrans-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libX11_jll.jl") + (synopsis "LibX11 library wrappers") + (description "This package provides a wrapper for the libx11 library.") + (license license:expat))) + (define-public julia-xorg-libxau-jll (package (name "julia-xorg-libxau-jll") -- cgit 1.4.1 From 7cb9173879aa814fd89e21d98035081f9f86e05b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:25:56 +0300 Subject: gnu: Add julia-xorg-libxext-jll. * gnu/packages/julia-jll.scm (julia-xorg-libxext-jll): New variable. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 33e7740298..7cf8899c94 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -1612,6 +1612,43 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the libxdmcp library.") (license license:expat))) +(define-public julia-xorg-libxext-jll + (package + (name "julia-xorg-libxext-jll") + (version "1.3.4+2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libXext_jll.jl") + (commit (string-append "Xorg_libXext-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1xmx86l54apvqv0xwy0rha7knjl4x5crllqra56nhi0arhw8ywfc")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_libXext\"") + (string-append "\"" (assoc-ref inputs "libxext") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxext" ,libxext))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libx11-jll" ,julia-xorg-libx11-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libXext_jll.jl") + (synopsis "LibXext library wrappers") + (description "This package provides a wrapper for the libxext library.") + (license license:expat))) + (define-public julia-xorg-xtrans-jll (package (name "julia-xorg-xtrans-jll") -- cgit 1.4.1 From d604f4fc5359cc887870c975bc8dcb8301b0e9b4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:26:49 +0300 Subject: gnu: Add julia-fontconfig-jll. * gnu/packages/julia-jll.scm (julia-fontconfig-jll): New variable. --- gnu/packages/julia-jll.scm | 43 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 7cf8899c94..80b6b4c5c3 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -222,6 +222,49 @@ build tree Yggdrasil.") (description "This package provides a wrapper for ffmpeg.") (license license:expat))) +(define-public julia-fontconfig-jll + (package + (name "julia-fontconfig-jll") + (version "2.13.93+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Fontconfig_jll.jl") + (commit (string-append "Fontconfig-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1p6mfci77bp31w3xzlwhjccln40g6g2rdpfp38v5xf8sz2aybpw2")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Fontconfig\", \"" + (assoc-ref inputs "fontconfig") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("fontconfig" ,fontconfig))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-bzip2-jll" ,julia-bzip2-jll) + ("julia-expat-jll" ,julia-expat-jll) + ("julia-freetype2-jll" ,julia-freetype2-jll) + ("julia-libuuid-jll" ,julia-libuuid-jll) + ("julia-zlib-jll" ,julia-zlib-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Fontconfig_jll.jl") + (synopsis "Fontconfig library wrappers") + (description "This package provides a wrapper for the fontconfig library.") + (license license:expat))) + (define-public julia-freetype2-jll (package (name "julia-freetype2-jll") -- cgit 1.4.1 From 390beddbc4ca74a3e4ea7573e8bc1f6f35d46375 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:28:17 +0300 Subject: gnu: Add julia-xorg-libxrender-jll. * gnu/packages/julia-jll.scm (julia-xorg-libxrender-jll): New variable. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 80b6b4c5c3..214b9d7644 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -1692,6 +1692,43 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the libxext library.") (license license:expat))) +(define-public julia-xorg-libxrender-jll + (package + (name "julia-xorg-libxrender-jll") + (version "0.9.10+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libXrender_jll.jl") + (commit (string-append "Xorg_libXrender-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "041kjqpkgcjf72msg4zm4wja623wfsy9gmkqjvsj46lj885qizz7")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_libXrender\"") + (string-append "\"" (assoc-ref inputs "libxrender") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxrender" ,libxrender))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libx11-jll" ,julia-xorg-libx11-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libXrender_jll.jl") + (synopsis "libXrender library wrappers") + (description "This package provides a wrapper for the libXrender library.") + (license license:expat))) + (define-public julia-xorg-xtrans-jll (package (name "julia-xorg-xtrans-jll") -- cgit 1.4.1 From 7f8cbd07a11cf7f60ae37626132cbafff477814c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:29:18 +0300 Subject: gnu: Add julia-cairo-jll. * gnu/packages/julia-jll.scm (julia-cairo-jll): New variable. --- gnu/packages/julia-jll.scm | 47 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 214b9d7644..71743e9082 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -34,6 +34,7 @@ #:use-module (gnu packages gettext) #:use-module (gnu packages glib) #:use-module (gnu packages gnupg) + #:use-module (gnu packages gtk) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages julia) @@ -93,6 +94,52 @@ compression program.") (license license:expat))) +(define-public julia-cairo-jll + (package + (name "julia-cairo-jll") + (version "1.16.0+5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Cairo_jll.jl") + (commit (string-append "Cairo-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1766k8f63qb4bgyl4g29qrcddwypqx0c4kdg3lji8bsimw3f1bay")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Cairo\"") + (string-append "\"" (assoc-ref inputs "cairo") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("cairo" ,cairo))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-bzip2-jll" ,julia-bzip2-jll) + ("julia-fontconfig-jll" ,julia-fontconfig-jll) + ("julia-freetype2-jll" ,julia-freetype2-jll) + ("julia-glib-jll" ,julia-glib-jll) + ("julia-libpng-jll" ,julia-libpng-jll) + ("julia-lzo-jll" ,julia-lzo-jll) + ("julia-pixman-jll" ,julia-pixman-jll) + ("julia-xorg-libxext-jll" ,julia-xorg-libxext-jll) + ("julia-xorg-libxrender-jll" ,julia-xorg-libxrender-jll) + ("julia-zlib-jll" ,julia-zlib-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Cairo_jll.jl") + (synopsis "Cairo library wrappers") + (description "This package provides a wrapper for the cairo library.") + (license license:expat))) + (define-public julia-compilersupportlibraries-jll (package (name "julia-compilersupportlibraries-jll") -- cgit 1.4.1 From 98cfe462c290219582de87eddeabc5671842891e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:32:09 +0300 Subject: gnu: Add julia-xorg-libxfixes-jll. * gnu/packages/julia-jll.scm (julia-xorg-libxfixes-jll): New variable. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 71743e9082..ac16c52693 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -1739,6 +1739,43 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the libxext library.") (license license:expat))) +(define-public julia-xorg-libxfixes-jll + (package + (name "julia-xorg-libxfixes-jll") + (version "5.0.3+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libXfixes_jll.jl") + (commit (string-append "Xorg_libXfixes-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0sjpclxinbcq3msnaqdfqlpfhnlvl15qn7dam968i4qwrpyv43dv")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_libXfixes\"") + (string-append "\"" (assoc-ref inputs "libxfixes") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxfixes" ,libxfixes))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libx11-jll" ,julia-xorg-libx11-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libXfixes_jll.jl") + (synopsis "Libxfixes library wrappers") + (description "This package provides a wrapper for the libxfixes library.") + (license license:expat))) + (define-public julia-xorg-libxrender-jll (package (name "julia-xorg-libxrender-jll") -- cgit 1.4.1 From 92873d3bfe2fd2016892801b10040d5b6f17e514 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:32:55 +0300 Subject: gnu: Add julia-xorg-libxcursor-jll. * gnu/packages/julia-jll.scm (julia-xorg-libxcursor-jll): New variable. --- gnu/packages/julia-jll.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index ac16c52693..32602f3f1b 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -1666,6 +1666,44 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the libxcb library.") (license license:expat))) +(define-public julia-xorg-libxcursor-jll + (package + (name "julia-xorg-libxcursor-jll") + (version "1.2.0+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libXcursor_jll.jl") + (commit (string-append "Xorg_libXcursor-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0hxhpsjw1zk30qphrp90g1wvqfs1hr47qifn1gqgx73ci5nmq0y7")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_libXcursor\"") + (string-append "\"" (assoc-ref inputs "libxcursor") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxcursor" ,libxcursor))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libxfixes-jll" ,julia-xorg-libxfixes-jll) + ("julia-xorg-libxrender-jll" ,julia-xorg-libxrender-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libXcursor_jll.jl") + (synopsis "Libxcursor library wrappers") + (description "This package provides a wrapper for the libxcursor library.") + (license license:expat))) + (define-public julia-xorg-libxdmcp-jll (package (name "julia-xorg-libxdmcp-jll") -- cgit 1.4.1 From 7946cd309bee1322986523290d30b40189be085b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:33:59 +0300 Subject: gnu: Add julia-libglvnd-jll. * gnu/packages/julia-jll.scm (julia-libglvnd-jll): New variable. --- gnu/packages/julia-jll.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 32602f3f1b..4cfe09d031 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -32,6 +32,7 @@ #:use-module (gnu packages fribidi) #:use-module (gnu packages gcc) #:use-module (gnu packages gettext) + #:use-module (gnu packages gl) #:use-module (gnu packages glib) #:use-module (gnu packages gnupg) #:use-module (gnu packages gtk) @@ -825,6 +826,44 @@ used in autogenerated packages via @code{BinaryBuilder.jl}.") (description "This package provides a wrapper for the libgcrypt library.") (license license:expat))) +(define-public julia-libglvnd-jll + (package + (name "julia-libglvnd-jll") + (version "1.3.0+2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Libglvnd_jll.jl") + (commit (string-append "Libglvnd-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1lrppqj836saryqxj9xrqn0cih513qhijkhgqdww5azw8w917d3w")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Libglvnd\"") + (string-append "\"" (assoc-ref inputs "libglvnd") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libglvnd" ,libglvnd))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libx11-jll" ,julia-xorg-libx11-jll) + ("julia-xorg-libxext-jll" ,julia-xorg-libxext-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Libglvnd_jll.jl") + (synopsis "Libglvnd library wrappers") + (description "This package provides a wrapper for the libglvnd library.") + (license license:expat))) + (define-public julia-libgpg-error-jll (package (name "julia-libgpg-error-jll") -- cgit 1.4.1 From 2cc2507d0e1d1bc30d4ad755dd1e73e21e8bcd1f Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:35:10 +0300 Subject: gnu: Add julia-xorg-libxi-jll. * gnu/packages/julia-jll.scm (julia-xorg-libxi-jll): New variable. --- gnu/packages/julia-jll.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 4cfe09d031..e6202dd4a6 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -1853,6 +1853,44 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the libxfixes library.") (license license:expat))) +(define-public julia-xorg-libxi-jll + (package + (name "julia-xorg-libxi-jll") + (version "1.7.10+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libXi_jll.jl") + (commit (string-append "Xorg_libXi-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1jhrng5sf44880x3pnw1gpb88z21c7nznfyzhs4a5z910ndrynd7")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_libXi\"") + (string-append "\"" (assoc-ref inputs "libxi") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxi" ,libxi))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libxext-jll" ,julia-xorg-libxext-jll) + ("julia-xorg-libxfixes-jll" ,julia-xorg-libxfixes-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libXi_jll.jl") + (synopsis "Libxi library wrappers") + (description "This package provides a wrapper for the libxi library.") + (license license:expat))) + (define-public julia-xorg-libxrender-jll (package (name "julia-xorg-libxrender-jll") -- cgit 1.4.1 From f7033423d3143373902461ef122a27a485432936 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:35:53 +0300 Subject: gnu: Add julia-xorg-libxinerama-jll. * gnu/packages/julia-jll.scm (julia-xorg-libxinerama-jll): New variable. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index e6202dd4a6..9708bd0175 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -1891,6 +1891,43 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the libxi library.") (license license:expat))) +(define-public julia-xorg-libxinerama-jll + (package + (name "julia-xorg-libxinerama-jll") + (version "1.1.4+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libXinerama_jll.jl") + (commit (string-append "Xorg_libXinerama-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0jybxbqxd4jc9ka3rk3v5yh8ps2fapdibldr7bymllzw1w2i25rn")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_libXinerama\"") + (string-append "\"" (assoc-ref inputs "libxinerama") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxinerama" ,libxinerama))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libxext-jll" ,julia-xorg-libxext-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libXinerama_jll.jl") + (synopsis "Libxinerama library wrappers") + (description "This package provides a wrapper for the libxinerama library.") + (license license:expat))) + (define-public julia-xorg-libxrender-jll (package (name "julia-xorg-libxrender-jll") -- cgit 1.4.1 From d3903306e883fc263e4e726c36624a0c3340849a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:36:47 +0300 Subject: gnu: Add julia-xorg-libxrandr-jll. * gnu/packages/julia-jll.scm (julia-xorg-libxrandr-jll): New variable. --- gnu/packages/julia-jll.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 9708bd0175..80ace85e87 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -1928,6 +1928,44 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the libxinerama library.") (license license:expat))) +(define-public julia-xorg-libxrandr-jll + (package + (name "julia-xorg-libxrandr-jll") + (version "1.5.2+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libXrandr_jll.jl") + (commit (string-append "Xorg_libXrandr-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0y4gsw5x643qdamf932agzdlyayzp63pn8j7j0lckd6dzqfdz46g")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_libXrandr\"") + (string-append "\"" (assoc-ref inputs "libxrandr") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxrandr" ,libxrandr))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libxext-jll" ,julia-xorg-libxext-jll) + ("julia-xorg-libxrender-jll" ,julia-xorg-libxrender-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libXrandr_jll.jl") + (synopsis "Libxrandr library wrappers") + (description "This package provides a wrapper for the libxrandr library.") + (license license:expat))) + (define-public julia-xorg-libxrender-jll (package (name "julia-xorg-libxrender-jll") -- cgit 1.4.1 From 46fafec9c68debce225035ac08aefaa793bfc0c9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:37:42 +0300 Subject: gnu: Add julia-glfw-jll. * gnu/packages/julia-jll.scm (julia-glfw-jll): New variable. --- gnu/packages/julia-jll.scm | 43 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 80ace85e87..500d7d0211 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -432,6 +432,49 @@ rendering library.") (description "This package provides a wrapper for the gettext library.") (license license:expat))) +(define-public julia-glfw-jll + (package + (name "julia-glfw-jll") + (version "3.3.4+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/GLFW_jll.jl") + (commit (string-append "GLFW-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "12r4g8x1pgfrx53wq1a2q0rj4p08q352mmci2px1j4bd0pwi8rc4")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"GLFW\", \"" + (assoc-ref inputs "glfw") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("glfw" ,glfw))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-libglvnd-jll" ,julia-libglvnd-jll) + ("julia-xorg-libxcursor-jll" ,julia-xorg-libxcursor-jll) + ("julia-xorg-libxinerama-jll" ,julia-xorg-libxinerama-jll) + ("julia-xorg-libxrandr-jll" ,julia-xorg-libxrandr-jll) + ("julia-xorg-libxi-jll" ,julia-xorg-libxi-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/GLFW_jll.jl") + (synopsis "Glfw library wrappers") + (description "This package provides a wrapper for the glfw library.") + (license license:expat))) + (define-public julia-glib-jll (package (name "julia-glib-jll") -- cgit 1.4.1 From 824f4bae6bbec359f795a9f22ccab2b96037b5ab Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:39:31 +0300 Subject: gnu: Add julia-wayland-jll. * gnu/packages/julia-jll.scm (julia-wayland-jll): New variable. --- gnu/packages/julia-jll.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 500d7d0211..7a2977e058 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -29,6 +29,7 @@ #:use-module (gnu packages base) #:use-module (gnu packages compression) #:use-module (gnu packages fontutils) + #:use-module (gnu packages freedesktop) #:use-module (gnu packages fribidi) #:use-module (gnu packages gcc) #:use-module (gnu packages gettext) @@ -1480,6 +1481,45 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the pixman library.") (license license:expat))) +(define-public julia-wayland-jll + (package + (name "julia-wayland-jll") + (version "1.17.0+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Wayland_jll.jl") + (commit (string-append "Wayland-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1w53inz62va3f022pgw3rfw5z5vgiv8z9dg3lfzpjrdb0lcd6ab6")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Wayland\"") + (string-append "\"" (assoc-ref inputs "wayland") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("wayland" ,wayland))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-expat-jll" ,julia-expat-jll) + ("julia-libffi-jll" ,julia-libffi-jll) + ("julia-xml2-jll" ,julia-xml2-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Wayland_jll.jl") + (synopsis "Wayland library wrappers") + (description "This package provides a wrapper for the wayland library.") + (license license:expat))) + (define-public julia-x264-jll (package (name "julia-x264-jll") -- cgit 1.4.1 From dfaddea2f3e271bbc2f8c7ff85955fe716a87d1c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:40:10 +0300 Subject: gnu: Add julia-wayland-protocols-jll. * gnu/packages/julia-jll.scm (julia-wayland-protocols-jll): New variable. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 7a2977e058..e06a281275 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -1520,6 +1520,43 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the wayland library.") (license license:expat))) +(define-public julia-wayland-protocols-jll + (package + (name "julia-wayland-protocols-jll") + (version "1.18.0+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Wayland_protocols_jll.jl") + (commit (string-append "Wayland_protocols-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1dc9d2wzgybqjlg8l7f4ridkv2d66dg3lb3zihnl0k64psibn4x9")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Wayland_protocols\"") + (string-append "\"" (assoc-ref inputs "wayland-protocols") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("wayland-protocols" ,wayland-protocols))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-wayland-jll" ,julia-wayland-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Wayland_protocols_jll.jl") + (synopsis "Wayland-protocols library wrappers") + (description "This package provides a wrapper for the wayland-protocols library.") + (license license:expat))) + (define-public julia-x264-jll (package (name "julia-x264-jll") -- cgit 1.4.1 From a2eb232b6ab7525af8d83964fd819b14b0a332ef Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:41:03 +0300 Subject: gnu: Add julia-xorg-libxkbfile-jll. * gnu/packages/julia-jll.scm (julia-xorg-libxkbfile-jll): New variable. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index e06a281275..25a78e8074 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -2048,6 +2048,43 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the libxinerama library.") (license license:expat))) +(define-public julia-xorg-libxkbfile-jll + (package + (name "julia-xorg-libxkbfile-jll") + (version "1.1.0+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libxkbfile_jll.jl") + (commit (string-append "Xorg_libxkbfile-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0zrnrixz34h54n0c06ziaxcajvndydzgxxh5jbvqx1xrij5rw5gy")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_libxkbfile\"") + (string-append "\"" (assoc-ref inputs "libxkbfile") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxkbfile" ,libxkbfile))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libx11-jll" ,julia-xorg-libx11-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libxkbfile_jll.jl") + (synopsis "Libxkbfile library wrappers") + (description "This package provides a wrapper for the libxkbfile library.") + (license license:expat))) + (define-public julia-xorg-libxrandr-jll (package (name "julia-xorg-libxrandr-jll") -- cgit 1.4.1 From d6227a3939821ade5192069e5b981ae61ee8de3f Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:41:54 +0300 Subject: gnu: Add julia-xorg-xkbcomp-jll. * gnu/packages/julia-jll.scm (julia-xorg-xkbcomp-jll): New variable. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 25a78e8074..0e32b46f8b 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -2160,6 +2160,43 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the libXrender library.") (license license:expat))) +(define-public julia-xorg-xkbcomp-jll + (package + (name "julia-xorg-xkbcomp-jll") + (version "1.4.2+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_xkbcomp_jll.jl") + (commit (string-append "Xorg_xkbcomp-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1rkb9525iq0jjpq8v333b728kfillgixxsim37mqdplad85l36wl")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_xkbcomp\"") + (string-append "\"" (assoc-ref inputs "xkbcomp") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("xkbcomp" ,xkbcomp))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libxkbfile-jll" ,julia-xorg-libxkbfile-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_xkbcomp_jll.jl") + (synopsis "xkbcomp library wrappers") + (description "This package provides a wrapper for the xkbcomp library.") + (license license:expat))) + (define-public julia-xorg-xtrans-jll (package (name "julia-xorg-xtrans-jll") -- cgit 1.4.1 From 845be82d03c55d186a0515cb9ba429e593bb177d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:42:43 +0300 Subject: gnu: Add julia-xorg-xkeyboard-config-jll. * gnu/packages/julia-jll.scm (julia-xorg-xkeyboard-config-jll): New variable. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 0e32b46f8b..4518aaa97f 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -2197,6 +2197,43 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the xkbcomp library.") (license license:expat))) +(define-public julia-xorg-xkeyboard-config-jll + (package + (name "julia-xorg-xkeyboard-config-jll") + (version "2.27.0+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_xkeyboard_config_jll.jl") + (commit (string-append "Xorg_xkeyboard_config-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1lgynzxd0mn64zbf0njqkd1hz1illqnl3p7hi9abwh5vbdf4pwhw")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_xkeyboard_config\"") + (string-append "\"" (assoc-ref inputs "xkeyboard-config") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("xkeyboard-config" ,xkeyboard-config))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-xkbcomp-jll" ,julia-xorg-xkbcomp-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_xkeyboard_config_jll.jl") + (synopsis "Xkeyboard-config library wrappers") + (description "This package provides a wrapper for the xkeyboard-config library.") + (license license:expat))) + (define-public julia-xorg-xtrans-jll (package (name "julia-xorg-xtrans-jll") -- cgit 1.4.1 From 4d6ef7eb2c8159e3ab8bf2e5d490960cd97958d0 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:44:51 +0300 Subject: gnu: Add julia-xkbcommon-jll. * gnu/packages/julia-jll.scm (julia-xkbcommon-jll): New variable. --- gnu/packages/julia-jll.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 4518aaa97f..3ec9ae6269 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -1634,6 +1634,46 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the x265 video library.") (license license:expat))) +(define-public julia-xkbcommon-jll + (package + (name "julia-xkbcommon-jll") + (version "0.9.1+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/xkbcommon_jll.jl") + (commit (string-append "xkbcommon-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1g2gmd3mj1p369kzvrd02ldgr9s712vs9774v1phb59jxlshc0zc")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"xkbcommon\"") + (string-append "\"" (assoc-ref inputs "libxkbcommon") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxkbcommon" ,libxkbcommon))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libxcb-jll" ,julia-xorg-libxcb-jll) + ("julia-xorg-xkeyboard-config-jll" ,julia-xorg-xkeyboard-config-jll) + ("julia-wayland-jll" ,julia-wayland-jll) + ("julia-wayland-protocols-jll" ,julia-wayland-protocols-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/xkbcommon_jll.jl") + (synopsis "Libxkbcommon library wrappers") + (description "This package provides a wrapper for the libxkbcommon library.") + (license license:expat))) + (define-public julia-xml2-jll (package (name "julia-xml2-jll") -- cgit 1.4.1 From 47bcda6d143f862c6bc12ba71735581e854edcab Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:45:50 +0300 Subject: gnu: Add julia-xorg-xcb-util-jll. * gnu/packages/julia-jll.scm (julia-xorg-xcb-util-jll): New variable. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 3ec9ae6269..6ce998707b 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -2200,6 +2200,43 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the libXrender library.") (license license:expat))) +(define-public julia-xorg-xcb-util-jll + (package + (name "julia-xorg-xcb-util-jll") + (version "0.4.0+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_jll.jl") + (commit (string-append "Xorg_xcb_util-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0jywbxwf9x2naqsh9hh231bqpphh15v7cdhijcspjfggwkyq1npi")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_xcb_util\"") + (string-append "\"" (assoc-ref inputs "xcb-util") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("xcb-util" ,xcb-util))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libxcb-jll" ,julia-xorg-libxcb-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_jll.jl") + (synopsis "Xcb-util library wrappers") + (description "This package provides a wrapper for the xcb-util library.") + (license license:expat))) + (define-public julia-xorg-xkbcomp-jll (package (name "julia-xorg-xkbcomp-jll") -- cgit 1.4.1 From d5c186e979ac2c745588fa1d14b1202c706b43c2 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:46:29 +0300 Subject: gnu: Add julia-xorg-xcb-util-wm-jll. * gnu/packages/julia-jll.scm (julia-xorg-xcb-util-wm-jll): New variable. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 6ce998707b..1edb1c73aa 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -2237,6 +2237,43 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the xcb-util library.") (license license:expat))) +(define-public julia-xorg-xcb-util-wm-jll + (package + (name "julia-xorg-xcb-util-wm-jll") + (version "0.4.1+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_wm_jll.jl") + (commit (string-append "Xorg_xcb_util_wm-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0g6jhfb3l04lrx3cm3b8wc0pp5271dpncwin5pg94nljdj4mgj53")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_xcb_util_wm\"") + (string-append "\"" (assoc-ref inputs "xcb-util-wm") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("xcb-util-wm" ,xcb-util-wm))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-xcb-util-jll" ,julia-xorg-xcb-util-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_wm_jll.jl") + (synopsis "Xcb-util-wm library wrappers") + (description "This package provides a wrapper for the xcb-util-wm library.") + (license license:expat))) + (define-public julia-xorg-xkbcomp-jll (package (name "julia-xorg-xkbcomp-jll") -- cgit 1.4.1 From 13b118108d011362b8f0ba1957326b2c5eedd422 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:47:06 +0300 Subject: gnu: Add julia-xorg-xcb-util-image-jll. * gnu/packages/julia-jll.scm (julia-xorg-xcb-util-image-jll): New variable. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 1edb1c73aa..f05ff7e75c 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -2237,6 +2237,43 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the xcb-util library.") (license license:expat))) +(define-public julia-xorg-xcb-util-image-jll + (package + (name "julia-xorg-xcb-util-image-jll") + (version "0.4.0+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_image_jll.jl") + (commit (string-append "Xorg_xcb_util_image-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1f9xx094nylg7dcfxm0qmph4xy492rd3yxa8arijqyi6rs8zrgxz")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_xcb_util_image\"") + (string-append "\"" (assoc-ref inputs "xcb-util-image") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("xcb-util-image" ,xcb-util-image))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-xcb-util-jll" ,julia-xorg-xcb-util-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_image_jll.jl") + (synopsis "Xcb-util-image library wrappers") + (description "This package provides a wrapper for the xcb-util-image library.") + (license license:expat))) + (define-public julia-xorg-xcb-util-wm-jll (package (name "julia-xorg-xcb-util-wm-jll") -- cgit 1.4.1 From 24ad2dc77c6a7748a3b0a0c428d26db848d7b0d9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:47:39 +0300 Subject: gnu: Add julia-xorg-xcb-util-keysyms-jll. * gnu/packages/julia-jll.scm (julia-xorg-xcb-util-keysyms-jll): New variable. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index f05ff7e75c..336de41aa5 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -2274,6 +2274,43 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the xcb-util-image library.") (license license:expat))) +(define-public julia-xorg-xcb-util-keysyms-jll + (package + (name "julia-xorg-xcb-util-keysyms-jll") + (version "0.4.0+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_keysyms_jll.jl") + (commit (string-append "Xorg_xcb_util_keysyms-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "03i3fw9p16rpjnki80w4rhmaiqvjlfsr94bf9yizndqsw1lcq42l")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_xcb_util_keysyms\"") + (string-append "\"" (assoc-ref inputs "xcb-util-keysyms") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("xcb-util-keysyms" ,xcb-util-keysyms))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-xcb-util-jll" ,julia-xorg-xcb-util-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_keysyms_jll.jl") + (synopsis "Xcb-util-keysyms library wrappers") + (description "This package provides a wrapper for the xcb-util-keysyms library.") + (license license:expat))) + (define-public julia-xorg-xcb-util-wm-jll (package (name "julia-xorg-xcb-util-wm-jll") -- cgit 1.4.1 From 274fb92686781ad2d1e438a42a9427ba52befb24 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:48:10 +0300 Subject: gnu: Add julia-xorg-xcb-util-renderutil-jll. * gnu/packages/julia-jll.scm (julia-xorg-xcb-util-renderutil-jll): New variable. --- gnu/packages/julia-jll.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 336de41aa5..5ce96d1a4c 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -2311,6 +2311,43 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the xcb-util-keysyms library.") (license license:expat))) +(define-public julia-xorg-xcb-util-renderutil-jll + (package + (name "julia-xorg-xcb-util-renderutil-jll") + (version "0.3.9+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_renderutil_jll.jl") + (commit (string-append "Xorg_xcb_util_renderutil-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1zxz459sxma7cv32x2y8fnvwdz1f37fq0xhkihdsnkfdl761gn1a")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_xcb_util_renderutil\"") + (string-append "\"" (assoc-ref inputs "xcb-util-renderutil") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("xcb-util-renderutil" ,xcb-util-renderutil))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-xcb-util-jll" ,julia-xorg-xcb-util-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_renderutil_jll.jl") + (synopsis "Xcb-util-renderutil library wrappers") + (description "This package provides a wrapper for the xcb-util-renderutil library.") + (license license:expat))) + (define-public julia-xorg-xcb-util-wm-jll (package (name "julia-xorg-xcb-util-wm-jll") -- cgit 1.4.1 From 0e7925f79cf6072a2f78187af1c2169e052a69f7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:49:33 +0300 Subject: gnu: Add julia-qt5base-jll. * gnu/packages/julia-jll.scm (julia-qt5base-jll): New variable. --- gnu/packages/julia-jll.scm | 52 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 5ce96d1a4c..edf53d18ac 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -45,6 +45,7 @@ #:use-module (gnu packages maths) #:use-module (gnu packages mp3) #:use-module (gnu packages pcre) + #:use-module (gnu packages qt) #:use-module (gnu packages tls) #:use-module (gnu packages video) #:use-module (gnu packages web) @@ -1481,6 +1482,57 @@ build tree Yggdrasil.") (description "This package provides a wrapper for the pixman library.") (license license:expat))) +(define-public julia-qt5base-jll + (package + (name "julia-qt5base-jll") + (version "5.15.2+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Qt5Base_jll.jl") + (commit (string-append "Qt5Base-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1hhs316dl2jy56y2j4809vwpfj6ffbjchl1a27x44mmh9bj7vxzy")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Qt5Base\", \"" + (assoc-ref inputs "qtbase") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("qtbase" ,qtbase))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-libglvnd-jll" ,julia-libglvnd-jll) + ("julia-compilersupportlibraries-jll" ,julia-compilersupportlibraries-jll) + ("julia-fontconfig-jll" ,julia-fontconfig-jll) + ("julia-glib-jll" ,julia-glib-jll) + ("julia-openssl-jll" ,julia-openssl-jll) + ("julia-xkbcommon-jll" ,julia-xkbcommon-jll) + ("julia-xorg-libxcb-jll" ,julia-xorg-libxcb-jll) + ("julia-xorg-libxext-jll" ,julia-xorg-libxext-jll) + ("julia-xorg-xcb-util-image-jll" ,julia-xorg-xcb-util-image-jll) + ("julia-xorg-xcb-util-keysyms-jll" ,julia-xorg-xcb-util-keysyms-jll) + ("julia-xorg-xcb-util-renderutil-jll" ,julia-xorg-xcb-util-renderutil-jll) + ("julia-xorg-xcb-util-wm-jll" ,julia-xorg-xcb-util-wm-jll) + ("julia-zlib-jll" ,julia-zlib-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/Qt5Base_jll.jl") + (synopsis "Qtbase library wrappers") + (description "This package provides a wrapper for the qtbase library.") + (license license:expat))) + (define-public julia-wayland-jll (package (name "julia-wayland-jll") -- cgit 1.4.1 From ab942d5c3a1a3cafc8132f1743a9c294c47f18f7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:51:40 +0300 Subject: gnu: Add julia-plotthemes. * gnu/packages/julia-xyz.scm (julia-plotthemes): New variable. --- gnu/packages/julia-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 60e518e251..b5f09c0751 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1201,6 +1201,29 @@ algorithms, while ensuring that the most efficient implementation is used in actual computation.") (license license:expat))) +(define-public julia-plotthemes + (package + (name "julia-plotthemes") + (version "2.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaPlots/PlotThemes.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1fd27w9z1vhz0d1bzrs5vcavpb5r5jviyh27d9c4ka37phz4xvmh")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-plotutils" ,julia-plotutils) + ("julia-requires" ,julia-requires))) + (home-page "https://github.com/JuliaPlots/PlotThemes.jl") + (synopsis "Themes for the Julia plotting package Plots.jl") + (description + "PlotThemes is a package to spice up the plots made with @code{Plots.jl}.") + (license license:expat))) + (define-public julia-plotutils (package (name "julia-plotutils") -- cgit 1.4.1 From 8f856c8008bfce845cad5085265d671532ed8ed8 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:53:20 +0300 Subject: gnu: Add julia-splitapplycombine. * gnu/packages/julia-xyz.scm (julia-splitapplycombine): New variable. --- gnu/packages/julia-xyz.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index b5f09c0751..bb394b04b6 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1458,6 +1458,32 @@ cosine) integrals, eta, zeta, digamma, inverse digamma, trigamma, and polygamma functions.") (license license:expat))) +(define-public julia-splitapplycombine + (package + (name "julia-splitapplycombine") + (version "1.1.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaData/SplitApplyCombine.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1qzaqvk57b0s5krzn8bxkzmr5kz6hi9dm3jbf2sl7z4vznsgbn9x")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-dictionaries" ,julia-dictionaries) + ("julia-indexing" ,julia-indexing))) + (home-page "https://github.com/JuliaData/SplitApplyCombine.jl") + (synopsis "Split-apply-combine strategies for Julia") + (description "@code{SplitApplyCombine.jl} provides high-level, generic tools +for manipulating data - particularly focussing on data in nested containers. An +emphasis is placed on ensuring split-apply-combine strategies are easy to apply, +and work reliably for arbitrary iterables and in an optimized way with the data +structures included in Julia's standard library.") + (license license:expat))) + (define-public julia-stablerngs (package (name "julia-stablerngs") -- cgit 1.4.1 From 9d6bf9a25364ea813ddf8c85674c4df5b269e4e5 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 30 May 2021 12:55:33 +0300 Subject: gnu: Add julia-measures. * gnu/packages/julia-xyz.scm (julia-measures): New variable. --- gnu/packages/julia-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index bb394b04b6..19ba80641d 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1045,6 +1045,28 @@ that let you do deep transformations of code.") TLS} and cryptography C library for Julia.") (license license:expat))) +(define-public julia-measures + (package + (name "julia-measures") + (version "0.3.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGraphics/Measures.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0j34psrdijnqqn9zv0r2sknr1p9q0mmbjvjhmjra37bb5fh2gk8l")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaGraphics/Measures.jl") + (synopsis "Unified measure and coordinates types") + (description "This library generalizes and unifies the notion of measures +used in Compose, Compose3D, and Escher. It allows building up and representing +expressions involving differing types of units that are then evaluated, +resolving them into absolute units.") + (license license:expat))) + (define-public julia-msgpack (package (name "julia-msgpack") -- cgit 1.4.1 From 296fe37aaa062799817f19429ea51e6be75aa588 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 30 May 2021 11:59:16 +0200 Subject: gnu: vapoursynth: Make python a regular input. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This follows up on c00b1760f605255719a525e52c268b222a1f5184, although meson-build-system's lack of cross-compilation makes it theoretical. * gnu/packages/video.scm (vapoursynth)[native-inputs]: Move python from here… [inputs]: …to here. --- gnu/packages/video.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 5975004049..50ede7cc0a 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2835,11 +2835,11 @@ capabilities.") ("cython" ,python-cython) ("libtool" ,libtool) ("pkg-config" ,pkg-config) - ("python" ,python) ("yasm" ,yasm))) (inputs `(("ffmpeg" ,ffmpeg) ("libass" ,libass) + ("python" ,python) ("tesseract-ocr" ,tesseract-ocr) ("zimg" ,zimg))) (home-page "http://www.vapoursynth.com/") -- cgit 1.4.1 From d9e429894662aa54850e5d956ed250c51327f797 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sun, 30 May 2021 13:09:02 +0200 Subject: gnu: emacs-consult: Update to 0.8. * gnu/packages/emacs-xyz.scm (emacs-consult): Update to 0.8. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 2bd75c0dde..3d546240b2 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -7768,7 +7768,7 @@ style, or as multiple word prefixes.") (define-public emacs-consult (package (name "emacs-consult") - (version "0.7") + (version "0.8") (source (origin (method git-fetch) @@ -7776,7 +7776,7 @@ style, or as multiple word prefixes.") (url "https://github.com/minad/consult") (commit version))) (sha256 - (base32 "1kzwybp87srckd1238drdcn9h7jyyqz9pzcwvw3ld8bgyyrwsxkj")) + (base32 "1460818fb6y086vgn1mzmrwhpa5jswlwi4v71zr86cg6y7yg4248")) (file-name (git-file-name name version)))) (build-system emacs-build-system) (propagated-inputs -- cgit 1.4.1 From 13df9f880302291418729f0ee26e6f86fbb58b03 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sun, 30 May 2021 13:11:01 +0200 Subject: gnu: emacs-marginalia: Update to 0.6. * gnu/packages/emacs-xyz.scm (emacs-marginalia): Update to 0.6. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 3d546240b2..efdc1cdac8 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -7792,7 +7792,7 @@ list of candidates.") (define-public emacs-marginalia (package (name "emacs-marginalia") - (version "0.5") + (version "0.6") (source (origin (method git-fetch) @@ -7801,7 +7801,7 @@ list of candidates.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "07vfidgq9am07zz2ydhdifmp4jmgs9jn5l1nfqiyp16sd1br6czj")))) + (base32 "1lisns2vghmqlg8wiv6jy15cfgnc8j83khz0vfnmrjwgcmjw3bbz")))) (build-system emacs-build-system) (home-page "https://github.com/minad/marginalia") (synopsis "Marginalia in the minibuffer completions") -- cgit 1.4.1 From 3c5a58cb0b244249e6da307167eeb3acdb37878f Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sun, 30 May 2021 14:41:59 +0200 Subject: gnu: mame: Update to 0.232. * gnu/packages/emulators.scm (mame): Update to 0.232. --- gnu/packages/emulators.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index 47dae86b51..1b401e66c9 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -1630,7 +1630,7 @@ This is a part of the TiLP project.") (define-public mame (package (name "mame") - (version "0.231") + (version "0.232") (source (origin (method git-fetch) @@ -1639,7 +1639,7 @@ This is a part of the TiLP project.") (commit (apply string-append "mame" (string-split version #\.))))) (file-name (git-file-name name version)) (sha256 - (base32 "0rgch8fg8ra48wa4gl5ah70q6191sxs28x39iyalb6ballmz8v1w")) + (base32 "1v6qka8k4smah08rp62kgjmc84hwsg1iqhms0369rhdh722bgpn7")) (modules '((guix build utils))) (snippet ;; Remove bundled libraries. -- cgit 1.4.1 From 17ace33aa61a10225e24691e1d0fd1b5b9c07804 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 30 May 2021 14:49:37 +0200 Subject: gnu: axoloti-runtime: Patch firmware Makefile. * gnu/packages/axoloti.scm (axoloti-runtime)[arguments]: Patch out whitespace substitution. --- gnu/packages/axoloti.scm | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/axoloti.scm b/gnu/packages/axoloti.scm index 0b12e4fe29..c6dd748773 100644 --- a/gnu/packages/axoloti.scm +++ b/gnu/packages/axoloti.scm @@ -125,6 +125,11 @@ (("arm-none-eabi-(gcc|g\\+\\+|objcopy|objdump)" tool) (which tool))) + ;; XXX: for some reason the whitespace substitution does not + ;; work, so we disable it. + (substitute* "firmware/Makefile.patch" + (("^BDIR=.*") "BDIR=${axoloti_home}/build\n")) + ;; Hardcode full path to compiler tools (substitute* '("firmware/Makefile" "firmware/flasher/Makefile" -- cgit 1.4.1 From 32a44fb581e80b3800c6f5481c3a5046cee6d7d9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 30 May 2021 14:19:30 +0200 Subject: gnu: vapoursynth: Update to 53. * gnu/packages/video.scm (vapoursynth): Update to 53. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 50ede7cc0a..2e9f9e3267 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2806,7 +2806,7 @@ capabilities.") (define-public vapoursynth (package (name "vapoursynth") - (version "52") + (version "53") (source (origin (method git-fetch) (uri (git-reference @@ -2815,7 +2815,7 @@ capabilities.") (file-name (git-file-name name version)) (sha256 (base32 - "1krfdzc2x2vxv4nq9kiv1c09hgj525qn120ah91fw2ikq8ldvmx4")))) + "0qcsfkpkry0cmvi60khjwvfz4fqhy23nqmn4pb9qrwll26sn9dcr")))) (build-system gnu-build-system) (arguments `(#:phases -- cgit 1.4.1 From e9cbb97ac85830e195005c025a5fc07c25e471cf Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 30 May 2021 14:32:22 +0200 Subject: gnu: cryptsetup: Update to 2.3.6. * gnu/packages/cryptsetup.scm (cryptsetup): Update to 2.3.6. --- gnu/packages/cryptsetup.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cryptsetup.scm b/gnu/packages/cryptsetup.scm index 1b3da5389c..cd0a3992a7 100644 --- a/gnu/packages/cryptsetup.scm +++ b/gnu/packages/cryptsetup.scm @@ -35,7 +35,7 @@ (define-public cryptsetup (package (name "cryptsetup") - (version "2.3.5") + (version "2.3.6") (source (origin (method url-fetch) (uri (string-append "mirror://kernel.org/linux/utils/cryptsetup/v" @@ -43,7 +43,7 @@ "/cryptsetup-" version ".tar.xz")) (sha256 (base32 - "1hbhzlv4vbib1da20vnrqaikhxi7ljnchbzrv8v2a4sd8ipr9nff")))) + "0pv34l6230ba1i5p0z6zmvfqvv3as0cwn731h2qw4xm53sibg5mj")))) (build-system gnu-build-system) (arguments `(#:configure-flags -- cgit 1.4.1 From bf2a36164375654c9ccb2bf96ada3f276da6b5eb Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 30 May 2021 14:39:15 +0200 Subject: gnu: cryptsetup: Rewrite synopsis & description. * gnu/packages/cryptsetup.scm (cryptsetup)[synopsis, description]: Be more explicit about stuff. --- gnu/packages/cryptsetup.scm | 22 +++++++++++++++------- 1 file changed, 15 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cryptsetup.scm b/gnu/packages/cryptsetup.scm index cd0a3992a7..4c4633fe0b 100644 --- a/gnu/packages/cryptsetup.scm +++ b/gnu/packages/cryptsetup.scm @@ -63,14 +63,22 @@ ("lvm2" ,lvm2) ; device-mapper ("popt" ,popt) ("util-linux" ,util-linux "lib"))) ;libuuid - (synopsis "Hard disk encryption tool") + (synopsis "Set up transparent encryption of block devices using dm-crypt") (description - "LUKS (Linux Unified Key Setup)/Cryptsetup provides a standard on-disk -encryption format, which does not only facilitate compatibility among -distributions, but which also provides secure management of multiple user -passwords. In contrast to existing solutions, LUKS stores all setup necessary -setup information in the partition header, enabling the users to transport -or migrate their data seamlessly.") + "Cryptsetup is a utility used to conveniently set up disk encryption based +on the @code{dm-crypt} Linux kernel module. It is most often used to manage +LUKS volumes but also supports plain dm-crypt volumes and loop-AES, TrueCrypt +(including VeraCrypt extension), and BitLocker formats. + +@acronym{LUKS, Linux Unified Key Setup} is the standard for hard disk encryption +with the kernel Linux. It provides a standard on-disk-format compatible amongst +distributions as well as secure management of multiple user passwords. LUKS +stores all necessary setup information in the partition header to facilitate +data transport and migration. + +The package also includes the @command{veritysetup} and @command{integritysetup} +utilities to conveniently configure the @code{dm-verity} and @code{dm-integrity} +block integrity kernel modules.") (license license:gpl2) (home-page "https://gitlab.com/cryptsetup/cryptsetup"))) -- cgit 1.4.1 From d342d06630c6d6e820a465edd621931023e58446 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 30 May 2021 15:02:34 +0200 Subject: gnu: julia-plotutils: Fix typo in description. * gnu/packages/julia-xyz.scm (julia-plotutils)[description]: Fix typo. --- gnu/packages/julia-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 19ba80641d..66289a78a7 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1269,7 +1269,7 @@ actual computation.") `(("julia-stablerngs" ,julia-stablerngs))) (home-page "https://github.com/JuliaPlots/PlotUtils.jl") (synopsis "Helper algorithms for building plotting components") - (description "This package containts generic helper algorithms for building + (description "This package contains generic helper algorithms for building plotting components.") (license license:expat))) -- cgit 1.4.1 From 836f5fc4c5bfa989dbc5d8b936bd87a3763ffb12 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 30 May 2021 15:04:33 +0200 Subject: gnu: zoxide: Fix typo in synopsis. * gnu/packages/rust-apps.scm (zoxide)[synopsis]: Fix typo. --- gnu/packages/rust-apps.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm index da61b8a582..b74e09c534 100644 --- a/gnu/packages/rust-apps.scm +++ b/gnu/packages/rust-apps.scm @@ -833,7 +833,7 @@ C-compatible) software.") (("rust-assert-cmd" ,rust-assert-cmd-1) ("rust-seq-macro" ,rust-seq-macro-0.2)))) (home-page "https://github.com/ajeetdsouza/zoxide/") - (synopsis "Fast way to navigate your filesystem") + (synopsis "Fast way to navigate your file system") (description "Zoxide is a fast replacement for your @command{cd} command. It keeps track of the directories you use most frequently, and uses a ranking algorithm -- cgit 1.4.1 From 6086e6ed1a038793e358becddded50d97593f691 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 30 May 2021 15:10:42 +0200 Subject: gnu: r-benchmarkmedata: Fix typo in description. * gnu/packages/cran.scm (r-benchmarkmedata)[description]: Fix typo. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 94966e8d41..878980a230 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -367,7 +367,7 @@ for authoring journal articles and conference submissions.") ("r-tibble" ,r-tibble))) (home-page "https://github.com/csgillespie/benchmarkme-data") (synopsis "Data set for the @code{benchmarkme} package") - (description "This pacakge contains the data set for the crowd sourced + (description "This package contains the data set for the crowd-sourced benchmarks from running the @code{benchmarkme} package.") (license license:gpl2+))) -- cgit 1.4.1 From 221141ca70c3692ff505602b08e05e8fe55407f2 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 09:44:47 +0300 Subject: gnu: gnuastro: Update to 0.15. * gnu/packages/astronomy.scm (gnuastro): Update to 0.15. --- gnu/packages/astronomy.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 6d1c4ddfe6..c4a686957d 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -228,7 +228,7 @@ astronomical image-processing packages like Drizzle, Swarp or SExtractor.") (define-public gnuastro (package (name "gnuastro") - (version "0.14") + (version "0.15") (source (origin (method url-fetch) @@ -236,7 +236,7 @@ astronomical image-processing packages like Drizzle, Swarp or SExtractor.") version ".tar.lz")) (sha256 (base32 - "1xp6n42qxv0x6yigi2w2l5k8006smv27lhrcssysgsvzbydghzg5")))) + "1jjr3ixxbpsr5m4s7ahh12ymcnlvjzwcp02ya16b1lvzrz1wmhy4")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("--disable-static"))) -- cgit 1.4.1 From ad7c7b5bf62440ee05ff4da908484721d75ca545 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Mon, 31 May 2021 09:21:45 +0200 Subject: gnu: Add python-google. * gnu/packages/python-web.scm (python-google): New variable. --- gnu/packages/python-web.scm | 21 ++++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index f20f1c1f55..81cd4daea2 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2013, 2014, 2015, 2016, 2020 Andreas Enge ;;; Copyright © 2016, 2017, 2019, 2020, 2021 Marius Bakke ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus -;;; Copyright © 2017 Roel Janssen +;;; Copyright © 2017, 2021 Roel Janssen ;;; Copyright © 2016, 2017, 2020 Julien Lepiller ;;; Copyright © 2016, 2017 Nikita ;;; Copyright © 2014, 2017, 2021 Eric Bavier @@ -4298,6 +4298,25 @@ name resolutions asynchronously.") for URL parsing and changing.") (license license:asl2.0))) +(define-public python-google + (package + (name "python-google") + (version "3.0.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "google" version)) + (sha256 + (base32 + "1gncv3l11za0mpxvmpaf5n5j3jzp282rz62yml4ha4z55q930d8l")))) + (build-system python-build-system) + (arguments + `(#:tests? #f)) ; There are no tests. + (home-page "https://breakingcode.wordpress.com/") + (synopsis "Python bindings to the Google search engine") + (description "This package provides Python bindings for using the +Google search engine. Its module is called @code{googlesearch}.") + (license license:bsd-3))) + (define-public python-google-api-client (package (name "python-google-api-client") -- cgit 1.4.1 From 47f31c0afec855e3158beb7467f9f20dcae02031 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Mon, 31 May 2021 09:30:51 +0200 Subject: gnu: Add python-pyflow. * gnu/packages/python-science.scm (python-pyflow): New variable. --- gnu/packages/python-science.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 79ee7c8bb2..fdfd03d424 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2020 Pierre Langlois ;;; Copyright © 2020, 2021 Vinicius Monego ;;; Copyright © 2021 Greg Hogan +;;; Copyright © 2021 Roel Janssen ;;; ;;; This file is part of GNU Guix. ;;; @@ -439,6 +440,27 @@ doing practical, real world data analysis in Python.") "if 'NULL byte' in msg or 'line contains NUL' in msg:")) #t))))))) +(define-public python-pyflow + (package + (name "python-pyflow") + (version "1.1.20") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/Illumina/pyflow/releases/download/v" + version "/pyflow-" version ".tar.gz")) + (sha256 + (base32 + "1bvfvviw58cndyn862qnv9nj3d9cd3a0dm4vc4sd9vwq8a6z1riv")))) + (build-system python-build-system) + (arguments + `(#:tests? #f)) ; There is no test suite. + (home-page "https://illumina.github.io/pyflow/") + (synopsis "Tool to manage tasks in a task dependency graph") + (description "This package is a Python module to manage tasks in the +context of a task dependency graph. It has some similarities to make.") + (license license:bsd-2))) + (define-public python-bottleneck (package (name "python-bottleneck") -- cgit 1.4.1 From c7f023723c1de3f82a3abfa47b8366fccbd3540a Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Tue, 4 May 2021 21:03:37 +0200 Subject: gnu: yml2: Update to 2.7.0. * gnu/packages/pep.scm (yml2): Update to 2.7.0. [source]: Switch to new git repo. --- gnu/packages/pep.scm | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/pep.scm b/gnu/packages/pep.scm index 289796a377..6d24534f7e 100644 --- a/gnu/packages/pep.scm +++ b/gnu/packages/pep.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2020 Hartmut Goebel +;;; Copyright © 2016, 2020, 2021 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -40,15 +40,16 @@ (define-public yml2 (package (name "yml2") - (version "2.6.3") - (source (origin - (method hg-fetch) - (uri (hg-reference - (url "https://pep.foundation/dev/repos/yml2") - (changeset version))) - (file-name (string-append name "-" version "-checkout")) + (version "2.7.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitea.pep.foundation/fdik/yml2") + (commit version))) + (file-name (git-file-name name version)) (sha256 - (base32 "10jjjyq1mz18zkzvxd62aba00h69gd9cglisqcvb81j67ml2v1bx")))) + (base32 "0fm1x1fv4lwcpbn59s55idzf7x173n59xpz8rlrxalmi6gvsjijr")))) (build-system python-build-system) (propagated-inputs `(("python-lxml" ,python-lxml))) -- cgit 1.4.1 From 85d80283b6d14b19dacdd687590eba494da4864f Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Tue, 4 May 2021 21:03:59 +0200 Subject: gnu: pep-engine: Update to 2.1.34. * gnu/packages/pep.scm (fdik-libetpan): Update to current development version. [source]: Switch to pep.foundation. (pep-engine): Update to 2.1.34. [source]: Switch to new git repo. [arguments]: Enable release-build. [inputs]: Use normal sequoia. * gnu/packages/sequoia.scm (sequoia4pEp): Remove variable. --- gnu/packages/pep.scm | 27 ++++++++--------- gnu/packages/sequoia.scm | 75 ------------------------------------------------ 2 files changed, 14 insertions(+), 88 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/pep.scm b/gnu/packages/pep.scm index 6d24534f7e..6ee01b9df5 100644 --- a/gnu/packages/pep.scm +++ b/gnu/packages/pep.scm @@ -65,9 +65,9 @@ shell provides options to redirect the output into a pipe or a file.") (define fdik-libetpan ;; pEp Engine requires libetpan with a set of patches that have not been ;; upstreamed yet. - (let ((commit "210ba2b3b310b8b7a6ee4a4e35e50f7fa379643f") ; 2020-06-03 - (checksum "00000nij3ray7nssvq0lzb352wmnab8ffzk7dgff2c68mvjbh1l6") - (revision "5")) + (let ((commit "0b80c39dd1504462ba3a39dc53db7c960c3a63f3") ; 2020-11-27 + (checksum "0gv3ivaziadybjlf6rfpv1j5z5418243v5cvl4swlxd2njsh7gjk") + (revision "6")) (package (inherit libetpan) (name "fdik-libetpan") @@ -77,7 +77,7 @@ shell provides options to redirect the output into a pipe or a file.") (inherit (package-source libetpan)) (method git-fetch) (uri (git-reference - (url "https://github.com/fdik/libetpan") + (url "https://gitea.pep.foundation/pEp.foundation/libetpan") (commit commit))) (file-name (string-append name "-" version)) (sha256 (base32 checksum))))))) @@ -85,23 +85,24 @@ shell provides options to redirect the output into a pipe or a file.") (define-public pep-engine (package (name "pep-engine") - (version "2.0.6") + (version "2.1.34") (source (origin - (method hg-fetch) - (uri (hg-reference - (url "https://pep.foundation/dev/repos/pEpEngine") - (changeset "ebb62ba262dd"))) ;; r4721 - (file-name (string-append name "-" version "-checkout")) + (method git-fetch) + (uri (git-reference + (url "https://gitea.pep.foundation/pEp.foundation/pEpEngine") + (commit (string-append "Release_" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "0ljf79j4ng7l8w6pbdcrfzb4yk51zslypvq0n72ib1d7grqvnagi")))) + (base32 "00q96y9j985qfa382acsz02i0zf6ayq2gmg8z70jzl04isg1h3cn")))) (build-system gnu-build-system) (arguments '(#:parallel-build? #f + #:make-flags '("NDEBUG=1") ; release build #:phases (modify-phases %standard-phases (replace 'configure - ;; pEpEngie does not use autotools and configure, + ;; pEpEngine does not use autotools and configure, ;; but a local.conf. We need to tweak the values there. (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out")) @@ -132,7 +133,7 @@ OPENPGP=SEQUOIA ("libiconv" ,libiconv) ("nettle" ,nettle) ("openssl" ,openssl) - ("sequoia" ,sequoia4pEp) + ("sequoia" ,sequoia) ("sqlite3" ,sqlite) ("util-linux" ,util-linux "lib"))) ;; uuid.h (home-page "https://pep.foundation/") diff --git a/gnu/packages/sequoia.scm b/gnu/packages/sequoia.scm index c83926ef6c..2c68f43e36 100644 --- a/gnu/packages/sequoia.scm +++ b/gnu/packages/sequoia.scm @@ -218,78 +218,3 @@ several crates, providing both a low-level and a high-level API for dealing with OpenPGP data.") (license license:gpl2+))) - -(define-public sequoia4pEp - ;; Currently pEp Engine requires sequoia in not-so-current version - (package - (inherit sequoia) - (name "sequoia") - (version "0.15.0-pEp") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://gitlab.com/sequoia-pgp/sequoia.git") - (commit "0eb1b6cd846ea8c36b3dfdf01ec88383fc64f2fe"))) - (sha256 - (base32 "06dqs9whwp9lfibwp8dqm0aw4nm3s3v4jp2n4fz51zcvsld40nfh")) - (file-name (git-file-name name version)))) - (arguments - (substitute-keyword-arguments (package-arguments sequoia) - ((#:cargo-inputs _) - `(("rust-anyhow" ,rust-anyhow-1) - ("rust-base64" ,rust-base64-0.11) - ("rust-bzip2" ,rust-bzip2-0.3) - ("rust-capnp" ,rust-capnp-0.10) - ("rust-capnp-rpc" ,rust-capnp-rpc-0.10) - ("rust-chrono" ,rust-chrono-0.4) - ("rust-clap" ,rust-clap-2) - ("rust-crossterm" ,rust-crossterm-0.13) - ("rust-dirs" ,rust-dirs-2) - ("rust-flate2" ,rust-flate2-1) - ("rust-fs2" ,rust-fs2-0.4) - ("rust-futures" ,rust-futures-0.1) - ("rust-http" ,rust-http-0.1) - ("rust-hyper" ,rust-hyper-0.12) - ("rust-hyper-tls" ,rust-hyper-tls-0.3) - ("rust-idna" ,rust-idna-0.2) - ("rust-itertools" ,rust-itertools-0.8) - ("rust-lalrpop" ,rust-lalrpop-0.17) - ("rust-lalrpop-util" ,rust-lalrpop-util-0.17) - ("rust-lazy-static" ,rust-lazy-static-1) - ("rust-libc" ,rust-libc-0.2) - ("rust-memsec" ,rust-memsec-0.5) - ("rust-native-tls" ,rust-native-tls-0.2) - ("rust-nettle" ,rust-nettle-7) - ("rust-percent-encoding" ,rust-percent-encoding-2) - ("rust-prettytable-rs" ,rust-prettytable-rs-0.8) - ("rust-proc-macro2" ,rust-proc-macro2-1) - ("rust-quickcheck" ,rust-quickcheck-0.9) - ("rust-quote" ,rust-quote-1) - ("rust-rand" ,rust-rand-0.7) - ("rust-regex" ,rust-regex-1) - ("rust-rpassword" ,rust-rpassword-4) - ("rust-rusqlite" ,rust-rusqlite-0.19) - ("rust-sha2" ,rust-sha2-0.8) - ("rust-syn" ,rust-syn-1) - ("rust-tempfile" ,rust-tempfile-3) - ("rust-thiserror" ,rust-thiserror-1) - ("rust-tokio" ,rust-tokio-0.1) - ("rust-tokio-core" ,rust-tokio-core-0.1) - ("rust-tokio-io" ,rust-tokio-io-0.1) - ("rust-unicode-normalization" ,rust-unicode-normalization-0.1) - ("rust-url" ,rust-url-2) - ("rust-zbase32" ,rust-zbase32-0.1))) - ((#:cargo-development-inputs _) - `(("rust-assert-cli" ,rust-assert-cli-0.6) - ("rust-colored" ,rust-colored-1) - ("rust-filetime" ,rust-filetime-0.2))) - ((#:phases phases) - `(modify-phases ,phases - (replace 'unpin-deps - (lambda _ - (substitute* (find-files "." "Cargo.toml") - (("= \"<") "= \"") - (("= \"=") "= \"")) - #t)))))) - (properties `((hidden? . #t))))) -- cgit 1.4.1 From c178f859b5f549da5d064e628a5906d505dd75ef Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Tue, 4 May 2021 21:04:24 +0200 Subject: gnu: libpEpAdapter: Update to 2.1.21. * gnu/packages/pep.scm (libpEpAdapter): Update to 2.1.21. [source]: Swicht to new git repo. [arguments]: Enable release-build. --- gnu/packages/pep.scm | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/pep.scm b/gnu/packages/pep.scm index 6ee01b9df5..fc6f299c4e 100644 --- a/gnu/packages/pep.scm +++ b/gnu/packages/pep.scm @@ -147,20 +147,21 @@ privacy).") (define-public libpepadapter (package (name "libpepadapter") - (version "2.0.2") + (version "2.1.21") (source (origin - (method hg-fetch) - (uri (hg-reference - (url "https://pep.foundation/dev/repos/libpEpAdapter") - (changeset "e8fe371c870a"))) ;; r168 - (file-name (string-append name "-" version "-checkout")) + (method git-fetch) + (uri (git-reference + (url "https://gitea.pep.foundation/pEp.foundation/libpEpAdapter") + (commit (string-append "Release_" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "1mlpavjbnmslvmr5jxcvpjgb2x40nhmxjb10hza3kn4qzj0k1pjz")))) + (base32 "09ljj3x09y99wc47n063hpn62zi8cdvdha82rnaypvirrlga6a5w")))) (build-system gnu-build-system) (arguments '(#:test-target "test" #:tests? #f ;; building the tests fails + #:make-flags '("NDEBUG=1") ; release build #:phases (modify-phases %standard-phases (replace 'configure @@ -170,7 +171,7 @@ privacy).") (let ((out (assoc-ref outputs "out")) (engine (assoc-ref inputs "pep-engine"))) (with-output-to-file "local.conf" - (lambda _ ;() + (lambda _ (format #t " PREFIX=~a ENGINE_LIB_PATH=~a/lib -- cgit 1.4.1 From 140087faa50414d5c03f5484b6622170a23a9bcd Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Tue, 4 May 2021 21:04:47 +0200 Subject: gnu: python-pep-adapter: Update to 2.1.3. * gnu/packages/pep.scm (python-pep-adapter): Update to 2.1.3. [source]: Switch to new git repo. [arguments]{remove-wheel-requirement}: New phase. [native-inputs]: Add python-pytest and python-pytest-forked. [inputs]: Remove asn1c, add python-setuptools-scm. util-linux. --- gnu/packages/pep.scm | 34 ++++++++++++++++++++++++---------- 1 file changed, 24 insertions(+), 10 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/pep.scm b/gnu/packages/pep.scm index fc6f299c4e..a6bcea7253 100644 --- a/gnu/packages/pep.scm +++ b/gnu/packages/pep.scm @@ -26,12 +26,14 @@ #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages boost) + #:use-module (gnu packages check) #:use-module (gnu packages documentation) #:use-module (gnu packages java) #:use-module (gnu packages linux) #:use-module (gnu packages mail) ; for libetpan #:use-module (gnu packages nettle) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages python-xyz) #:use-module (gnu packages sequoia) #:use-module (gnu packages sqlite) #:use-module (gnu packages tls) @@ -189,16 +191,16 @@ ENGINE_INC_PATH=~a/include (define-public python-pep-adapter (package (name "python-pep-adapter") - (version "2.0.5") + (version "2.1.3") (source (origin - (method hg-fetch) - (uri (hg-reference - (url "https://pep.foundation/dev/repos/pEpPythonAdapter") - (changeset "66df0e5b9405"))) ;; r374 - (file-name (string-append name "-" version "-checkout")) + (method git-fetch) + (uri (git-reference + (url "https://gitea.pep.foundation/pEp.foundation/pEpPythonAdapter") + (commit version))) + (file-name (git-file-name name version)) (sha256 - (base32 "107i1s8jf8gyhpmqcs64q9csxa3fwc8g7s57iyccqb4czw8gph6d")))) + (base32 "0ssz21p1k7xx3snmd4g3ggzq565rlzdmp90l2mph6yfp1y65p39s")))) (build-system python-build-system) (arguments `(;; Adding configure-flags does not work, running `build_ext` @@ -226,12 +228,24 @@ ENGINE_INC_PATH=~a/include (string-append a "os.getenv('LIBRARY_PATH', '').split(os.pathsep)\n")) (("^(\\s+SYS_SHARES = )\\['/usr.*" _ a) (string-append a "['" (assoc-ref %build-inputs "asn1c") "/share']\n"))) + #t)) + (add-before 'build 'remove-wheel-requirement + ;; we dont't build a wheel + (lambda _ + (substitute* "setup.cfg" + ((" wheel *>= [0-9.]*") "")) + (substitute* "pyproject.toml" + (("\"wheel *>=.*\"") "")) #t))))) + (native-inputs + `(("python-pytest" ,python-pytest) + ("python-pytest-forked" ,python-pytest-forked))) (inputs - `(("asn1c" ,asn1c) - ("boost-python" ,boost-with-python3) + `(("boost-python" ,boost-with-python3) ("libpepadapter" ,libpepadapter) - ("pep-engine" ,pep-engine))) + ("pep-engine" ,pep-engine) + ("python-setuptools-scm" ,python-setuptools-scm/next) + ("util-linux" ,util-linux "lib"))) ;; uuid.h (home-page "https://pep.foundation/") (synopsis "Python adapter for p≡p (pretty Easy Privacy)") (description "The p≡p Python adapter is an adaptor interface to the p≡p -- cgit 1.4.1 From c85edf2ca47a10634faba15848cca7b4558a82ab Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Tue, 4 May 2021 21:05:30 +0200 Subject: gnu: java-pep-adapter 2.1.23. * gnu/packages/pep.scm (java-pep-adapter): Update to 2.1.23. [source]: Switch to new git repo. [arguments]: Enable release-build, use new target names. [arguments]{fix-includes}: Remove phase. {pin-shared-lib-path}: Update file paths. {build-codegen}: New phase. {install}: Use "(install)". [native-inputs]: Add graphviz. [inputs]: Fix input util-linux. --- gnu/packages/pep.scm | 46 ++++++++++++++++++++-------------------------- 1 file changed, 20 insertions(+), 26 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/pep.scm b/gnu/packages/pep.scm index a6bcea7253..aa0d786d87 100644 --- a/gnu/packages/pep.scm +++ b/gnu/packages/pep.scm @@ -20,7 +20,6 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix git-download) - #:use-module (guix hg-download) #:use-module (guix build-system gnu) #:use-module (guix build-system python) #:use-module (gnu packages) @@ -28,6 +27,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages documentation) + #:use-module (gnu packages graphviz) #:use-module (gnu packages java) #:use-module (gnu packages linux) #:use-module (gnu packages mail) ; for libetpan @@ -255,35 +255,26 @@ ENGINE_INC_PATH=~a/include (define-public java-pep-adapter (package (name "java-pep-adapter") - (version "2.0.5") + (version "2.1.23") (source (origin - (method hg-fetch) - (uri (hg-reference - (url "https://pep.foundation/dev/repos/pEpJNIAdapter") - (changeset "534537c9cd50"))) ;; r763 - (file-name (string-append name "-" version "-checkout")) + (method git-fetch) + (uri (git-reference + (url "https://gitea.pep.foundation/pEp.foundation/pEpJNIAdapter") + (commit (string-append "Release_" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "107ldpssc80bq8kndn2n000000gphj4lqagaiv3fddlfph4vji48")))) + (base32 "1sw3a5ggxcrkghvpp0a6h2lz461x55ldgfw5y4pw7c3gk5wynvjk")))) (build-system gnu-build-system) (outputs '("out" "doc")) (arguments `(#:test-target "test" - #:make-flags (list "doxy-all") + #:make-flags '("NDEBUG=1" "all" "doc") ; release build #:phases (modify-phases %standard-phases - (add-before 'configure 'fix-includes - (lambda _ - (substitute* "src/jniutils.hh" - (("#pragma once\n" line) - (string-append line - "#include \n" - "#include \n" - "#include \n"))) - #t)) (add-before 'configure 'pin-shared-lib-path (lambda* (#:key outputs #:allow-other-keys) - (substitute* "src/foundation/pEp/jniadapter/AbstractEngine.java" + (substitute* "src/java/foundation/pEp/jniadapter/AbstractEngine.java" (("System.loadLibrary\\(\"pEpJNI\"\\);") (string-append "System.load(\"" (assoc-ref outputs "out") @@ -298,7 +289,7 @@ ENGINE_INC_PATH=~a/include (libadapter (assoc-ref inputs "libpepadapter")) (openjdk (assoc-ref inputs "openjdk"))) (with-output-to-file "local.conf" - (lambda _ ;() + (lambda _ (format #t " PREFIX=~a ENGINE_LIB_PATH=~a/lib @@ -313,16 +304,18 @@ JAVA_HOME=~a (substitute* "src/Makefile" ;; suppress some warnings (("^\\s+OLD_JAVA=") " xxx_OLD_JAVA=")) #t))) + (add-before 'build 'build-codegen + ;; run codegen first to allow parallel build of other parts + (lambda _ + (invoke "make" "-C" "src" "create-dirs" "codegen"))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (libout (string-append out "/lib/")) (javaout (string-append out "/share/java/"))) - (mkdir-p libout) - (mkdir-p javaout) - (copy-file "src/libpEpJNI.so" - (string-append libout "/libpEpJNI.so")) - (copy-file "src/pEp.jar" (string-append javaout "/pEp.jar")) + (install-file "dist/libpEpJNI.a" libout) + (install-file "dist/libpEpJNI.so" libout) + (install-file "dist/pEp.jar" javaout) #t))) (add-after 'install 'install-docs (lambda* (#:key outputs #:allow-other-keys) @@ -337,13 +330,14 @@ JAVA_HOME=~a #t)))))) (native-inputs `(("doxygen" ,doxygen) + ("graphviz" ,graphviz) ("openjdk" ,openjdk9 "jdk") ("which" ,which) ("yml2" ,yml2))) (inputs `(("libpepadapter" ,libpepadapter) ("pep-engine" ,pep-engine) - ("util-linux" ,util-linux))) ;; uuid.h + ("util-linux" ,util-linux "lib"))) ;; uuid.h (home-page "https://pep.foundation/") (synopsis "Java adapter for p≡p (pretty Easy Privacy)") (description "The p≡p JNI adapter is a Java adapter interface to the p≡p -- cgit 1.4.1 From ccbf9c450e50a31081d2865aba700e823c21ef35 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 10:25:24 +0300 Subject: gnu: Add julia-dataapi. * gnu/packages/julia-xyz.scm (julia-dataapi): New variable. --- gnu/packages/julia-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 66289a78a7..dd8e2390c8 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -440,6 +440,29 @@ both the 256 color and 24 bit true color extensions, and the different text styles available to terminals.") (license license:expat))) +(define-public julia-dataapi + (package + (name "julia-dataapi") + (version "1.6.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaData/DataAPI.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "14sfvkz169zcbap3gdwpj16qsap783h86fd07flfxk822abam11w")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaData/DataAPI.jl") + (synopsis "Data-focused namespace for packages to share functions") + (description "This package provides a namespace for data-related generic +function definitions to solve the optional dependency problem; packages wishing +to share and/or extend functions can avoid depending directly on each other by +moving the function definition to DataAPI.jl and each package taking a +dependency on it.") + (license license:expat))) + (define-public julia-datastructures (package (name "julia-datastructures") -- cgit 1.4.1 From 21df298ec9195b3e6c34162002fcb08a012f24aa Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 10:51:44 +0300 Subject: gnu: Add julia-datavalueinterfaces. * gnu/packages/julia-xyz.scm (julia-datavalueinterfaces): New variable. --- gnu/packages/julia-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index dd8e2390c8..9f916b1cfc 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -487,6 +487,27 @@ including, @code{CircularBuffer}, @code{Queue}, @code{Stack}, @code{Accumulators}, @code{LinkedLists}, @code{SortedDicts} and many others.") (license license:expat))) +(define-public julia-datavalueinterfaces + (package + (name "julia-datavalueinterfaces") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/queryverse/DataValueInterfaces.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0g2wj6q7jj956nx6g7dk8x7w1c4l2xcmnr1kq5x8s8fild9kslg8")))) + (build-system julia-build-system) + (home-page "https://github.com/queryverse/DataValueInterfaces.jl") + (synopsis "Interface for DataValues.jl") + (description "This package allows a few \"forward\" definitions for the +@code{DataValues.jl} package that other packages can utilize for integration +without having to take direct dependencies.") + (license license:expat))) + (define-public julia-dictionaries (package (name "julia-dictionaries") -- cgit 1.4.1 From 43f26eaeaa50b75907fe390180acba5ed60c30b1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 10:54:06 +0300 Subject: gnu: Add julia-iteratorinterfaceextensions. * gnu/packages/julia-xyz.scm (julia-iteratorinterfaceextensions): New variable. --- gnu/packages/julia-xyz.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 9f916b1cfc..f5797f632b 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1013,6 +1013,26 @@ external IRs. It can be used with Julia metaprogramming tools such as Cassette.") (license license:expat))) +(define-public julia-iteratorinterfaceextensions + (package + (name "julia-iteratorinterfaceextensions") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/queryverse/IteratorInterfaceExtensions.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1slpay1dhja8f9gy6z7b3psgvgcknn963dvfqqakvg1grk9ppa09")))) + (build-system julia-build-system) + (home-page "https://github.com/queryverse/IteratorInterfaceExtensions.jl") + (synopsis "Traits for Julia iterators") + (description "IteratorInterfaceExtensions defines a small number of +extensions to the iterator interface.") + (license license:expat))) + (define-public julia-json (package (name "julia-json") -- cgit 1.4.1 From 3f40ba72c6437b56f7bdced8d7c419dc14b990cf Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 10:54:58 +0300 Subject: gnu: Add julia-tabletraits. * gnu/packages/julia-xyz.scm (julia-tabletraits): New variable. --- gnu/packages/julia-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index f5797f632b..f13f2aa399 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1683,6 +1683,27 @@ extensions. It is intended to be the base both for @code{TableIO.jl} and for the @code{Pluto.jl} tabular data import functionality.") (license license:expat))) +(define-public julia-tabletraits + (package + (name "julia-tabletraits") + (version "1.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/queryverse/TableTraits.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "08ssb2630wm6j8f2qa985mn2vfibfm5kjcn4ayl2qkhfcyp8daw4")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-iteratorinterfaceextensions" ,julia-iteratorinterfaceextensions))) + (home-page "https://github.com/queryverse/TableTraits.jl") + (synopsis "Traits for Julia tables") + (description "TableTraits defines a generic interface for tabular data.") + (license license:expat))) + (define-public julia-unpack (package (name "julia-unpack") -- cgit 1.4.1 From e886181bb6c1b94c5fe5f79cb011de76a5c76951 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 10:58:00 +0300 Subject: gnu: Add julia-datavalues. * gnu/packages/julia-xyz.scm (julia-datavalues): New variable. --- gnu/packages/julia-xyz.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index f13f2aa399..d8cf906d7e 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -508,6 +508,39 @@ including, @code{CircularBuffer}, @code{Queue}, @code{Stack}, without having to take direct dependencies.") (license license:expat))) +(define-public julia-datavalues + (package + (name "julia-datavalues") + (version "0.4.13") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/queryverse/DataValues.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "15j3hrqq6nazn533bfsvg32xznacbzsl303j1qs48av59ppnvhhv")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'skip-known-failing-tests + (lambda _ + ;; See upstream report: + ;; https://github.com/queryverse/DataValues.jl/issues/83 + (substitute* "test/array/test_reduce.jl" + ((".*DataValue\\(mapreduce.*") "") + ((".*DataValue\\(method\\(f.*") "")) + #t))))) + (propagated-inputs + `(("julia-datavalueinterfaces" ,julia-datavalueinterfaces))) + (home-page "https://github.com/queryverse/DataValues.jl") + (synopsis "Missing values for Julia") + (description "This package provides the type @code{DataValue} that is used +to represent missing data.") + (license license:expat))) + (define-public julia-dictionaries (package (name "julia-dictionaries") -- cgit 1.4.1 From a61e13f7776040e860740bb36c8dda64456e9107 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 11:01:59 +0300 Subject: gnu: Add julia-tableshowutils. * gnu/packages/julia-xyz.scm (julia-tableshowutils): New variable. --- gnu/packages/julia-xyz.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index d8cf906d7e..648dd204f8 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1716,6 +1716,33 @@ extensions. It is intended to be the base both for @code{TableIO.jl} and for the @code{Pluto.jl} tabular data import functionality.") (license license:expat))) +(define-public julia-tableshowutils + ;; The 0.2.5 release is not fully compatable with newer versions of Julia. + (let ((commit "c4e02d8b9bbb31fc81ed6618955e9b1c7cb04460") + (revision "1")) + (package + (name "julia-tableshowutils") + (version "0.2.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/queryverse/TableShowUtils.jl") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0gp3hpj3jvzfhkp9r345vfic2j2n2s60729wv38hwn75csp74cg5")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-datavalues" ,julia-datavalues) + ("julia-json" ,julia-json))) + (home-page "https://github.com/queryverse/TableShowUtils.jl") + (synopsis "Implement show for TableTraits.jl types") + (description "This package provides some common helper functions that make +it easier to implement various @code{Base.show} functions for types that +participate in the @code{TableTraits.jl} ecosystem.") + (license license:expat)))) + (define-public julia-tabletraits (package (name "julia-tabletraits") -- cgit 1.4.1 From 209a80c109b8ec742cef12c69e1a6a6943b3570e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 11:02:54 +0300 Subject: gnu: Add julia-queryoperators. * gnu/packages/julia-xyz.scm (julia-queryoperators): New variable. --- gnu/packages/julia-xyz.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 648dd204f8..0aaa7cd1e0 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1370,6 +1370,30 @@ actual computation.") plotting components.") (license license:expat))) +(define-public julia-queryoperators + (package + (name "julia-queryoperators") + (version "0.9.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/queryverse/QueryOperators.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "06zm4cbn3x49lbpgshhdfvvmgz066qkc8q0d57igm5p8bcp6js22")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-datastructures" ,julia-datastructures) + ("julia-iteratorinterfaceextensions" ,julia-iteratorinterfaceextensions) + ("julia-tableshowutils" ,julia-tableshowutils))) + (home-page "https://github.com/queryverse/QueryOperators.jl") + (synopsis "Query operators for Julia") + (description "This package contains the underlying query operators that are +exposed to users in @code{Query.jl}.") + (license license:expat))) + (define-public julia-recipesbase (package (name "julia-recipesbase") -- cgit 1.4.1 From db2bfcb90d83324f33cfa6c224bfe504decf9056 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 11:08:00 +0300 Subject: gnu: Add julia-missings. * gnu/packages/julia-xyz.scm (julia-missings): New variable. --- gnu/packages/julia-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 0aaa7cd1e0..d262460f79 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1164,6 +1164,28 @@ expressions involving differing types of units that are then evaluated, resolving them into absolute units.") (license license:expat))) +(define-public julia-missings + (package + (name "julia-missings") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaData/Missings.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "131ma44yvswvj85jdjhm37frzfz46cc60lwj65a9jcmgc77dshsm")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-dataapi" ,julia-dataapi))) + (home-page "https://github.com/JuliaData/Missings.jl") + (synopsis "Additional missing value support for Julia") + (description "This package provides additional functionality for working +with @code{missing} values in Julia.") + (license license:expat))) + (define-public julia-msgpack (package (name "julia-msgpack") -- cgit 1.4.1 From 2bd2406cd902a9ef4715269e12ddb551f9255b41 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 11:09:02 +0300 Subject: gnu: Add julia-tables. * gnu/packages/julia-xyz.scm (julia-tables): New variable. --- gnu/packages/julia-xyz.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index d262460f79..cfa6b5ef43 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1762,6 +1762,34 @@ extensions. It is intended to be the base both for @code{TableIO.jl} and for the @code{Pluto.jl} tabular data import functionality.") (license license:expat))) +(define-public julia-tables + (package + (name "julia-tables") + (version "1.4.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaData/Tables.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0yfjl4v1vglsk9wr7gbqgya4kk3a0q0i6zhi9xdgvnqsqzqrsc7c")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-dataapi" ,julia-dataapi) + ("julia-datavalueinterfaces" ,julia-datavalueinterfaces) + ("julia-iteratorinterfaceextensions" ,julia-iteratorinterfaceextensions) + ("julia-tabletraits" ,julia-tabletraits))) + (native-inputs + `(("julia-datavalues" ,julia-datavalues) + ("julia-queryoperators" ,julia-queryoperators))) + (home-page "https://github.com/JuliaData/Tables.jl") + (synopsis "Interface for tables in Julia") + (description "The @code{Tables.jl} package provides simple, yet powerful +interface functions for working with all kinds tabular data.") + (license license:expat))) + (define-public julia-tableshowutils ;; The 0.2.5 release is not fully compatable with newer versions of Julia. (let ((commit "c4e02d8b9bbb31fc81ed6618955e9b1c7cb04460") -- cgit 1.4.1 From f7f1efeaa78d157562eda3cfb1d1cd1e2d98153a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 11:12:41 +0300 Subject: gnu: Add julia-statsapi. * gnu/packages/julia-xyz.scm (julia-statsapi): New variable. --- gnu/packages/julia-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index cfa6b5ef43..9d43ffb8af 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1721,6 +1721,29 @@ statically sized arrays in Julia, using the abstract type linear algebra operations.") (license license:expat))) +(define-public julia-statsapi + (package + (name "julia-statsapi") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaStats/StatsAPI.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1k1c3s7i5wzkz4r9fyy4gd7wb97p0qgbc7bmaajm16zqipfmy2bv")))) + (build-system julia-build-system) + (home-page "https://juliastats.org/") + (synopsis "Statistics-focused namespace for packages to share functions") + (description "This package provides a namespace for data-related generic +function definitions to solve the optional dependency problem; packages wishing +to share and/or extend functions can avoid depending directly on each other by +moving the function definition to @code{StatsAPI.jl} and each package taking a +dependency on it.") + (license license:expat))) + (define-public julia-suppressor (package (name "julia-suppressor") -- cgit 1.4.1 From 6dd2634da42ae61120015e98879d4f7bc8a4b7bb Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 11:18:45 +0300 Subject: gnu: Add julia-arraylayouts. * gnu/packages/julia-xyz.scm (julia-arraylayouts): New variable. --- gnu/packages/julia-xyz.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 9d43ffb8af..bb8854acb1 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -115,6 +115,30 @@ be GPU compatible without throwing away the wrapper.") provides functions to run a few automatable checks for Julia packages.") (license license:expat))) +(define-public julia-arraylayouts + (package + (name "julia-arraylayouts") + (version "0.7.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaMatrices/ArrayLayouts.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "01725v4jp8h8zwn85splw907r206h1hnp205pchmzjin7h4659xz")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-fillarrays" ,julia-fillarrays))) + (home-page "https://github.com/JuliaMatrices/ArrayLayouts.jl") + (synopsis "Array layouts and general fast linear algebra") + (description "This package implements a trait-based framework for describing +array layouts such as column major, row major, etc. that can be dispatched to +appropriate BLAS or optimised Julia linear algebra routines. This supports a +much wider class of matrix types than Julia's in-built @code{StridedArray}.") + (license license:expat))) + (define-public julia-benchmarktools (package (name "julia-benchmarktools") -- cgit 1.4.1 From fa945a540cb2a36a63d50b349a9ea697bf4b8340 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 11:20:27 +0300 Subject: gnu: Add julia-matrixfactorizations. * gnu/packages/julia-xyz.scm (julia-matrixfactorizations): New variable. --- gnu/packages/julia-xyz.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index bb8854acb1..8fe4f8bac1 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1136,6 +1136,41 @@ expressions. This includes a template-matching system and code-walking tools that let you do deep transformations of code.") (license license:expat))) +(define-public julia-matrixfactorizations + (package + (name "julia-matrixfactorizations") + (version "0.8.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaMatrices/MatrixFactorizations.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "14c6w1vhyf4pi4454pdp6ryczsxn9pgjg99fg9bkdj03xg5fsxb8")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'skip-failing-test + (lambda _ + ;; Tests with math functions are hard. + (substitute* "test/test_ul.jl" + (("@test @inferred\\(logdet") "@test @test_nowarn(logdet") + ;; Also skip the REPL test. + (("test String") "test_nowarn String")) + #t))))) + (propagated-inputs + `(("julia-arraylayouts" ,julia-arraylayouts))) + (home-page "https://github.com/JuliaMatrices/MatrixFactorizations.jl") + (synopsis "Julia package to contain non-standard matrix factorizations") + (description "A Julia package to contain non-standard matrix factorizations. +At the moment it implements the QL, RQ, and UL factorizations, a combined +Cholesky factorization with inverse, and polar decompositions. In the future it +may include other factorizations such as the LQ factorization.") + (license license:expat))) + (define-public julia-mbedtls (package (name "julia-mbedtls") -- cgit 1.4.1 From 2615a8bad5171d5802067ee98b00472f6a71c57a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 11:25:06 +0300 Subject: gnu: Add julia-optimtestproblems. * gnu/packages/julia-xyz.scm (julia-optimtestproblems): New variable. --- gnu/packages/julia-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 8fe4f8bac1..9676466527 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1285,6 +1285,28 @@ Julia, with type-driven, overloadable packing/unpacking functionality.") @code{NaN} instead of throwing a @code{DomainError}.") (license license:expat))) +(define-public julia-optimtestproblems + (package + (name "julia-optimtestproblems") + (version "2.0.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaNLSolvers/OptimTestProblems.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "10h47x5ws42pkqjccimaz0yxfvz41w0yazq6inamfk4lg5g2g3d9")))) + (build-system julia-build-system) + (arguments + `(#:julia-package-name "OptimTestProblems")) + (home-page "https://github.com/JuliaNLSolvers/OptimTestProblems.jl") + (synopsis "Collection of optimization test problems") + (description "The purpose of this package is to provide test problems for +JuliaNLSolvers packages.") + (license license:expat))) + (define-public julia-orderedcollections (package (name "julia-orderedcollections") -- cgit 1.4.1 From 73b6f78c98405797aa85e884df4a17d4cf195ce9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 11:31:50 +0300 Subject: gnu: Add julia-exprtools. * gnu/packages/julia-xyz.scm (julia-exprtools): New variable. --- gnu/packages/julia-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 9676466527..aeccbf3353 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -697,6 +697,27 @@ stressing the robustness of differentiation tools.") (description "This package provides various examples.") (license license:expat)))) +(define-public julia-exprtools + (package + (name "julia-exprtools") + (version "0.1.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/invenia/ExprTools.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1lwxi9fx9farf1jdv42gv43xs3f3i3js2xnvr5gf6d0xfx0g6b6a")))) + (build-system julia-build-system) + (home-page "https://github.com/invenia/ExprTools.jl") + (synopsis "Light-weight expression manipulation tools") + (description "@code{ExprTools} provides tooling for working with Julia +expressions during metaprogramming. This package aims to provide light-weight +performant tooling without requiring additional package dependencies.") + (license license:expat))) + (define-public julia-ffmpeg (package (name "julia-ffmpeg") -- cgit 1.4.1 From f273a4b799e5cb3976785f2ea3e8a36074dc6724 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 11:35:34 +0300 Subject: gnu: Add julia-mocking. * gnu/packages/julia-xyz.scm (julia-mocking): New variable. --- gnu/packages/julia-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index aeccbf3353..51bd9241b0 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1266,6 +1266,28 @@ resolving them into absolute units.") with @code{missing} values in Julia.") (license license:expat))) +(define-public julia-mocking + (package + (name "julia-mocking") + (version "0.7.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/invenia/Mocking.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "10jz716v6i3gpd403rmcrip6cncjl9lqr12cdl321x1994a5g8ck")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-exprtools" ,julia-exprtools))) + (home-page "https://github.com/invenia/Mocking.jl") + (synopsis "Overload Julia function calls") + (description "The purpose of this package is to allow Julia function calls +to be temporarily overloaded for the purpose of testing.") + (license license:expat))) + (define-public julia-msgpack (package (name "julia-msgpack") -- cgit 1.4.1 From 277fef2026024c90518e0eff12a06b9593782f40 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 11:48:36 +0300 Subject: gnu: Add julia-quadmath. * gnu/packages/julia-xyz.scm (julia-quadmath): New variable. --- gnu/packages/julia-xyz.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 51bd9241b0..33f597ca3f 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -23,6 +23,7 @@ #:use-module (guix packages) #:use-module (guix git-download) #:use-module (guix build-system julia) + #:use-module (gnu packages gcc) #:use-module (gnu packages julia-jll)) (define-public julia-abstractffts @@ -1516,6 +1517,43 @@ actual computation.") plotting components.") (license license:expat))) +(define-public julia-quadmath + (package + (name "julia-quadmath") + (version "0.5.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaMath/Quadmath.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "051biw4b9zni7cmh2f1yzifp1v8wazlfxrdz4p44lyd1wba6379w")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'hardcode-libmath-location + (lambda* (#:key inputs #:allow-other-keys) + (let ((gcclib (assoc-ref inputs "gcc:lib"))) + (substitute* "src/Quadmath.jl" + (("libgcc_s.so.1" lib) (string-append gcclib "/lib/" lib)) + (("libquadmath.so.0" lib) (string-append gcclib "/lib/" lib))) + #t)))))) + (propagated-inputs + `(("julia-requires" ,julia-requires))) + (inputs + `(("gcc:lib" ,gcc "lib"))) + (native-inputs + `(("julia-specialfunctions" ,julia-specialfunctions))) + (home-page "https://github.com/JuliaMath/Quadmath.jl") + (synopsis "Float128 and libquadmath for the Julia language") + (description "This is a Julia interface to @code{libquadmath}, providing a +@code{Float128} type corresponding to the IEEE754 binary128 floating point +format.") + (license license:expat))) + (define-public julia-queryoperators (package (name "julia-queryoperators") -- cgit 1.4.1 From 6a2d36c734a5c5ab7e1826ce9372f680c0fe772d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 12:07:54 +0300 Subject: gnu: Add julia-tensorcore. * gnu/packages/julia-xyz.scm (julia-tensorcore): New variable. --- gnu/packages/julia-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 33f597ca3f..c802c2b0c5 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -2023,6 +2023,29 @@ participate in the @code{TableTraits.jl} ecosystem.") (description "TableTraits defines a generic interface for tabular data.") (license license:expat))) +(define-public julia-tensorcore + (package + (name "julia-tensorcore") + (version "0.1.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaMath/TensorCore.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1sy3in4a1rl3l2vk0cm9mzg2nkva7syhr7i35si0kbzhkdwpbqjy")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaMath/TensorCore.jl") + (synopsis "Tensor-algebra definitions") + (description "This package is intended as a lightweight foundation for +tensor operations across the Julia ecosystem. Currently it exports three +operations: @acronym{hadamard, elementwise multiplication}, @acronym{tensor, +product preserves all dimensions}, and @acronym{boxdot, contracts neighboring +dimensions}.") + (license license:expat))) + (define-public julia-unpack (package (name "julia-unpack") -- cgit 1.4.1 From ea03851b019b699d1f48d39cfd7e681d9fbd3991 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 12:22:58 +0300 Subject: gnu: Add julia-mappedarrays. * gnu/packages/julia-xyz.scm (julia-mappedarrays): New variable. --- gnu/packages/julia-xyz.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index c802c2b0c5..553dbfca7b 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1158,6 +1158,36 @@ expressions. This includes a template-matching system and code-walking tools that let you do deep transformations of code.") (license license:expat))) +(define-public julia-mappedarrays + (package + (name "julia-mappedarrays") + (version "0.4.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaArrays/MappedArrays.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0l5adird8m1cmnsxwhzi5hcr7q9bm1rf7a6018zc7kcn2yxdshy3")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-fixedpointnumbers" ,julia-fixedpointnumbers))) + (native-inputs + `(("julia-colortypes" ,julia-colortypes) + ("julia-fixedpointnumbers" ,julia-fixedpointnumbers) + ("julia-offsetarrays" ,julia-offsetarrays))) + (home-page "https://github.com/JuliaArrays/MappedArrays.jl") + (synopsis "Lazy in-place transformations of arrays") + (description "This package implements \"lazy\" in-place elementwise +transformations of arrays for the Julia programming language. Explicitly, it +provides a \"view\" M of an array A so that @code{M[i] = f(A[i])} for a +specified (but arbitrary) function f, without ever having to compute M +explicitly (in the sense of allocating storage for M). The name of the package +comes from the fact that @code{M == map(f, A)}.") + (license license:expat))) + (define-public julia-matrixfactorizations (package (name "julia-matrixfactorizations") -- cgit 1.4.1 From 2262f7991764477ab330e570defa3847952bdf32 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 12:36:16 +0300 Subject: gnu: Add julia-graphics. * gnu/packages/julia-xyz.scm (julia-graphics): New variable. --- gnu/packages/julia-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 553dbfca7b..bc4c1db5dc 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -880,6 +880,29 @@ differentiation (AD).") "FuzzyCompletions provides fuzzy completions for a Julia runtime session.") (license license:expat))) +(define-public julia-graphics + (package + (name "julia-graphics") + (version "1.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGraphics/Graphics.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "10h1s09v7qkvrjr6l678zamb1p248n8jv4rrwkf8g7d2bpfz9amn")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-colors" ,julia-colors) + ("julia-nanmath" ,julia-nanmath))) + (home-page "https://github.com/JuliaGraphics/Graphics.jl") + (synopsis "Base graphics in Julia") + (description "@code{Graphics.jl} is an abstraction layer for graphical +operations in Julia.") + (license license:expat))) + (define-public julia-gumbo (package (name "julia-gumbo") -- cgit 1.4.1 From a33695945c9d762b0a5568cbfb18274736d36186 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 12:39:25 +0300 Subject: gnu: Add julia-rangearrays. * gnu/packages/julia-xyz.scm (julia-rangearrays): New variable. --- gnu/packages/julia-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index bc4c1db5dc..71f2019ec8 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1631,6 +1631,27 @@ format.") exposed to users in @code{Query.jl}.") (license license:expat))) +(define-public julia-rangearrays + (package + (name "julia-rangearrays") + (version "0.3.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaArrays/RangeArrays.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1ihzfyfq1xihkjcvn7xmzfbn6igzidb4fkzdcxwfr5qkvi52gnmg")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaArrays/RangeArrays.jl") + (synopsis "Array data structures with autogenerated columns") + (description "The goal of RangeArrays is to provide efficient and convenient +array data structures where the columns of the arrays are generated (on the fly) +by Ranges.") + (license license:expat))) + (define-public julia-recipesbase (package (name "julia-recipesbase") -- cgit 1.4.1 From 4541cda7d76b8fdea39b2abfda283e1e392d12fd Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 12:43:32 +0300 Subject: gnu: Add julia-indirectarrays. * gnu/packages/julia-xyz.scm (julia-indirectarrays): New variable. --- gnu/packages/julia-xyz.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 71f2019ec8..82e7be95ab 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1025,6 +1025,33 @@ out of dictionaries, tuples, etc, extending this ability beyond @code{AbstractArray}.") (license license:expat))) +(define-public julia-indirectarrays + (package + (name "julia-indirectarrays") + (version "0.5.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaArrays/IndirectArrays.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0l0jq0jnr9z3k431ni82xycq7mqapgxrbrx4yyk6lycvi41ipm4s")))) + (build-system julia-build-system) + (native-inputs + `(("julia-colors" ,julia-colors) + ("julia-fixedpointnumbers" ,julia-fixedpointnumbers) + ("julia-mappedarrays" ,julia-mappedarrays))) + (home-page "https://github.com/JuliaArrays/IndirectArrays.jl") + (synopsis "Julia implementation of indexed arrays") + (description "An @code{IndirectArray} is one that encodes data using a +combination of an @code{index} and a @code{value} table. Each element is +assigned its own index, which is used to retrieve the value from the +@code{value} table. Among other uses, @code{IndirectArrays} can represent +indexed images, sometimes called \"colormap images\" or \"paletted images.\"") + (license license:expat))) + (define-public julia-inifile (package (name "julia-inifile") -- cgit 1.4.1 From 9f92c8b51f099d90b1e1d834298319e17b04d829 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 12:45:30 +0300 Subject: gnu: Add julia-pooledarrays. * gnu/packages/julia-xyz.scm (julia-pooledarrays): New variable. --- gnu/packages/julia-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 82e7be95ab..35c3e416f1 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1597,6 +1597,28 @@ actual computation.") plotting components.") (license license:expat))) +(define-public julia-pooledarrays + (package + (name "julia-pooledarrays") + (version "1.2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaData/PooledArrays.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ihvhzkxdw4qf0i6sbrickhdcwkmlin9zyixxn9xvgzm8nc0iwqy")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-dataapi" ,julia-dataapi))) + (home-page "https://github.com/JuliaData/PooledArrays.jl") + (synopsis "Pooled representation of arrays in Julia") + (description "This package provides a pooled representation of arrays for +purposes of compression when there are few unique elements.") + (license license:expat))) + (define-public julia-quadmath (package (name "julia-quadmath") -- cgit 1.4.1 From f34f8a3d22fc522ea9f9dccd4a96c390f7e17863 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 12:46:20 +0300 Subject: gnu: Add julia-weakrefstrings. * gnu/packages/julia-xyz.scm (julia-weakrefstrings): New variable. --- gnu/packages/julia-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 35c3e416f1..d0b1617815 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -2270,6 +2270,28 @@ useful in order to support @code{VersionNumber} comparisons applied to \"foreign\" version numbers from external packages.") (license license:expat))) +(define-public julia-weakrefstrings + (package + (name "julia-weakrefstrings") + (version "0.6.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaData/WeakRefStrings.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0129mf1axxycb1ans3idlvw8ch0hmdrl80q98jw63f99zz3ddipr")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-dataapi" ,julia-dataapi))) + (home-page "https://github.com/JuliaData/WeakRefStrings.jl") + (synopsis "Efficient string representation and transfer in Julia") + (description "This package provides a minimal String type for Julia that +allows for efficient string representation and transfer") + (license license:expat))) + (define-public julia-zipfile (package (name "julia-zipfile") -- cgit 1.4.1 From adedfd077381fb6ef370ed00baf5a8cc582ef101 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 12:47:02 +0300 Subject: gnu: Add julia-typedtables. * gnu/packages/julia-xyz.scm (julia-typedtables): New variable. --- gnu/packages/julia-xyz.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index d0b1617815..da3a61f12f 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -2169,6 +2169,32 @@ product preserves all dimensions}, and @acronym{boxdot, contracts neighboring dimensions}.") (license license:expat))) +(define-public julia-typedtables + (package + (name "julia-typedtables") + (version "1.2.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaData/TypedTables.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "06k5h7ybsh29b6kiy0p62rp9b2q3xi9jk8p9wf0kq907p5kvfnfy")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-adapt" ,julia-adapt) + ("julia-splitapplycombine" ,julia-splitapplycombine) + ("julia-tables" ,julia-tables))) + (home-page "https://github.com/JuliaData/TypedTables.jl") + (synopsis "Column-based storage for data analysis in Julia") + (description "@code{TypedTables.jl} provides two column-based storage +containers: @code{Table} and @code{FlexTable}, both of which represent an array +of @code{NamedTuples}. This package is designed to be lightweight, easy-to-use +and fast, and presents a very minimal new interface to learn.") + (license license:expat))) + (define-public julia-unpack (package (name "julia-unpack") -- cgit 1.4.1 From 9bb2e649a66271f00756143c2a07015e83f471b3 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 12:47:57 +0300 Subject: gnu: Add julia-formatting. * gnu/packages/julia-xyz.scm (julia-formatting): New variable. --- gnu/packages/julia-xyz.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index da3a61f12f..53bd0e0b64 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -828,6 +828,26 @@ scaled by a constant factor. Consequently, they have a fixed number of digits (bits) after the decimal (radix) point.") (license license:expat))) +(define-public julia-formatting + (package + (name "julia-formatting") + (version "0.4.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaIO/Formatting.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ma3q9my51rr38bb5712xkc4h3rq0wsfjb4ac6mdh9ywn8rqvrmh")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaIO/Formatting.jl") + (synopsis "Julia package to provide Python-like formatting support") + (description "This package offers Python-style general formatting and +c-style numerical formatting.") + (license license:expat))) + (define-public julia-forwarddiff (package (name "julia-forwarddiff") -- cgit 1.4.1 From d2d1f8bfae5bd8b60178141a7199189356fd892e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 31 May 2021 12:48:45 +0300 Subject: gnu: Add julia-prettytables. * gnu/packages/julia-xyz.scm (julia-prettytables): New variable. --- gnu/packages/julia-xyz.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 53bd0e0b64..816ca9c85b 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1639,6 +1639,39 @@ plotting components.") purposes of compression when there are few unique elements.") (license license:expat))) +(define-public julia-prettytables + (package + (name "julia-prettytables") + (version "1.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ronisbr/PrettyTables.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1d1sd87kkwbar3l608h0adzws42cwdrmp1idxx7an6mfqcsdrijw")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'skip-color-tests + (lambda _ + (substitute* "test/text_backend.jl" + ((".*colors\\.jl.*") "")) + #t))))) + (propagated-inputs + `(("julia-crayons" ,julia-crayons) + ("julia-formatting" ,julia-formatting) + ("julia-reexport" ,julia-reexport) + ("julia-tables" ,julia-tables))) + (home-page "https://github.com/ronisbr/PrettyTables.jl") + (synopsis "Print data in formatted tables") + (description "This package has the purpose to print data in matrices in a +human-readable format.") + (license license:expat))) + (define-public julia-quadmath (package (name "julia-quadmath") -- cgit 1.4.1 From ca1a015777565f1098d56ac3b5873226e50c067d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:33 +0200 Subject: gnu: r-genomicalignments: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-genomicalignments): Move from here... * gnu/packages/bioconductor.scm (r-genomicalignments): ...to here. --- gnu/packages/bioconductor.scm | 35 ++++++++++++++++++++++++++++++++++- gnu/packages/bioinformatics.scm | 33 --------------------------------- 2 files changed, 34 insertions(+), 34 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b58c5bc11f..eef0811d4e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft @@ -2280,6 +2280,39 @@ translation between different chromosome sequence naming conventions (e.g., names in their natural, rather than lexicographic, order.") (license license:artistic2.0))) +(define-public r-genomicalignments + (package + (name "r-genomicalignments") + (version "1.26.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicAlignments" version)) + (sha256 + (base32 + "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr")))) + (properties + `((upstream-name . "GenomicAlignments"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/GenomicAlignments") + (synopsis "Representation and manipulation of short genomic alignments") + (description + "This package provides efficient containers for storing and manipulating +short genomic alignments (typically obtained by aligning short reads to a +reference genome). This includes read counting, computing the coverage, +junction detection, and working with the nucleotide content of the +alignments.") + (license license:artistic2.0))) + (define-public r-genomicranges (package (name "r-genomicranges") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2a7443314a..ba284759a0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7952,39 +7952,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomicalignments - (package - (name "r-genomicalignments") - (version "1.26.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "GenomicAlignments" version)) - (sha256 - (base32 - "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr")))) - (properties - `((upstream-name . "GenomicAlignments"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (home-page "https://bioconductor.org/packages/GenomicAlignments") - (synopsis "Representation and manipulation of short genomic alignments") - (description - "This package provides efficient containers for storing and manipulating -short genomic alignments (typically obtained by aligning short reads to a -reference genome). This includes read counting, computing the coverage, -junction detection, and working with the nucleotide content of the -alignments.") - (license license:artistic2.0))) - (define-public r-rtracklayer (package (name "r-rtracklayer") -- cgit 1.4.1 From a88230a1bc332ee41eb1e0080f020e0178f78d5a Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:34 +0200 Subject: gnu: r-rtracklayer: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-rtracklayer): Move from here... * gnu/packages/bioconductor.scm (r-rtracklayer): ...to here. --- gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 48 ----------------------------------------- 2 files changed, 48 insertions(+), 48 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eef0811d4e..2b3c232d53 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2590,6 +2590,54 @@ Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.") (license license:expat))) +(define-public r-rtracklayer + (package + (name "r-rtracklayer") + (version "1.50.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "rtracklayer" version)) + (sha256 + (base32 + "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-zlib + (lambda _ + (substitute* "DESCRIPTION" + ((" zlibbioc,") "")) + (substitute* "NAMESPACE" + (("import\\(zlibbioc\\)") "")) + #t))))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcurl" ,r-rcurl) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-xml" ,r-xml) + ("r-xvector" ,r-xvector) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/rtracklayer") + (synopsis "R interface to genome browsers and their annotation tracks") + (description + "rtracklayer is an extensible framework for interacting with multiple +genome browsers (currently UCSC built-in) and manipulating annotation tracks +in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit +built-in). The user may export/import tracks to/from the supported browsers, +as well as query and modify the browser state, such as the current viewport.") + (license license:artistic2.0))) + (define-public r-shortread (package (name "r-shortread") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ba284759a0..f9d2d125bf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7952,54 +7952,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-rtracklayer - (package - (name "r-rtracklayer") - (version "1.50.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "rtracklayer" version)) - (sha256 - (base32 - "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8")))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-system-zlib - (lambda _ - (substitute* "DESCRIPTION" - ((" zlibbioc,") "")) - (substitute* "NAMESPACE" - (("import\\(zlibbioc\\)") "")) - #t))))) - (native-inputs - `(("pkg-config" ,pkg-config))) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) - (home-page "https://bioconductor.org/packages/rtracklayer") - (synopsis "R interface to genome browsers and their annotation tracks") - (description - "rtracklayer is an extensible framework for interacting with multiple -genome browsers (currently UCSC built-in) and manipulating annotation tracks -in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit -built-in). The user may export/import tracks to/from the supported browsers, -as well as query and modify the browser state, such as the current viewport.") - (license license:artistic2.0))) - (define-public r-genomicfeatures (package (name "r-genomicfeatures") -- cgit 1.4.1 From f78ff75b411fe2d07b18529db6fb1da231bcc4cd Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:35 +0200 Subject: gnu: r-genomicfeatures: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-genomicfeatures): Move from here... * gnu/packages/bioconductor.scm (r-genomicfeatures): ...to here. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 43 ----------------------------------------- 2 files changed, 43 insertions(+), 43 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2b3c232d53..7278bb486b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2313,6 +2313,49 @@ junction detection, and working with the nucleotide content of the alignments.") (license license:artistic2.0))) +(define-public r-genomicfeatures + (package + (name "r-genomicfeatures") + (version "1.42.3") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicFeatures" version)) + (sha256 + (base32 + "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz")))) + (properties + `((upstream-name . "GenomicFeatures"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biomart" ,r-biomart) + ("r-biostrings" ,r-biostrings) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcurl" ,r-rcurl) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/GenomicFeatures") + (synopsis "Tools for working with transcript centric annotations") + (description + "This package provides a set of tools and methods for making and +manipulating transcript centric annotations. With these tools the user can +easily download the genomic locations of the transcripts, exons and cds of a +given organism, from either the UCSC Genome Browser or a BioMart +database (more sources will be supported in the future). This information is +then stored in a local database that keeps track of the relationship between +transcripts, exons, cds and genes. Flexible methods are provided for +extracting the desired features in a convenient format.") + (license license:artistic2.0))) + (define-public r-genomicranges (package (name "r-genomicranges") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f9d2d125bf..fe81959ef0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7952,49 +7952,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomicfeatures - (package - (name "r-genomicfeatures") - (version "1.42.3") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "GenomicFeatures" version)) - (sha256 - (base32 - "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz")))) - (properties - `((upstream-name . "GenomicFeatures"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/GenomicFeatures") - (synopsis "Tools for working with transcript centric annotations") - (description - "This package provides a set of tools and methods for making and -manipulating transcript centric annotations. With these tools the user can -easily download the genomic locations of the transcripts, exons and cds of a -given organism, from either the UCSC Genome Browser or a BioMart -database (more sources will be supported in the future). This information is -then stored in a local database that keeps track of the relationship between -transcripts, exons, cds and genes. Flexible methods are provided for -extracting the desired features in a convenient format.") - (license license:artistic2.0))) - (define-public r-go-db (package (name "r-go-db") -- cgit 1.4.1 From 90bbab5cff337c522003adde870f127179f25f3d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:36 +0200 Subject: gnu: r-topgo: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-topgo): Move from here... * gnu/packages/bioconductor.scm (r-topgo): ...to here. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 33 --------------------------------- 2 files changed, 33 insertions(+), 33 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7278bb486b..a0f5222937 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2873,6 +2873,39 @@ experimental designs is facilitated by a consistently implemented sample annotation infrastructure.") (license license:artistic2.0))) +(define-public r-topgo + (package + (name "r-topgo") + (version "2.42.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "topGO" version)) + (sha256 + (base32 + "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl")))) + (properties + `((upstream-name . "topGO"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-dbi" ,r-dbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-go-db" ,r-go-db) + ("r-graph" ,r-graph) + ("r-lattice" ,r-lattice) + ("r-matrixstats" ,r-matrixstats) + ("r-sparsem" ,r-sparsem))) + (home-page "https://bioconductor.org/packages/topGO") + (synopsis "Enrichment analysis for gene ontology") + (description + "The topGO package provides tools for testing @dfn{gene ontology} (GO) +terms while accounting for the topology of the GO graph. Different test +statistics and different methods for eliminating local similarities and +dependencies between GO terms can be implemented and applied.") + ;; Any version of the LGPL applies. + (license license:lgpl2.1+))) + (define-public r-variantannotation (package (name "r-variantannotation") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fe81959ef0..e78769b1d3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7976,39 +7976,6 @@ including VCF header and contents in RDF and JSON.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-topgo - (package - (name "r-topgo") - (version "2.42.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "topGO" version)) - (sha256 - (base32 - "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl")))) - (properties - `((upstream-name . "topGO"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dbi" ,r-dbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-lattice" ,r-lattice) - ("r-matrixstats" ,r-matrixstats) - ("r-sparsem" ,r-sparsem))) - (home-page "https://bioconductor.org/packages/topGO") - (synopsis "Enrichment analysis for gene ontology") - (description - "The topGO package provides tools for testing @dfn{gene ontology} (GO) -terms while accounting for the topology of the GO graph. Different test -statistics and different methods for eliminating local similarities and -dependencies between GO terms can be implemented and applied.") - ;; Any version of the LGPL applies. - (license license:lgpl2.1+))) - (define-public r-bsgenome (package (name "r-bsgenome") -- cgit 1.4.1 From 537d48d8695cf54da8957277aaac12b3991167c8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:37 +0200 Subject: gnu: r-bsgenome: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-bsgenome): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome): ...to here. --- gnu/packages/bioconductor.scm | 33 ++++++++++++++++++++++++++++++++- gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 32 insertions(+), 32 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a0f5222937..5825a69d18 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017 Efraim Flashner -;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu @@ -2080,6 +2080,37 @@ matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.") (license license:artistic2.0))) +(define-public r-bsgenome + (package + (name "r-bsgenome") + (version "1.58.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome" version)) + (sha256 + (base32 + "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq")))) + (properties + `((upstream-name . "BSgenome"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/BSgenome") + (synopsis "Infrastructure for Biostrings-based genome data packages") + (description + "This package provides infrastructure shared by all Biostrings-based +genome data packages and support for efficient SNP representation.") + (license license:artistic2.0))) + (define-public r-category (package (name "r-category") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e78769b1d3..7a55ebd559 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7976,37 +7976,6 @@ including VCF header and contents in RDF and JSON.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-bsgenome - (package - (name "r-bsgenome") - (version "1.58.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "BSgenome" version)) - (sha256 - (base32 - "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq")))) - (properties - `((upstream-name . "BSgenome"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (home-page "https://bioconductor.org/packages/BSgenome") - (synopsis "Infrastructure for Biostrings-based genome data packages") - (description - "This package provides infrastructure shared by all Biostrings-based -genome data packages and support for efficient SNP representation.") - (license license:artistic2.0))) - (define-public r-impute (package (name "r-impute") -- cgit 1.4.1 From 8c7c78bfced859bc636752b03384f7f380398f71 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:38 +0200 Subject: gnu: r-msnid: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-msnid): Move from here... * gnu/packages/bioconductor.scm (r-msnid): ...to here. --- gnu/packages/bioconductor.scm | 52 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 52 ----------------------------------------- 2 files changed, 52 insertions(+), 52 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5825a69d18..f16e01261a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2517,6 +2517,58 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-msnid + (package + (name "r-msnid") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MSnID" version)) + (sha256 + (base32 + "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d")))) + (properties `((upstream-name . "MSnID"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationhub" ,r-annotationhub) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocstyle" ,r-biocstyle) + ("r-biostrings" ,r-biostrings) + ("r-data-table" ,r-data-table) + ("r-doparallel" ,r-doparallel) + ("r-dplyr" ,r-dplyr) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-iterators" ,r-iterators) + ("r-msnbase" ,r-msnbase) + ("r-msmstests" ,r-msmstests) + ("r-mzid" ,r-mzid) + ("r-mzr" ,r-mzr) + ("r-protgenerics" ,r-protgenerics) + ("r-purrr" ,r-purrr) + ("r-r-cache" ,r-r-cache) + ("r-rcpp" ,r-rcpp) + ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) + ("r-runit" ,r-runit) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-xtable" ,r-xtable))) + (home-page "https://bioconductor.org/packages/MSnID") + (synopsis "Utilities for LC-MSn proteomics identifications") + (description + "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data +from mzIdentML (leveraging the mzID package) or text files. After collating +the search results from multiple datasets it assesses their identification +quality and optimize filtering criteria to achieve the maximum number of +identifications while not exceeding a specified false discovery rate. It also +contains a number of utilities to explore the MS/MS results and assess missed +and irregular enzymatic cleavages, mass measurement accuracy, etc.") + (license license:artistic2.0))) + (define-public r-rbgl (package (name "r-rbgl") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7a55ebd559..478de5634e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9449,58 +9449,6 @@ structure (pcaRes) to provide a common interface to the PCA results.") of mass spectrometry based proteomics data.") (license license:artistic2.0))) -(define-public r-msnid - (package - (name "r-msnid") - (version "1.24.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "MSnID" version)) - (sha256 - (base32 - "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d")))) - (properties `((upstream-name . "MSnID"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocstyle" ,r-biocstyle) - ("r-biostrings" ,r-biostrings) - ("r-data-table" ,r-data-table) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-iterators" ,r-iterators) - ("r-msnbase" ,r-msnbase) - ("r-msmstests" ,r-msmstests) - ("r-mzid" ,r-mzid) - ("r-mzr" ,r-mzr) - ("r-protgenerics" ,r-protgenerics) - ("r-purrr" ,r-purrr) - ("r-r-cache" ,r-r-cache) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-runit" ,r-runit) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-xtable" ,r-xtable))) - (home-page "https://bioconductor.org/packages/MSnID") - (synopsis "Utilities for LC-MSn proteomics identifications") - (description - "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data -from mzIdentML (leveraging the mzID package) or text files. After collating -the search results from multiple datasets it assesses their identification -quality and optimize filtering criteria to achieve the maximum number of -identifications while not exceeding a specified false discovery rate. It also -contains a number of utilities to explore the MS/MS results and assess missed -and irregular enzymatic cleavages, mass measurement accuracy, etc.") - (license license:artistic2.0))) - (define-public r-aroma-light (package (name "r-aroma-light") -- cgit 1.4.1 From 4f030cc0db4806def4bb434817daee0e6c1cfa7d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:39 +0200 Subject: gnu: r-msnbase: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-msnbase): Move from here... * gnu/packages/bioconductor.scm (r-msnbase): ...to here. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 45 ----------------------------------------- 2 files changed, 45 insertions(+), 45 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f16e01261a..0db6590be3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2517,6 +2517,51 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-msnbase + (package + (name "r-msnbase") + (version "2.16.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MSnbase" version)) + (sha256 + (base32 + "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h")))) + (properties `((upstream-name . "MSnbase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-digest" ,r-digest) + ("r-ggplot2" ,r-ggplot2) + ("r-impute" ,r-impute) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-maldiquant" ,r-maldiquant) + ("r-mass" ,r-mass) + ("r-mzid" ,r-mzid) + ("r-mzr" ,r-mzr) + ("r-pcamethods" ,r-pcamethods) + ("r-plyr" ,r-plyr) + ("r-preprocesscore" ,r-preprocesscore) + ("r-protgenerics" ,r-protgenerics) + ("r-rcpp" ,r-rcpp) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-vsn" ,r-vsn) + ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/lgatto/MSnbase") + (synopsis "Base functions and classes for MS-based proteomics") + (description + "This package provides basic plotting, data manipulation and processing +of mass spectrometry based proteomics data.") + (license license:artistic2.0))) + (define-public r-msnid (package (name "r-msnid") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 478de5634e..e402efa4ad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9404,51 +9404,6 @@ the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results.") (license license:gpl3+))) -(define-public r-msnbase - (package - (name "r-msnbase") - (version "2.16.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "MSnbase" version)) - (sha256 - (base32 - "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h")))) - (properties `((upstream-name . "MSnbase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-digest" ,r-digest) - ("r-ggplot2" ,r-ggplot2) - ("r-impute" ,r-impute) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-maldiquant" ,r-maldiquant) - ("r-mass" ,r-mass) - ("r-mzid" ,r-mzid) - ("r-mzr" ,r-mzr) - ("r-pcamethods" ,r-pcamethods) - ("r-plyr" ,r-plyr) - ("r-preprocesscore" ,r-preprocesscore) - ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-vsn" ,r-vsn) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/lgatto/MSnbase") - (synopsis "Base functions and classes for MS-based proteomics") - (description - "This package provides basic plotting, data manipulation and processing -of mass spectrometry based proteomics data.") - (license license:artistic2.0))) - (define-public r-aroma-light (package (name "r-aroma-light") -- cgit 1.4.1 From a2a1d86a77b513dc2d49f6ae8735f2e3d9e2f8c0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:40 +0200 Subject: gnu: r-samr: Move to (gnu packages bioconductor). * gnu/packages/cran.scm (r-samr): Move from here... * gnu/packages/bioconductor.scm (r-samr): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/cran.scm | 30 ------------------------------ 2 files changed, 31 insertions(+), 30 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0db6590be3..9c6ba94838 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10,6 +10,7 @@ ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2021 Hong Li +;;; Copyright © 2021 Tim Howes ;;; ;;; This file is part of GNU Guix. ;;; @@ -2809,6 +2810,36 @@ built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.") (license license:artistic2.0))) +;; This is a CRAN package, but it depends on a Bioconductor package. +(define-public r-samr + (package + (name "r-samr") + (version "3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "samr" version)) + (sha256 + (base32 + "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15")))) + (properties `((upstream-name . "samr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gsa" ,r-gsa) + ("r-impute" ,r-impute) + ("r-matrixstats" ,r-matrixstats) + ("r-openxlsx" ,r-openxlsx) + ("r-shiny" ,r-shiny) + ("r-shinyfiles" ,r-shinyfiles))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://statweb.stanford.edu/~tibs/SAM/") + (synopsis "Significance analysis of Microarrays") + (description + "This is a package for significance analysis of Microarrays for +differential expression analysis, RNAseq data and related problems.") + ;; Any version of the LGPL + (license license:lgpl3+))) + (define-public r-shortread (package (name "r-shortread") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 878980a230..711792958c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33,7 +33,6 @@ ;;; Copyright © 2020 Magali Lemes ;;; Copyright © 2020 Simon Tournier ;;; Copyright © 2020 Aniket Patil -;;; Copyright © 2021 Tim Howes ;;; ;;; This file is part of GNU Guix. ;;; @@ -29153,35 +29152,6 @@ indicator, a quantitative variable or a survival time.") ;; Any version of the LGPL (license license:lgpl3+))) -(define-public r-samr - (package - (name "r-samr") - (version "3.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "samr" version)) - (sha256 - (base32 - "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15")))) - (properties `((upstream-name . "samr"))) - (build-system r-build-system) - (propagated-inputs - `(("r-gsa" ,r-gsa) - ("r-impute" ,r-impute) - ("r-matrixstats" ,r-matrixstats) - ("r-openxlsx" ,r-openxlsx) - ("r-shiny" ,r-shiny) - ("r-shinyfiles" ,r-shinyfiles))) - (native-inputs `(("gfortran" ,gfortran))) - (home-page "https://statweb.stanford.edu/~tibs/SAM/") - (synopsis "Significance analysis of Microarrays") - (description - "This is a package for significance analysis of Microarrays for -differential expression analysis, RNAseq data and related problems.") - ;; Any version of the LGPL - (license license:lgpl3+))) - (define-public r-randomforestsrc (package (name "r-randomforestsrc") -- cgit 1.4.1 From b832fddbfc83dfc1b13a4f113a9d3f86754e4c57 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:41 +0200 Subject: gnu: r-impute: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-impute): Move from here... * gnu/packages/bioconductor.scm (r-impute): ...to here. --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ gnu/packages/bioinformatics.scm | 20 -------------------- 2 files changed, 20 insertions(+), 20 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9c6ba94838..a4a3fbd39a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2499,6 +2499,26 @@ Enrichment Analysis} (GSEA).") the Human Protein Atlas project.") (license license:artistic2.0))) +(define-public r-impute + (package + (name "r-impute") + (version "1.64.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "impute" version)) + (sha256 + (base32 + "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa")))) + (native-inputs + `(("gfortran" ,gfortran))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/impute") + (synopsis "Imputation for microarray data") + (description + "This package provides a function to impute missing gene expression +microarray data, using nearest neighbor averaging.") + (license license:gpl2+))) + (define-public r-limma (package (name "r-limma") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e402efa4ad..566370c37f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7976,26 +7976,6 @@ including VCF header and contents in RDF and JSON.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-impute - (package - (name "r-impute") - (version "1.64.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "impute" version)) - (sha256 - (base32 - "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa")))) - (native-inputs - `(("gfortran" ,gfortran))) - (build-system r-build-system) - (home-page "https://bioconductor.org/packages/impute") - (synopsis "Imputation for microarray data") - (description - "This package provides a function to impute missing gene expression -microarray data, using nearest neighbor averaging.") - (license license:gpl2+))) - (define-public r-seqpattern (package (name "r-seqpattern") -- cgit 1.4.1 From 14fb30e5f68dca6c64508ce3accce0a1722b118b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:42 +0200 Subject: gnu: r-seqpattern: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-seqpattern): Move from here... * gnu/packages/bioconductor.scm (r-seqpattern): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a4a3fbd39a..d386f2270e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2860,6 +2860,33 @@ differential expression analysis, RNAseq data and related problems.") ;; Any version of the LGPL (license license:lgpl3+))) +(define-public r-seqpattern + (package + (name "r-seqpattern") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "seqPattern" version)) + (sha256 + (base32 + "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq")))) + (properties + `((upstream-name . "seqPattern"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-kernsmooth" ,r-kernsmooth) + ("r-plotrix" ,r-plotrix))) + (home-page "https://bioconductor.org/packages/seqPattern") + (synopsis "Visualising oligonucleotide patterns and motif occurrences") + (description + "This package provides tools to visualize oligonucleotide patterns and +sequence motif occurrences across a large set of sequences centred at a common +reference point and sorted by a user defined feature.") + (license license:gpl3+))) + (define-public r-shortread (package (name "r-shortread") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 566370c37f..fa57451bdc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7976,33 +7976,6 @@ including VCF header and contents in RDF and JSON.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-seqpattern - (package - (name "r-seqpattern") - (version "1.22.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "seqPattern" version)) - (sha256 - (base32 - "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq")))) - (properties - `((upstream-name . "seqPattern"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-plotrix" ,r-plotrix))) - (home-page "https://bioconductor.org/packages/seqPattern") - (synopsis "Visualising oligonucleotide patterns and motif occurrences") - (description - "This package provides tools to visualize oligonucleotide patterns and -sequence motif occurrences across a large set of sequences centred at a common -reference point and sorted by a user defined feature.") - (license license:gpl3+))) - (define-public r-spp (package (name "r-spp") -- cgit 1.4.1 From f3b50aa4fd0c431814c70f02fea62bfcffeebbd4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:43 +0200 Subject: gnu: r-go-db: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-go-db): Move from here... * gnu/packages/bioconductor.scm (r-go-db): ...to here. [source]: Replace 'string-append' by 'bioconductor-uri' with 'annotation. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 24 ------------------------ 2 files changed, 22 insertions(+), 24 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d386f2270e..8cf8b43ed4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -436,6 +436,28 @@ in Biostrings objects.") ID and species. It is used by functions in the GenomeInfoDb package.") (license license:artistic2.0))) +(define-public r-go-db + (package + (name "r-go-db") + (version "3.7.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GO.db" version 'annotation)) + (sha256 + (base32 + "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5")))) + (properties + `((upstream-name . "GO.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/GO.db") + (synopsis "Annotation maps describing the entire Gene Ontology") + (description + "The purpose of this GO.db annotation package is to provide detailed +information about the latest version of the Gene Ontologies.") + (license license:artistic2.0))) + (define-public r-homo-sapiens (package (name "r-homo-sapiens") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fa57451bdc..1396631591 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7952,30 +7952,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-go-db - (package - (name "r-go-db") - (version "3.7.0") - (source (origin - (method url-fetch) - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/GO.db_" - version ".tar.gz")) - (sha256 - (base32 - "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5")))) - (properties - `((upstream-name . "GO.db"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) - (home-page "https://bioconductor.org/packages/GO.db") - (synopsis "Annotation maps describing the entire Gene Ontology") - (description - "The purpose of this GO.db annotation package is to provide detailed -information about the latest version of the Gene Ontologies.") - (license license:artistic2.0))) - (define-public r-spp (package (name "r-spp") -- cgit 1.4.1 From f8fe5497c7b9f598786d46d96fd1bd5002e7e57f Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:44 +0200 Subject: gnu: r-genomation: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-genomation): Move from here... * gnu/packages/bioconductor.scm (r-genomation): ...to here. --- gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 48 ----------------------------------------- 2 files changed, 48 insertions(+), 48 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8cf8b43ed4..b90e315267 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2304,6 +2304,54 @@ CAGE.") high-throughput sequencing experiments.") (license license:artistic2.0))) +(define-public r-genomation + (package + (name "r-genomation") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "genomation" version)) + (sha256 + (base32 + "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-data-table" ,r-data-table) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-gridbase" ,r-gridbase) + ("r-impute" ,r-impute) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-plotrix" ,r-plotrix) + ("r-plyr" ,r-plyr) + ("r-rcpp" ,r-rcpp) + ("r-readr" ,r-readr) + ("r-reshape2" ,r-reshape2) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-runit" ,r-runit) + ("r-s4vectors" ,r-s4vectors) + ("r-seqpattern" ,r-seqpattern))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioinformatics.mdc-berlin.de/genomation/") + (synopsis "Summary, annotation and visualization of genomic data") + (description + "This package provides a package for summary and annotation of genomic +intervals. Users can visualize and quantify genomic intervals over +pre-defined functional regions, such as promoters, exons, introns, etc. The +genomic intervals represent regions with a defined chromosome position, which +may be associated with a score, such as aligned reads from HT-seq experiments, +TF binding sites, methylation scores, etc. The package can use any tabular +genomic feature data as long as it has minimal information on the locations of +genomic intervals. In addition, it can use BAM or BigWig files as input.") + (license license:artistic2.0))) + (define-public r-genomeinfodb (package (name "r-genomeinfodb") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1396631591..cc6e1b1594 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8023,54 +8023,6 @@ used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.") (license license:bsd-3))) -(define-public r-genomation - (package - (name "r-genomation") - (version "1.22.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "genomation" version)) - (sha256 - (base32 - "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-data-table" ,r-data-table) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gridbase" ,r-gridbase) - ("r-impute" ,r-impute) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-plotrix" ,r-plotrix) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-runit" ,r-runit) - ("r-s4vectors" ,r-s4vectors) - ("r-seqpattern" ,r-seqpattern))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioinformatics.mdc-berlin.de/genomation/") - (synopsis "Summary, annotation and visualization of genomic data") - (description - "This package provides a package for summary and annotation of genomic -intervals. Users can visualize and quantify genomic intervals over -pre-defined functional regions, such as promoters, exons, introns, etc. The -genomic intervals represent regions with a defined chromosome position, which -may be associated with a score, such as aligned reads from HT-seq experiments, -TF binding sites, methylation scores, etc. The package can use any tabular -genomic feature data as long as it has minimal information on the locations of -genomic intervals. In addition, it can use BAM or BigWig files as input.") - (license license:artistic2.0))) - (define-public r-genomationdata (package (name "r-genomationdata") -- cgit 1.4.1 From d7fa9c1ffdbd0ab4d4412020c925be39503ce9e8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:45 +0200 Subject: gnu: r-genomationdata: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-genomationdata): Move from here... * gnu/packages/bioconductor.scm (r-genomationdata): ...to here. [source]: Replace 'string-append' by 'bioconductor-uri' with 'experiment. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 28 ---------------------------- 2 files changed, 26 insertions(+), 28 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b90e315267..b25cc8e019 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1170,6 +1170,32 @@ genomes and gene ID formats, largely based on the UCSC table browser.") and visualize the results.") (license license:gpl3))) +(define-public r-genomationdata + (package + (name "r-genomationdata") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "genomationData" version 'experiment)) + (sha256 + (base32 + "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g")))) + (properties + `((upstream-name . "genomationData"))) + (build-system r-build-system) + ;; As this package provides little more than large data files, it doesn't + ;; make sense to build substitutes. + (arguments `(#:substitutable? #f)) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioinformatics.mdc-berlin.de/genomation/") + (synopsis "Experimental data for use with the genomation package") + (description + "This package contains experimental genetic data for use with the +genomation package. Included are Chip Seq, Methylation and Cage data, +downloaded from Encode.") + (license license:gpl3+))) + (define-public r-pasilla (package (name "r-pasilla") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cc6e1b1594..1b94b62b1d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8023,34 +8023,6 @@ used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.") (license license:bsd-3))) -(define-public r-genomationdata - (package - (name "r-genomationdata") - (version "1.22.0") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://bioconductor.org/packages/" - "release/data/experiment/src/contrib/" - "genomationData_" version ".tar.gz")) - (sha256 - (base32 - "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g")))) - (build-system r-build-system) - ;; As this package provides little more than large data files, it doesn't - ;; make sense to build substitutes. - (arguments `(#:substitutable? #f)) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioinformatics.mdc-berlin.de/genomation/") - (synopsis "Experimental data for use with the genomation package") - (description - "This package contains experimental genetic data for use with the -genomation package. Included are Chip Seq, Methylation and Cage data, -downloaded from Encode.") - (license license:gpl3+))) - (define-public r-seqlogo (package (name "r-seqlogo") -- cgit 1.4.1 From ad46c8aa7f8ae74aa8f594b4cd663ea2ea9a8115 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:46 +0200 Subject: gnu: r-pcamethods: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-pcamethods): Move from here... * gnu/packages/bioconductor.scm (r-pcamethods): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b25cc8e019..e70f2bc13d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2731,6 +2731,36 @@ contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) +(define-public r-pcamethods + (package + (name "r-pcamethods") + (version "1.82.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "pcaMethods" version)) + (sha256 + (base32 + "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0")))) + (properties `((upstream-name . "pcaMethods"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/hredestig/pcamethods") + (synopsis "Collection of PCA methods") + (description + "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, +Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method +for missing value estimation is included for comparison. BPCA, PPCA and +NipalsPCA may be used to perform PCA on incomplete data as well as for +accurate missing value estimation. A set of methods for printing and plotting +the results is also provided. All PCA methods make use of the same data +structure (pcaRes) to provide a common interface to the PCA results.") + (license license:gpl3+))) + (define-public r-rbgl (package (name "r-rbgl") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1b94b62b1d..a2c99ecbd6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9227,36 +9227,6 @@ mzIdentML files with the drawback of having less pretty output than a vendor specific parser.") (license license:gpl2+))) -(define-public r-pcamethods - (package - (name "r-pcamethods") - (version "1.82.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "pcaMethods" version)) - (sha256 - (base32 - "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0")))) - (properties `((upstream-name . "pcaMethods"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp))) - (home-page "https://github.com/hredestig/pcamethods") - (synopsis "Collection of PCA methods") - (description - "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, -Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method -for missing value estimation is included for comparison. BPCA, PPCA and -NipalsPCA may be used to perform PCA on incomplete data as well as for -accurate missing value estimation. A set of methods for printing and plotting -the results is also provided. All PCA methods make use of the same data -structure (pcaRes) to provide a common interface to the PCA results.") - (license license:gpl3+))) - (define-public r-aroma-light (package (name "r-aroma-light") -- cgit 1.4.1 From 7756e08b44b40ff46357572befa81fb173ca7edc Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:47 +0200 Subject: gnu: r-mzid: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-mzid): Move from here... * gnu/packages/bioconductor.scm (r-mzid): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e70f2bc13d..8fc035b623 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2731,6 +2731,37 @@ contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) +(define-public r-mzid + (package + (name "r-mzid") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mzID" version)) + (sha256 + (base32 + "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2")))) + (properties `((upstream-name . "mzID"))) + (build-system r-build-system) + (propagated-inputs + `(("r-doparallel" ,r-doparallel) + ("r-foreach" ,r-foreach) + ("r-iterators" ,r-iterators) + ("r-plyr" ,r-plyr) + ("r-protgenerics" ,r-protgenerics) + ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/mzID") + (synopsis "Parser for mzIdentML files") + (description + "This package provides a parser for mzIdentML files implemented using the +XML package. The parser tries to be general and able to handle all types of +mzIdentML files with the drawback of having less pretty output than a vendor +specific parser.") + (license license:gpl2+))) + (define-public r-pcamethods (package (name "r-pcamethods") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a2c99ecbd6..f6ec7e32c4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9196,37 +9196,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-mzid - (package - (name "r-mzid") - (version "1.28.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "mzID" version)) - (sha256 - (base32 - "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2")))) - (properties `((upstream-name . "mzID"))) - (build-system r-build-system) - (propagated-inputs - `(("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-iterators" ,r-iterators) - ("r-plyr" ,r-plyr) - ("r-protgenerics" ,r-protgenerics) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/mzID") - (synopsis "Parser for mzIdentML files") - (description - "This package provides a parser for mzIdentML files implemented using the -XML package. The parser tries to be general and able to handle all types of -mzIdentML files with the drawback of having less pretty output than a vendor -specific parser.") - (license license:gpl2+))) - (define-public r-aroma-light (package (name "r-aroma-light") -- cgit 1.4.1 From bb118f20fe6581a4acbd3799ed31ab0d21e72e78 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:48 +0200 Subject: gnu: r-aroma-light: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-aroma-light): Move from here... * gnu/packages/bioconductor.scm (r-aroma-light): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8fc035b623..3f057a3a4d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1987,6 +1987,33 @@ annotation data packages using SQLite data storage.") databases. Packages produced are intended to be used with AnnotationDbi.") (license license:artistic2.0))) +(define-public r-aroma-light + (package + (name "r-aroma-light") + (version "3.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "aroma.light" version)) + (sha256 + (base32 + "0pi37rlfqh24p9wd7l1xb3f7c7938xdscgcc5agp8c9qhajq25a0")))) + (properties `((upstream-name . "aroma.light"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrixstats" ,r-matrixstats) + ("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo) + ("r-r-utils" ,r-r-utils))) + (home-page "https://github.com/HenrikBengtsson/aroma.light") + (synopsis "Methods for normalization and visualization of microarray data") + (description + "This package provides methods for microarray analysis that take basic +data types such as matrices and lists of vectors. These methods can be used +standalone, be utilized in other packages, or be wrapped up in higher-level +classes.") + (license license:gpl2+))) + (define-public r-biobase (package (name "r-biobase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f6ec7e32c4..687da8086e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9196,33 +9196,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-aroma-light - (package - (name "r-aroma-light") - (version "3.20.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "aroma.light" version)) - (sha256 - (base32 - "0pi37rlfqh24p9wd7l1xb3f7c7938xdscgcc5agp8c9qhajq25a0")))) - (properties `((upstream-name . "aroma.light"))) - (build-system r-build-system) - (propagated-inputs - `(("r-matrixstats" ,r-matrixstats) - ("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo) - ("r-r-utils" ,r-r-utils))) - (home-page "https://github.com/HenrikBengtsson/aroma.light") - (synopsis "Methods for normalization and visualization of microarray data") - (description - "This package provides methods for microarray analysis that take basic -data types such as matrices and lists of vectors. These methods can be used -standalone, be utilized in other packages, or be wrapped up in higher-level -classes.") - (license license:gpl2+))) - (define-public r-deseq (package (name "r-deseq") -- cgit 1.4.1 From ef954bb4884185466bc4833c365ecb01be3a0a20 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:49 +0200 Subject: gnu: r-deseq: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-deseq): Move from here... * gnu/packages/bioconductor.scm (r-deseq): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3f057a3a4d..65dfce04bd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2218,6 +2218,37 @@ genome data packages and support for efficient SNP representation.") analysis.") (license license:artistic2.0))) +(define-public r-deseq + (package + (name "r-deseq") + (version "1.39.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DESeq" version)) + (sha256 + (base32 + "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1")))) + (properties `((upstream-name . "DESeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genefilter" ,r-genefilter) + ("r-geneplotter" ,r-geneplotter) + ("r-lattice" ,r-lattice) + ("r-locfit" ,r-locfit) + ("r-mass" ,r-mass) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "https://www-huber.embl.de/users/anders/DESeq/") + (synopsis "Differential gene expression analysis") + (description + "This package provides tools for estimating variance-mean dependence in +count data from high-throughput genetic sequencing assays and for testing for +differential expression based on a model using the negative binomial +distribution.") + (license license:gpl3+))) + (define-public r-deseq2 (package (name "r-deseq2") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 687da8086e..d23c3cb94e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9196,37 +9196,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-deseq - (package - (name "r-deseq") - (version "1.39.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "DESeq" version)) - (sha256 - (base32 - "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1")))) - (properties `((upstream-name . "DESeq"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-lattice" ,r-lattice) - ("r-locfit" ,r-locfit) - ("r-mass" ,r-mass) - ("r-rcolorbrewer" ,r-rcolorbrewer))) - (home-page "https://www-huber.embl.de/users/anders/DESeq/") - (synopsis "Differential gene expression analysis") - (description - "This package provides tools for estimating variance-mean dependence in -count data from high-throughput genetic sequencing assays and for testing for -differential expression based on a model using the negative binomial -distribution.") - (license license:gpl3+))) - (define-public r-edaseq (package (name "r-edaseq") -- cgit 1.4.1 From f6f43a2d40e830243d118f740d164d3fe1b79bba Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:50 +0200 Subject: gnu: r-edaseq: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-edaseq): Move from here... * gnu/packages/bioconductor.scm (r-edaseq): ...to here. --- gnu/packages/bioconductor.scm | 40 ++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 40 ---------------------------------------- 2 files changed, 40 insertions(+), 40 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 65dfce04bd..7e6b48eb19 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2332,6 +2332,46 @@ testing. The package also provides functions for the visualization and exploration of the results.") (license license:gpl3+))) +(define-public r-edaseq + (package + (name "r-edaseq") + (version "2.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EDASeq" version)) + (sha256 + (base32 + "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip")))) + (properties `((upstream-name . "EDASeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-aroma-light" ,r-aroma-light) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-biomart" ,r-biomart) + ("r-biostrings" ,r-biostrings) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-shortread" ,r-shortread))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/drisso/EDASeq") + (synopsis "Exploratory data analysis and normalization for RNA-Seq") + (description + "This package provides support for numerical and graphical summaries of +RNA-Seq genomic read data. Provided within-lane normalization procedures to +adjust for GC-content effect (or other gene-level effects) on read counts: +loess robust local regression, global-scaling, and full-quantile +normalization. Between-lane normalization procedures to adjust for +distributional differences between lanes (e.g., sequencing depth): +global-scaling and full-quantile normalization.") + (license license:artistic2.0))) + (define-public r-edger (package (name "r-edger") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d23c3cb94e..87ba47e2e4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9196,46 +9196,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-edaseq - (package - (name "r-edaseq") - (version "2.24.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "EDASeq" version)) - (sha256 - (base32 - "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip")))) - (properties `((upstream-name . "EDASeq"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-aroma-light" ,r-aroma-light) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-shortread" ,r-shortread))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/drisso/EDASeq") - (synopsis "Exploratory data analysis and normalization for RNA-Seq") - (description - "This package provides support for numerical and graphical summaries of -RNA-Seq genomic read data. Provided within-lane normalization procedures to -adjust for GC-content effect (or other gene-level effects) on read counts: -loess robust local regression, global-scaling, and full-quantile -normalization. Between-lane normalization procedures to adjust for -distributional differences between lanes (e.g., sequencing depth): -global-scaling and full-quantile normalization.") - (license license:artistic2.0))) - (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") -- cgit 1.4.1 From dfe6224f5f42993eb8bcf2659d6da99f8c7fd1ac Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:51 +0200 Subject: gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Move from here... * gnu/packages/bioconductor.scm (r-interactivedisplaybase): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7e6b48eb19..53f1005d7b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2713,6 +2713,33 @@ the Human Protein Atlas project.") microarray data, using nearest neighbor averaging.") (license license:gpl2+))) +(define-public r-interactivedisplaybase + (package + (name "r-interactivedisplaybase") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "interactiveDisplayBase" version)) + (sha256 + (base32 + "08id2hkx4ssxj34dildx00a4j3z0nv171b7b0wl6xjks7wk6lv01")))) + (properties + `((upstream-name . "interactiveDisplayBase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-dt" ,r-dt) + ("r-shiny" ,r-shiny))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/interactiveDisplayBase") + (synopsis "Base package for web displays of Bioconductor objects") + (description + "This package contains the basic methods needed to generate interactive +Shiny-based display methods for Bioconductor objects.") + (license license:artistic2.0))) + (define-public r-limma (package (name "r-limma") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 87ba47e2e4..38286fb974 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9196,33 +9196,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-interactivedisplaybase - (package - (name "r-interactivedisplaybase") - (version "1.28.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "interactiveDisplayBase" version)) - (sha256 - (base32 - "08id2hkx4ssxj34dildx00a4j3z0nv171b7b0wl6xjks7wk6lv01")))) - (properties - `((upstream-name . "interactiveDisplayBase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-dt" ,r-dt) - ("r-shiny" ,r-shiny))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/interactiveDisplayBase") - (synopsis "Base package for web displays of Bioconductor objects") - (description - "This package contains the basic methods needed to generate interactive -Shiny-based display methods for Bioconductor objects.") - (license license:artistic2.0))) - (define-public r-annotationhub (package (name "r-annotationhub") -- cgit 1.4.1 From 9644745692aa2407e66f2ce4671356c3231c462d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:52 +0200 Subject: gnu: r-annotationhub: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-annotationhub): Move from here... * gnu/packages/bioconductor.scm (r-annotationhub): ...to here. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 41 ----------------------------------------- 2 files changed, 41 insertions(+), 41 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 53f1005d7b..42a01a4dc3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1987,6 +1987,47 @@ annotation data packages using SQLite data storage.") databases. Packages produced are intended to be used with AnnotationDbi.") (license license:artistic2.0))) +(define-public r-annotationhub + (package + (name "r-annotationhub") + (version "2.22.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationHub" version)) + (sha256 + (base32 + "08d7m0n4jkpajsj0bvi5xd4vi1zqczl6lnrh8kqi2fbjkrvwdqp5")))) + (properties `((upstream-name . "AnnotationHub"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocfilecache" ,r-biocfilecache) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-biocversion" ,r-biocversion) + ("r-curl" ,r-curl) + ("r-dplyr" ,r-dplyr) + ("r-httr" ,r-httr) + ("r-interactivedisplaybase" ,r-interactivedisplaybase) + ("r-rappdirs" ,r-rappdirs) + ("r-rsqlite" ,r-rsqlite) + ("r-s4vectors" ,r-s4vectors) + ("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/AnnotationHub") + (synopsis "Client to access AnnotationHub resources") + (description + "This package provides a client for the Bioconductor AnnotationHub web +resource. The AnnotationHub web resource provides a central location where +genomic files (e.g. VCF, bed, wig) and other resources from standard +locations (e.g. UCSC, Ensembl) can be discovered. The resource includes +metadata about each resource, e.g., a textual description, tags, and date of +modification. The client creates and manages a local cache of files retrieved +by the user, helping with quick and reproducible access.") + (license license:artistic2.0))) + (define-public r-aroma-light (package (name "r-aroma-light") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 38286fb974..104a37acaa 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9196,47 +9196,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-annotationhub - (package - (name "r-annotationhub") - (version "2.22.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "AnnotationHub" version)) - (sha256 - (base32 - "08d7m0n4jkpajsj0bvi5xd4vi1zqczl6lnrh8kqi2fbjkrvwdqp5")))) - (properties `((upstream-name . "AnnotationHub"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biocversion" ,r-biocversion) - ("r-curl" ,r-curl) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-interactivedisplaybase" ,r-interactivedisplaybase) - ("r-rappdirs" ,r-rappdirs) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/AnnotationHub") - (synopsis "Client to access AnnotationHub resources") - (description - "This package provides a client for the Bioconductor AnnotationHub web -resource. The AnnotationHub web resource provides a central location where -genomic files (e.g. VCF, bed, wig) and other resources from standard -locations (e.g. UCSC, Ensembl) can be discovered. The resource includes -metadata about each resource, e.g., a textual description, tags, and date of -modification. The client creates and manages a local cache of files retrieved -by the user, helping with quick and reproducible access.") - (license license:artistic2.0))) - (define-public r-fastseg (package (name "r-fastseg") -- cgit 1.4.1 From 32ae36e96f9b076901af94c723e3d156595d5bc5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:53 +0200 Subject: gnu: r-fastseg: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-fastseg): Move from here... * gnu/packages/bioconductor.scm (r-fastseg): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 42a01a4dc3..07ce719d7d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2441,6 +2441,36 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.") (license license:gpl2+))) +(define-public r-fastseg + (package + (name "r-fastseg") + (version "1.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "fastseg" version)) + (sha256 + (base32 + "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://www.bioinf.jku.at/software/fastseg/index.html") + (synopsis "Fast segmentation algorithm for genetic sequencing data") + (description + "Fastseg implements a very fast and efficient segmentation algorithm. +It can segment data from DNA microarrays and data from next generation +sequencing for example to detect copy number segments. Further it can segment +data from RNA microarrays like tiling arrays to identify transcripts. Most +generally, it can segment data given as a matrix or as a vector. Various data +formats can be used as input to fastseg like expression set objects for +microarrays or GRanges for sequencing data.") + (license license:lgpl2.0+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 104a37acaa..54c3945489 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9196,36 +9196,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-fastseg - (package - (name "r-fastseg") - (version "1.36.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "fastseg" version)) - (sha256 - (base32 - "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://www.bioinf.jku.at/software/fastseg/index.html") - (synopsis "Fast segmentation algorithm for genetic sequencing data") - (description - "Fastseg implements a very fast and efficient segmentation algorithm. -It can segment data from DNA microarrays and data from next generation -sequencing for example to detect copy number segments. Further it can segment -data from RNA microarrays like tiling arrays to identify transcripts. Most -generally, it can segment data given as a matrix or as a vector. Various data -formats can be used as input to fastseg like expression set objects for -microarrays or GRanges for sequencing data.") - (license license:lgpl2.0+))) - (define-public r-keggrest (package (name "r-keggrest") -- cgit 1.4.1 From 22cda2e4320a59a4c26fbbbadf4064526d2b2c82 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:54 +0200 Subject: gnu: r-affy: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-affy): Move from here... * gnu/packages/bioconductor.scm (r-affy): ...to here. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 28 ---------------------------- 2 files changed, 28 insertions(+), 28 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 07ce719d7d..25094e771e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1755,6 +1755,34 @@ optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.") (license license:gpl2+))) +(define-public r-affy + (package + (name "r-affy") + (version "1.68.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affy" version)) + (sha256 + (base32 + "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06")))) + (build-system r-build-system) + (propagated-inputs + `(("r-affyio" ,r-affyio) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-preprocesscore" ,r-preprocesscore) + ("r-zlibbioc" ,r-zlibbioc))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://bioconductor.org/packages/affy") + (synopsis "Methods for affymetrix oligonucleotide arrays") + (description + "This package contains functions for exploratory oligonucleotide array +analysis.") + (license license:lgpl2.0+))) + (define-public r-affycomp (package (name "r-affycomp") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 54c3945489..df0d4e73c1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9132,34 +9132,6 @@ upon file format information. The primary focus is on accessing the CEL and CDF file formats.") (license license:lgpl2.0+))) -(define-public r-affy - (package - (name "r-affy") - (version "1.68.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "affy" version)) - (sha256 - (base32 - "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06")))) - (build-system r-build-system) - (propagated-inputs - `(("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-preprocesscore" ,r-preprocesscore) - ("r-zlibbioc" ,r-zlibbioc))) - (inputs - `(("zlib" ,zlib))) - (home-page "https://bioconductor.org/packages/affy") - (synopsis "Methods for affymetrix oligonucleotide arrays") - (description - "This package contains functions for exploratory oligonucleotide array -analysis.") - (license license:lgpl2.0+))) - (define-public r-vsn (package (name "r-vsn") -- cgit 1.4.1 From d0a5503752cab62efbaa06bd00fb92145e015732 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:55 +0200 Subject: gnu: r-keggrest: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-keggrest): Move from here... * gnu/packages/bioconductor.scm (r-keggrest): ...to here. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 25094e771e..28e8810bbc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2839,6 +2839,32 @@ microarray data, using nearest neighbor averaging.") Shiny-based display methods for Bioconductor objects.") (license license:artistic2.0))) +(define-public r-keggrest + (package + (name "r-keggrest") + (version "1.30.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "KEGGREST" version)) + (sha256 + (base32 + "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s")))) + (properties `((upstream-name . "KEGGREST"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-httr" ,r-httr) + ("r-png" ,r-png))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/KEGGREST") + (synopsis "Client-side REST access to KEGG") + (description + "This package provides a package that provides a client interface to the +@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.") + (license license:artistic2.0))) + (define-public r-limma (package (name "r-limma") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index df0d4e73c1..8188b50ad6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9168,32 +9168,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-keggrest - (package - (name "r-keggrest") - (version "1.30.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "KEGGREST" version)) - (sha256 - (base32 - "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s")))) - (properties `((upstream-name . "KEGGREST"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-httr" ,r-httr) - ("r-png" ,r-png))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/KEGGREST") - (synopsis "Client-side REST access to KEGG") - (description - "This package provides a package that provides a client interface to the -@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.") - (license license:artistic2.0))) - (define-public r-gage (package (name "r-gage") -- cgit 1.4.1 From 84019edf38fea7ded047464fa4a6c79675934ae4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:56 +0200 Subject: gnu: r-gage: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-gage): Move from here... * gnu/packages/bioconductor.scm (r-gage): ...to here. --- gnu/packages/bioconductor.scm | 33 ++++++++++++++++++++++++++++++++- gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 32 insertions(+), 32 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 28e8810bbc..a0ee8a8c18 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017 Efraim Flashner -;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu @@ -2499,6 +2499,37 @@ formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data.") (license license:lgpl2.0+))) +(define-public r-gage + (package + (name "r-gage") + (version "2.40.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gage" version)) + (sha256 + (base32 + "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-go-db" ,r-go-db) + ("r-graph" ,r-graph) + ("r-keggrest" ,r-keggrest))) + (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/" + "articles/10.1186/1471-2105-10-161")) + (synopsis "Generally applicable gene-set enrichment for pathway analysis") + (description + "GAGE is a published method for gene set (enrichment or GSEA) or pathway +analysis. GAGE is generally applicable independent of microarray or RNA-Seq +data attributes including sample sizes, experimental designs, assay platforms, +and other types of heterogeneity. The gage package provides functions for +basic GAGE analysis, result processing and presentation. In addition, it +provides demo microarray data and commonly used gene set data based on KEGG +pathways and GO terms. These functions and data are also useful for gene set +analysis using other methods.") + (license license:gpl2+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8188b50ad6..a857c1ccc5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9168,37 +9168,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-gage - (package - (name "r-gage") - (version "2.40.2") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "gage" version)) - (sha256 - (base32 - "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-keggrest" ,r-keggrest))) - (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/" - "articles/10.1186/1471-2105-10-161")) - (synopsis "Generally applicable gene-set enrichment for pathway analysis") - (description - "GAGE is a published method for gene set (enrichment or GSEA) or pathway -analysis. GAGE is generally applicable independent of microarray or RNA-Seq -data attributes including sample sizes, experimental designs, assay platforms, -and other types of heterogeneity. The gage package provides functions for -basic GAGE analysis, result processing and presentation. In addition, it -provides demo microarray data and commonly used gene set data based on KEGG -pathways and GO terms. These functions and data are also useful for gene set -analysis using other methods.") - (license license:gpl2+))) - (define-public r-genomicfiles (package (name "r-genomicfiles") -- cgit 1.4.1 From ff65fa90d268bbe3f868be4cb5d9e2bb5ab6c3dd Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:57 +0200 Subject: gnu: r-complexheatmap: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-complexheatmap): Move from here... * gnu/packages/bioconductor.scm (r-complexheatmap): ...to here. --- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 39 --------------------------------------- 2 files changed, 39 insertions(+), 39 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a0ee8a8c18..3e536e0299 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2287,6 +2287,45 @@ genome data packages and support for efficient SNP representation.") analysis.") (license license:artistic2.0))) +(define-public r-complexheatmap + (package + (name "r-complexheatmap") + (version "2.6.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ComplexHeatmap" version)) + (sha256 + (base32 + "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x")))) + (properties + `((upstream-name . "ComplexHeatmap"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cairo" ,r-cairo) + ("r-circlize" ,r-circlize) + ("r-clue" ,r-clue) + ("r-colorspace" ,r-colorspace) + ("r-digest" ,r-digest) + ("r-getoptlong" ,r-getoptlong) + ("r-globaloptions" ,r-globaloptions) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-png" ,r-png) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page + "https://github.com/jokergoo/ComplexHeatmap") + (synopsis "Making Complex Heatmaps") + (description + "Complex heatmaps are efficient to visualize associations between +different sources of data sets and reveal potential structures. This package +provides a highly flexible way to arrange multiple heatmaps and supports +self-defined annotation graphics.") + (license license:gpl2+))) + (define-public r-deseq (package (name "r-deseq") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a857c1ccc5..a57c420a07 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9202,45 +9202,6 @@ distributed by file or by range. User defined mapper and reducer functions provide added flexibility for data combination and manipulation.") (license license:artistic2.0))) -(define-public r-complexheatmap - (package - (name "r-complexheatmap") - (version "2.6.2") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ComplexHeatmap" version)) - (sha256 - (base32 - "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x")))) - (properties - `((upstream-name . "ComplexHeatmap"))) - (build-system r-build-system) - (propagated-inputs - `(("r-cairo" ,r-cairo) - ("r-circlize" ,r-circlize) - ("r-clue" ,r-clue) - ("r-colorspace" ,r-colorspace) - ("r-digest" ,r-digest) - ("r-getoptlong" ,r-getoptlong) - ("r-globaloptions" ,r-globaloptions) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page - "https://github.com/jokergoo/ComplexHeatmap") - (synopsis "Making Complex Heatmaps") - (description - "Complex heatmaps are efficient to visualize associations between -different sources of data sets and reveal potential structures. This package -provides a highly flexible way to arrange multiple heatmaps and supports -self-defined annotation graphics.") - (license license:gpl2+))) - (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") -- cgit 1.4.1 From 0b5b41c5614be969e611f3dc3e1462eb8135b3e8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:58 +0200 Subject: gnu: r-genomicfiles: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-genomicfiles): Move from here... * gnu/packages/bioconductor.scm (r-genomicfiles): ...to here. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 34 ---------------------------------- 2 files changed, 34 insertions(+), 34 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3e536e0299..c369ac0cb4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2751,6 +2751,40 @@ transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.") (license license:artistic2.0))) +(define-public r-genomicfiles + (package + (name "r-genomicfiles") + (version "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicFiles" version)) + (sha256 + (base32 + "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz")))) + (properties `((upstream-name . "GenomicFiles"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrixgenerics" ,r-matrixgenerics) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/GenomicFiles") + (synopsis "Distributed computing by file or by range") + (description + "This package provides infrastructure for parallel computations +distributed by file or by range. User defined mapper and reducer functions +provide added flexibility for data combination and manipulation.") + (license license:artistic2.0))) + (define-public r-genomicranges (package (name "r-genomicranges") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a57c420a07..38f3298c23 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9168,40 +9168,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-genomicfiles - (package - (name "r-genomicfiles") - (version "1.26.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "GenomicFiles" version)) - (sha256 - (base32 - "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz")))) - (properties `((upstream-name . "GenomicFiles"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (home-page "https://bioconductor.org/packages/GenomicFiles") - (synopsis "Distributed computing by file or by range") - (description - "This package provides infrastructure for parallel computations -distributed by file or by range. User defined mapper and reducer functions -provide added flexibility for data combination and manipulation.") - (license license:artistic2.0))) - (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") -- cgit 1.4.1 From d1ea2b7c8b76dea810102379112b05d344b02530 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:59 +0200 Subject: gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Move from here... * gnu/packages/bioconductor.scm (r-dirichletmultinomial): ...to here. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 29 insertions(+), 29 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c369ac0cb4..fea0fe78ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2440,6 +2440,35 @@ testing. The package also provides functions for the visualization and exploration of the results.") (license license:gpl3+))) +(define-public r-dirichletmultinomial + (package + (name "r-dirichletmultinomial") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DirichletMultinomial" version)) + (sha256 + (base32 + "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk")))) + (properties + `((upstream-name . "DirichletMultinomial"))) + (build-system r-build-system) + (inputs + `(("gsl" ,gsl))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/DirichletMultinomial") + (synopsis "Dirichlet-Multinomial mixture models for microbiome data") + (description + "Dirichlet-multinomial mixture models can be used to describe variability +in microbial metagenomic data. This package is an interface to code +originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): +1-15.") + (license license:lgpl3))) + (define-public r-edaseq (package (name "r-edaseq") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 38f3298c23..dd095b6e05 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9168,35 +9168,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-dirichletmultinomial - (package - (name "r-dirichletmultinomial") - (version "1.32.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "DirichletMultinomial" version)) - (sha256 - (base32 - "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk")))) - (properties - `((upstream-name . "DirichletMultinomial"))) - (build-system r-build-system) - (inputs - `(("gsl" ,gsl))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://bioconductor.org/packages/DirichletMultinomial") - (synopsis "Dirichlet-Multinomial mixture models for microbiome data") - (description - "Dirichlet-multinomial mixture models can be used to describe variability -in microbial metagenomic data. This package is an interface to code -originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): -1-15.") - (license license:lgpl3))) - (define-public r-ensembldb (package (name "r-ensembldb") -- cgit 1.4.1 From 8182e6a6fd10bc6e8fb04a4a95df19266aa0b6b2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:00 +0200 Subject: gnu: r-organismdbi: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-organismdbi): Move from here... * gnu/packages/bioconductor.scm (r-organismdbi): ...to here. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 32 -------------------------------- 2 files changed, 32 insertions(+), 32 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fea0fe78ac..659c8f5c82 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3145,6 +3145,38 @@ mzIdentML files with the drawback of having less pretty output than a vendor specific parser.") (license license:gpl2+))) +(define-public r-organismdbi + (package + (name "r-organismdbi") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "OrganismDbi" version)) + (sha256 + (base32 + "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw")))) + (properties `((upstream-name . "OrganismDbi"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-dbi" ,r-dbi) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-graph" ,r-graph) + ("r-iranges" ,r-iranges) + ("r-rbgl" ,r-rbgl) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/OrganismDbi") + (synopsis "Software to enable the smooth interfacing of database packages") + (description "The package enables a simple unified interface to several +annotation packages each of which has its own schema by taking advantage of +the fact that each of these packages implements a select methods.") + (license license:artistic2.0))) + (define-public r-pcamethods (package (name "r-pcamethods") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dd095b6e05..9e7bae2525 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9213,38 +9213,6 @@ chromosome region or transcript models of lincRNA genes.") ;; No version specified (license license:lgpl3+))) -(define-public r-organismdbi - (package - (name "r-organismdbi") - (version "1.32.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "OrganismDbi" version)) - (sha256 - (base32 - "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw")))) - (properties `((upstream-name . "OrganismDbi"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-dbi" ,r-dbi) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-graph" ,r-graph) - ("r-iranges" ,r-iranges) - ("r-rbgl" ,r-rbgl) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://bioconductor.org/packages/OrganismDbi") - (synopsis "Software to enable the smooth interfacing of database packages") - (description "The package enables a simple unified interface to several -annotation packages each of which has its own schema by taking advantage of -the fact that each of these packages implements a select methods.") - (license license:artistic2.0))) - (define-public r-biovizbase (package (name "r-biovizbase") -- cgit 1.4.1 From 96ae9822c4c641587ea151e6a58eddbdb6e66590 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:01 +0200 Subject: gnu: r-affyio: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-affyio): Move from here... * gnu/packages/bioconductor.scm (r-affyio): ...to here. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 24 ------------------------ 2 files changed, 24 insertions(+), 24 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 659c8f5c82..9faf7021da 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1899,6 +1899,30 @@ problems in CEL-level data to help evaluate performance of quality metrics.") to streamline the more common analyses that a Biostatistician might see.") (license license:artistic2.0))) +(define-public r-affyio + (package + (name "r-affyio") + (version "1.60.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affyio" version)) + (sha256 + (base32 + "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h")))) + (build-system r-build-system) + (propagated-inputs + `(("r-zlibbioc" ,r-zlibbioc))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/bmbolstad/affyio") + (synopsis "Tools for parsing Affymetrix data files") + (description + "This package provides routines for parsing Affymetrix data files based +upon file format information. The primary focus is on accessing the CEL and +CDF file formats.") + (license license:lgpl2.0+))) + (define-public r-affxparser (package (name "r-affxparser") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9e7bae2525..0dd362c8ee 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9108,30 +9108,6 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) -(define-public r-affyio - (package - (name "r-affyio") - (version "1.60.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "affyio" version)) - (sha256 - (base32 - "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h")))) - (build-system r-build-system) - (propagated-inputs - `(("r-zlibbioc" ,r-zlibbioc))) - (inputs - `(("zlib" ,zlib))) - (home-page "https://github.com/bmbolstad/affyio") - (synopsis "Tools for parsing Affymetrix data files") - (description - "This package provides routines for parsing Affymetrix data files based -upon file format information. The primary focus is on accessing the CEL and -CDF file formats.") - (license license:lgpl2.0+))) - (define-public r-vsn (package (name "r-vsn") -- cgit 1.4.1 From 8d4311bb8e0e7ae68f0182bf232f598ebe2835e5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:02 +0200 Subject: gnu: r-vsn: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-vsn): Move from here... * gnu/packages/bioconductor.scm (r-vsn): ...to here. --- gnu/packages/bioconductor.scm | 36 ++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 36 ------------------------------------ 2 files changed, 36 insertions(+), 36 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9faf7021da..a631143102 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3746,6 +3746,42 @@ dependencies between GO terms can be implemented and applied.") coding changes and predict coding outcomes.") (license license:artistic2.0))) +(define-public r-vsn + (package + (name "r-vsn") + (version "3.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "vsn" version)) + (sha256 + (base32 + "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-ggplot2" ,r-ggplot2) + ("r-lattice" ,r-lattice) + ("r-limma" ,r-limma))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") + (synopsis "Variance stabilization and calibration for microarray data") + (description + "The package implements a method for normalising microarray intensities, +and works for single- and multiple-color arrays. It can also be used for data +from other technologies, as long as they have similar format. The method uses +a robust variant of the maximum-likelihood estimator for an +additive-multiplicative error model and affine calibration. The model +incorporates data calibration step (a.k.a. normalization), a model for the +dependence of the variance on the mean intensity and a variance stabilizing +data transformation. Differences between transformed intensities are +analogous to \"normalized log-ratios\". However, in contrast to the latter, +their variance is independent of the mean, and they are usually more sensitive +and specific in detecting differential transcription.") + (license license:artistic2.0))) + (define-public r-xvector (package (name "r-xvector") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0dd362c8ee..d133764963 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9108,42 +9108,6 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) -(define-public r-vsn - (package - (name "r-vsn") - (version "3.58.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "vsn" version)) - (sha256 - (base32 - "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb")))) - (build-system r-build-system) - (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-ggplot2" ,r-ggplot2) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma))) - (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes - (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") - (synopsis "Variance stabilization and calibration for microarray data") - (description - "The package implements a method for normalising microarray intensities, -and works for single- and multiple-color arrays. It can also be used for data -from other technologies, as long as they have similar format. The method uses -a robust variant of the maximum-likelihood estimator for an -additive-multiplicative error model and affine calibration. The model -incorporates data calibration step (a.k.a. normalization), a model for the -dependence of the variance on the mean intensity and a variance stabilizing -data transformation. Differences between transformed intensities are -analogous to \"normalized log-ratios\". However, in contrast to the latter, -their variance is independent of the mean, and they are usually more sensitive -and specific in detecting differential transcription.") - (license license:artistic2.0))) - (define-public r-ensembldb (package (name "r-ensembldb") -- cgit 1.4.1 From fea33b9d1e35c18fb214c12653b7624a627271d9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:03 +0200 Subject: gnu: r-biovizbase: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-biovizbase): Move from here... * gnu/packages/bioconductor.scm (r-biovizbase): ...to here. --- gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 42 ----------------------------------------- 2 files changed, 42 insertions(+), 42 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a631143102..56e7186209 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2249,6 +2249,48 @@ matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.") (license license:artistic2.0))) +(define-public r-biovizbase + (package + (name "r-biovizbase") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biovizBase" version)) + (sha256 + (base32 + "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq")))) + (properties `((upstream-name . "biovizBase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationfilter" ,r-annotationfilter) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-dichromat" ,r-dichromat) + ("r-ensembldb" ,r-ensembldb) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-hmisc" ,r-hmisc) + ("r-iranges" ,r-iranges) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rlang" ,r-rlang) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/biovizBase") + (synopsis "Basic graphic utilities for visualization of genomic data") + (description + "The biovizBase package is designed to provide a set of utilities, color +schemes and conventions for genomic data. It serves as the base for various +high-level packages for biological data visualization. This saves development +effort and encourages consistency.") + (license license:artistic2.0))) + (define-public r-bsgenome (package (name "r-bsgenome") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d133764963..b17ca0fabd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9153,48 +9153,6 @@ chromosome region or transcript models of lincRNA genes.") ;; No version specified (license license:lgpl3+))) -(define-public r-biovizbase - (package - (name "r-biovizbase") - (version "1.38.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "biovizBase" version)) - (sha256 - (base32 - "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq")))) - (properties `((upstream-name . "biovizBase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dichromat" ,r-dichromat) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (home-page "https://bioconductor.org/packages/biovizBase") - (synopsis "Basic graphic utilities for visualization of genomic data") - (description - "The biovizBase package is designed to provide a set of utilities, color -schemes and conventions for genomic data. It serves as the base for various -high-level packages for biological data visualization. This saves development -effort and encourages consistency.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit 1.4.1 From 88cf24febb43768c780d55cd496034d227096550 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:04 +0200 Subject: gnu: r-ensembldb: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-ensembldb): Move from here... * gnu/packages/bioconductor.scm (r-ensembldb): ...to here. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 45 ----------------------------------------- 2 files changed, 45 insertions(+), 45 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 56e7186209..eb0bcb22c6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2603,6 +2603,51 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.") (license license:gpl2+))) +(define-public r-ensembldb + (package + (name "r-ensembldb") + (version "2.14.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ensembldb" version)) + (sha256 + (base32 + "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationfilter" ,r-annotationfilter) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-curl" ,r-curl) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-protgenerics" ,r-protgenerics) + ("r-rsamtools" ,r-rsamtools) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/jotsetung/ensembldb") + (synopsis "Utilities to create and use Ensembl-based annotation databases") + (description + "The package provides functions to create and use transcript-centric +annotation databases/packages. The annotation for the databases are directly +fetched from Ensembl using their Perl API. The functionality and data is +similar to that of the TxDb packages from the @code{GenomicFeatures} package, +but, in addition to retrieve all gene/transcript models and annotations from +the database, the @code{ensembldb} package also provides a filter framework +allowing to retrieve annotations for specific entries like genes encoded on a +chromosome region or transcript models of lincRNA genes.") + ;; No version specified + (license license:lgpl3+))) + (define-public r-fastseg (package (name "r-fastseg") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b17ca0fabd..4be61522b6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9108,51 +9108,6 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) -(define-public r-ensembldb - (package - (name "r-ensembldb") - (version "2.14.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ensembldb" version)) - (sha256 - (base32 - "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-curl" ,r-curl) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-protgenerics" ,r-protgenerics) - ("r-rsamtools" ,r-rsamtools) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/jotsetung/ensembldb") - (synopsis "Utilities to create and use Ensembl-based annotation databases") - (description - "The package provides functions to create and use transcript-centric -annotation databases/packages. The annotation for the databases are directly -fetched from Ensembl using their Perl API. The functionality and data is -similar to that of the TxDb packages from the @code{GenomicFeatures} package, -but, in addition to retrieve all gene/transcript models and annotations from -the database, the @code{ensembldb} package also provides a filter framework -allowing to retrieve annotations for specific entries like genes encoded on a -chromosome region or transcript models of lincRNA genes.") - ;; No version specified - (license license:lgpl3+))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit 1.4.1 From 720d2694a5e50fac5d86f67a5faae61881ad4b38 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:05 +0200 Subject: gnu: r-mzr: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-mzr): Move from here... * gnu/packages/bioconductor.scm (r-mzr): ...to here. --- gnu/packages/bioconductor.scm | 62 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 61 ---------------------------------------- 2 files changed, 62 insertions(+), 61 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eb0bcb22c6..08d4545257 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -36,6 +36,7 @@ #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages boost) #:use-module (gnu packages cran) #:use-module (gnu packages compression) #:use-module (gnu packages gcc) @@ -3256,6 +3257,67 @@ mzIdentML files with the drawback of having less pretty output than a vendor specific parser.") (license license:gpl2+))) +(define-public r-mzr + (package + (name "r-mzr") + (version "2.24.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mzR" version)) + (sha256 + (base32 + "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "src/boost") + #t)))) + (properties `((upstream-name . "mzR"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-boost + (lambda _ + (substitute* "src/Makevars" + (("\\./boost/libs.*") "") + ;; This is to avoid having a plain directory on the list of + ;; libraries to link. + (("\\(RHDF5_LIBS\\)" match) + (string-append match "/libhdf5.a")) + (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ") + (("\\ARCH_OBJS=" line) + (string-append line + "\nBOOST_LIBS=-lboost_system -lboost_regex \ +-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) + #t))))) + (inputs + `(;; Our default boost package won't work here, unfortunately, even with + ;; mzR version 2.24.1. + ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources + ("zlib" ,zlib))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-ncdf4" ,r-ncdf4) + ("r-protgenerics" ,r-protgenerics) + ("r-rcpp" ,r-rcpp) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/sneumann/mzR/") + (synopsis "Parser for mass spectrometry data files") + (description + "The mzR package provides a unified API to the common file formats and +parsers available for mass spectrometry data. It comes with a wrapper for the +ISB random access parser for mass spectrometry mzXML, mzData and mzML files. +The package contains the original code written by the ISB, and a subset of the +proteowizard library for mzML and mzIdentML. The netCDF reading code has +previously been used in XCMS.") + (license license:artistic2.0))) + (define-public r-organismdbi (package (name "r-organismdbi") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4be61522b6..b356a76681 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9047,67 +9047,6 @@ trait.") proteomics packages.") (license license:artistic2.0))) -(define-public r-mzr - (package - (name "r-mzr") - (version "2.24.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "mzR" version)) - (sha256 - (base32 - "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg")) - (modules '((guix build utils))) - (snippet - '(begin - (delete-file-recursively "src/boost") - #t)))) - (properties `((upstream-name . "mzR"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-system-boost - (lambda _ - (substitute* "src/Makevars" - (("\\./boost/libs.*") "") - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\(RHDF5_LIBS\\)" match) - (string-append match "/libhdf5.a")) - (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ") - (("\\ARCH_OBJS=" line) - (string-append line - "\nBOOST_LIBS=-lboost_system -lboost_regex \ --lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) - #t))))) - (inputs - `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.24.1. - ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources - ("zlib" ,zlib))) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-ncdf4" ,r-ncdf4) - ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/sneumann/mzR/") - (synopsis "Parser for mass spectrometry data files") - (description - "The mzR package provides a unified API to the common file formats and -parsers available for mass spectrometry data. It comes with a wrapper for the -ISB random access parser for mass spectrometry mzXML, mzData and mzML files. -The package contains the original code written by the ISB, and a subset of the -proteowizard library for mzML and mzIdentML. The netCDF reading code has -previously been used in XCMS.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit 1.4.1 From 900ef8fb1ea8a85966a1a81ea01a9f3670fc8c58 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:06 +0200 Subject: gnu: r-protgenerics: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-protgenerics): Move from here... * gnu/packages/bioconductor.scm (r-protgenerics): ...to here. --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ gnu/packages/bioinformatics.scm | 20 -------------------- 2 files changed, 20 insertions(+), 20 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 08d4545257..8e0182691b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3380,6 +3380,26 @@ the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results.") (license license:gpl3+))) +(define-public r-protgenerics + (package + (name "r-protgenerics") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ProtGenerics" version)) + (sha256 + (base32 + "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz")))) + (properties `((upstream-name . "ProtGenerics"))) + (build-system r-build-system) + (home-page "https://github.com/lgatto/ProtGenerics") + (synopsis "S4 generic functions for proteomics infrastructure") + (description + "This package provides S4 generic functions needed by Bioconductor +proteomics packages.") + (license license:artistic2.0))) + (define-public r-rbgl (package (name "r-rbgl") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b356a76681..ca0952895c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9027,26 +9027,6 @@ for analyzing gene-level association tests in meta-analyses for binary trait.") (license license:gpl3))) -(define-public r-protgenerics - (package - (name "r-protgenerics") - (version "1.22.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ProtGenerics" version)) - (sha256 - (base32 - "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz")))) - (properties `((upstream-name . "ProtGenerics"))) - (build-system r-build-system) - (home-page "https://github.com/lgatto/ProtGenerics") - (synopsis "S4 generic functions for proteomics infrastructure") - (description - "This package provides S4 generic functions needed by Bioconductor -proteomics packages.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit 1.4.1 From 621aa3b442341c81305d2d56835203ff517a7bb9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:07 +0200 Subject: gnu: r-sva: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-sva): Move from here... * gnu/packages/bioconductor.scm (r-sva): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8e0182691b..a4d99dd929 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3790,6 +3790,37 @@ typically represent genomic ranges of interest and the columns represent samples.") (license license:artistic2.0))) +(define-public r-sva + (package + (name "r-sva") + (version "3.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "sva" version)) + (sha256 + (base32 + "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy")))) + (build-system r-build-system) + (propagated-inputs + `(("r-edger" ,r-edger) + ("r-genefilter" ,r-genefilter) + ("r-mgcv" ,r-mgcv) + ("r-biocparallel" ,r-biocparallel) + ("r-matrixstats" ,r-matrixstats) + ("r-limma" ,r-limma))) + (home-page "https://bioconductor.org/packages/sva") + (synopsis "Surrogate variable analysis") + (description + "This package contains functions for removing batch effects and other +unwanted variation in high-throughput experiment. It also contains functions +for identifying and building surrogate variables for high-dimensional data +sets. Surrogate variables are covariates constructed directly from +high-dimensional data like gene expression/RNA sequencing/methylation/brain +imaging data that can be used in subsequent analyses to adjust for unknown, +unmodeled, or latent sources of noise.") + (license license:artistic2.0))) + (define-public r-systempiper (package (name "r-systempiper") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ca0952895c..cb0fe505cb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8964,37 +8964,6 @@ resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq.") (license license:artistic2.0))) -(define-public r-sva - (package - (name "r-sva") - (version "3.38.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "sva" version)) - (sha256 - (base32 - "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy")))) - (build-system r-build-system) - (propagated-inputs - `(("r-edger" ,r-edger) - ("r-genefilter" ,r-genefilter) - ("r-mgcv" ,r-mgcv) - ("r-biocparallel" ,r-biocparallel) - ("r-matrixstats" ,r-matrixstats) - ("r-limma" ,r-limma))) - (home-page "https://bioconductor.org/packages/sva") - (synopsis "Surrogate variable analysis") - (description - "This package contains functions for removing batch effects and other -unwanted variation in high-throughput experiment. It also contains functions -for identifying and building surrogate variables for high-dimensional data -sets. Surrogate variables are covariates constructed directly from -high-dimensional data like gene expression/RNA sequencing/methylation/brain -imaging data that can be used in subsequent analyses to adjust for unknown, -unmodeled, or latent sources of noise.") - (license license:artistic2.0))) - (define-public r-raremetals2 (package (name "r-raremetals2") -- cgit 1.4.1 From c2a18aee16a59330a005bf6818df733a2f56c425 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:08 +0200 Subject: gnu: r-motifrg: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-motifrg): Move from here... * gnu/packages/bioconductor.scm (r-motifrg): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a4d99dd929..c9f72c5492 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3129,6 +3129,33 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-motifrg + (package + (name "r-motifrg") + (version "1.31.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "motifRG" version)) + (sha256 + (base32 + "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn")))) + (properties `((upstream-name . "motifRG"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-iranges" ,r-iranges) + ("r-seqlogo" ,r-seqlogo) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/motifRG") + (synopsis "Discover motifs in high throughput sequencing data") + (description + "This package provides tools for discriminative motif discovery in high +throughput genetic sequencing data sets using regression methods.") + (license license:artistic2.0))) + (define-public r-msnbase (package (name "r-msnbase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cb0fe505cb..8f011f0c78 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8046,33 +8046,6 @@ plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).") (license license:lgpl2.0+))) -(define-public r-motifrg - (package - (name "r-motifrg") - (version "1.31.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "motifRG" version)) - (sha256 - (base32 - "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn")))) - (properties `((upstream-name . "motifRG"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-iranges" ,r-iranges) - ("r-seqlogo" ,r-seqlogo) - ("r-xvector" ,r-xvector))) - (home-page "https://bioconductor.org/packages/motifRG") - (synopsis "Discover motifs in high throughput sequencing data") - (description - "This package provides tools for discriminative motif discovery in high -throughput genetic sequencing data sets using regression methods.") - (license license:artistic2.0))) - (define-public r-zlibbioc (package (name "r-zlibbioc") -- cgit 1.4.1 From 0006a664155c7d556ac773b254fd09205412c172 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:09 +0200 Subject: gnu: r-seqlogo: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-seqlogo): Move from here... * gnu/packages/bioconductor.scm (r-seqlogo): ...to here. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 23 ----------------------- 2 files changed, 23 insertions(+), 23 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c9f72c5492..b53267e80d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3652,6 +3652,29 @@ differential expression analysis, RNAseq data and related problems.") ;; Any version of the LGPL (license license:lgpl3+))) +(define-public r-seqlogo + (package + (name "r-seqlogo") + (version "1.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "seqLogo" version)) + (sha256 + (base32 + "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1")))) + (properties `((upstream-name . "seqLogo"))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/seqLogo") + (synopsis "Sequence logos for DNA sequence alignments") + (description + "seqLogo takes the position weight matrix of a DNA sequence motif and +plots the corresponding sequence logo as introduced by Schneider and +Stephens (1990).") + (license license:lgpl2.0+))) + (define-public r-seqpattern (package (name "r-seqpattern") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8f011f0c78..832de0baad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8023,29 +8023,6 @@ used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.") (license license:bsd-3))) -(define-public r-seqlogo - (package - (name "r-seqlogo") - (version "1.56.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "seqLogo" version)) - (sha256 - (base32 - "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1")))) - (properties `((upstream-name . "seqLogo"))) - (build-system r-build-system) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/seqLogo") - (synopsis "Sequence logos for DNA sequence alignments") - (description - "seqLogo takes the position weight matrix of a DNA sequence motif and -plots the corresponding sequence logo as introduced by Schneider and -Stephens (1990).") - (license license:lgpl2.0+))) - (define-public r-zlibbioc (package (name "r-zlibbioc") -- cgit 1.4.1 From e0c81584ea47ebce218a9ef37accab0889860fc1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:10 +0200 Subject: gnu: r-zlibbioc: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-zlibbioc): Move from here... * gnu/packages/bioconductor.scm (r-zlibbioc): ...to here. --- gnu/packages/bioconductor.scm | 19 +++++++++++++++++++ gnu/packages/bioinformatics.scm | 19 ------------------- 2 files changed, 19 insertions(+), 19 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b53267e80d..ea4e373b49 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4068,6 +4068,25 @@ and specific in detecting differential transcription.") \"externally\" (behind an R external pointer, or on disk).") (license license:artistic2.0))) +(define-public r-zlibbioc + (package + (name "r-zlibbioc") + (version "1.36.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "zlibbioc" version)) + (sha256 + (base32 + "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg")))) + (properties + `((upstream-name . "zlibbioc"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/zlibbioc") + (synopsis "Provider for zlib-1.2.5 to R packages") + (description "This package uses the source code of zlib-1.2.5 to create +libraries for systems that do not have these available via other means.") + (license license:artistic2.0))) + (define-public r-geneplotter (package (name "r-geneplotter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 832de0baad..3bd982ae31 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8023,25 +8023,6 @@ used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.") (license license:bsd-3))) -(define-public r-zlibbioc - (package - (name "r-zlibbioc") - (version "1.36.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "zlibbioc" version)) - (sha256 - (base32 - "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg")))) - (properties - `((upstream-name . "zlibbioc"))) - (build-system r-build-system) - (home-page "https://bioconductor.org/packages/zlibbioc") - (synopsis "Provider for zlib-1.2.5 to R packages") - (description "This package uses the source code of zlib-1.2.5 to create -libraries for systems that do not have these available via other means.") - (license license:artistic2.0))) - (define-public r-r4rna (package (name "r-r4rna") -- cgit 1.4.1 From 043c309d154a69455e0fa7624afa98b912bffb6d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:11 +0200 Subject: gnu: r-rhtslib: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-rhtslib): Move from here... * gnu/packages/bioconductor.scm (r-rhtslib): ...to here. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 32 insertions(+), 31 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ea4e373b49..cb42c0bed2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -39,6 +39,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages cran) #:use-module (gnu packages compression) + #:use-module (gnu packages curl) #:use-module (gnu packages gcc) #:use-module (gnu packages graph) #:use-module (gnu packages graphviz) @@ -3037,6 +3038,37 @@ Enrichment Analysis} (GSEA).") the Human Protein Atlas project.") (license license:artistic2.0))) +(define-public r-rhtslib + (package + (name "r-rhtslib") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Rhtslib" version)) + (sha256 + (base32 + "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4")))) + (properties `((upstream-name . "Rhtslib"))) + (build-system r-build-system) + ;; Without this a temporary directory ends up in the Rhtslib.so binary, + ;; which makes R abort the build. + (arguments '(#:configure-flags '("--no-staged-install"))) + (propagated-inputs + `(("curl" ,curl) + ("zlib" ,zlib) ; packages using rhtslib need to link with zlib + ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) + (home-page "https://github.com/nhayden/Rhtslib") + (synopsis "High-throughput sequencing library as an R package") + (description + "This package provides the HTSlib C library for high-throughput +nucleotide sequence analysis. The package is primarily useful to developers +of other R packages who wish to make use of HTSlib.") + (license license:lgpl2.0+))) + (define-public r-impute (package (name "r-impute") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3bd982ae31..fd83c4dd48 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8046,37 +8046,6 @@ characteristic tag shift values in these assays.") secondary structure and comparative analysis in R.") (license license:gpl3+))) -(define-public r-rhtslib - (package - (name "r-rhtslib") - (version "1.22.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "Rhtslib" version)) - (sha256 - (base32 - "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4")))) - (properties `((upstream-name . "Rhtslib"))) - (build-system r-build-system) - ;; Without this a temporary directory ends up in the Rhtslib.so binary, - ;; which makes R abort the build. - (arguments '(#:configure-flags '("--no-staged-install"))) - (propagated-inputs - `(("curl" ,curl) - ("zlib" ,zlib) ; packages using rhtslib need to link with zlib - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) - (home-page "https://github.com/nhayden/Rhtslib") - (synopsis "High-throughput sequencing library as an R package") - (description - "This package provides the HTSlib C library for high-throughput -nucleotide sequence analysis. The package is primarily useful to developers -of other R packages who wish to make use of HTSlib.") - (license license:lgpl2.0+))) - (define-public r-bamsignals (package (name "r-bamsignals") -- cgit 1.4.1 From 45b6db4fb4b6963be6fca4dc747d763673edce3c Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:12 +0200 Subject: gnu: r-bamsignals: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-bamsignals): Move from here... * gnu/packages/bioconductor.scm (r-bamsignals): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cb42c0bed2..382e3b6d28 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2109,6 +2109,36 @@ standalone, be utilized in other packages, or be wrapped up in higher-level classes.") (license license:gpl2+))) +(define-public r-bamsignals + (package + (name "r-bamsignals") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bamsignals" version)) + (sha256 + (base32 + "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcpp" ,r-rcpp) + ("r-rhtslib" ,r-rhtslib) + ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/bamsignals") + (synopsis "Extract read count signals from bam files") + (description + "This package efficiently obtains count vectors from indexed bam +files. It counts the number of nucleotide sequence reads in given genomic +ranges and it computes reads profiles and coverage profiles. It also handles +paired-end data.") + (license license:gpl2+))) + (define-public r-biobase (package (name "r-biobase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fd83c4dd48..998541434f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8046,36 +8046,6 @@ characteristic tag shift values in these assays.") secondary structure and comparative analysis in R.") (license license:gpl3+))) -(define-public r-bamsignals - (package - (name "r-bamsignals") - (version "1.22.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "bamsignals" version)) - (sha256 - (base32 - "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/bamsignals") - (synopsis "Extract read count signals from bam files") - (description - "This package efficiently obtains count vectors from indexed bam -files. It counts the number of nucleotide sequence reads in given genomic -ranges and it computes reads profiles and coverage profiles. It also handles -paired-end data.") - (license license:gpl2+))) - (define-public r-rcas (package (name "r-rcas") -- cgit 1.4.1 From 7360dea62449d5c4f5ce897ee8f642090326ebc9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:13 +0200 Subject: gnu: r-rcas: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-rcas): Move from here... * gnu/packages/bioconductor.scm (r-rcas): ...to here. --- gnu/packages/bioconductor.scm | 49 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 49 ----------------------------------------- 2 files changed, 49 insertions(+), 49 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 382e3b6d28..ca9e15d53e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3512,6 +3512,55 @@ proteomics packages.") the graph algorithms contained in the Boost library.") (license license:artistic2.0))) +(define-public r-rcas + (package + (name "r-rcas") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "RCAS" version)) + (sha256 + (base32 + "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m")))) + (properties `((upstream-name . "RCAS"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-cowplot" ,r-cowplot) + ("r-data-table" ,r-data-table) + ("r-dt" ,r-dt) + ("r-genomation" ,r-genomation) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-ggseqlogo" ,r-ggseqlogo) + ("r-gprofiler2" ,r-gprofiler2) + ("r-iranges" ,r-iranges) + ("r-pbapply" ,r-pbapply) + ("r-pheatmap" ,r-pheatmap) + ("r-plotly" ,r-plotly) + ("r-plotrix" ,r-plotrix) + ("r-proxy" ,r-proxy) + ("r-ranger" ,r-ranger) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-rmarkdown" ,r-rmarkdown) + ("r-s4vectors" ,r-s4vectors) + ("pandoc" ,pandoc))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (synopsis "RNA-centric annotation system") + (description + "RCAS aims to be a standalone RNA-centric annotation system that provides +intuitive reports and publication-ready graphics. This package provides the R +library implementing most of the pipeline's features.") + (home-page "https://github.com/BIMSBbioinfo/RCAS") + (license license:artistic2.0))) + (define-public r-regioner (package (name "r-regioner") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 998541434f..e9eebd35b5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8046,55 +8046,6 @@ characteristic tag shift values in these assays.") secondary structure and comparative analysis in R.") (license license:gpl3+))) -(define-public r-rcas - (package - (name "r-rcas") - (version "1.16.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "RCAS" version)) - (sha256 - (base32 - "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m")))) - (properties `((upstream-name . "RCAS"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-cowplot" ,r-cowplot) - ("r-data-table" ,r-data-table) - ("r-dt" ,r-dt) - ("r-genomation" ,r-genomation) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggseqlogo" ,r-ggseqlogo) - ("r-gprofiler2" ,r-gprofiler2) - ("r-iranges" ,r-iranges) - ("r-pbapply" ,r-pbapply) - ("r-pheatmap" ,r-pheatmap) - ("r-plotly" ,r-plotly) - ("r-plotrix" ,r-plotrix) - ("r-proxy" ,r-proxy) - ("r-ranger" ,r-ranger) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rmarkdown" ,r-rmarkdown) - ("r-s4vectors" ,r-s4vectors) - ("pandoc" ,pandoc))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (synopsis "RNA-centric annotation system") - (description - "RCAS aims to be a standalone RNA-centric annotation system that provides -intuitive reports and publication-ready graphics. This package provides the R -library implementing most of the pipeline's features.") - (home-page "https://github.com/BIMSBbioinfo/RCAS") - (license license:artistic2.0))) - (define-public rcas-web (package (name "rcas-web") -- cgit 1.4.1 From bf8f50295696a95a0ae3dca14188709b4330efac Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:14 +0200 Subject: gnu: r-mutationalpatterns: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-mutationalpatterns): Move from here... * gnu/packages/bioconductor.scm (r-mutationalpatterns): ...to here. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 45 ----------------------------------------- 2 files changed, 45 insertions(+), 45 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ca9e15d53e..f66ba6ce5f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3218,6 +3218,51 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") throughput genetic sequencing data sets using regression methods.") (license license:artistic2.0))) +(define-public r-mutationalpatterns + (package + (name "r-mutationalpatterns") + (version "3.0.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MutationalPatterns" version)) + (sha256 + (base32 + "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ;; These two packages are suggested packages + ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-cowplot" ,r-cowplot) + ("r-dplyr" ,r-dplyr) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggalluvial" ,r-ggalluvial) + ("r-ggdendro" ,r-ggdendro) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-magrittr" ,r-magrittr) + ("r-nmf" ,r-nmf) + ("r-pracma" ,r-pracma) + ("r-purrr" ,r-purrr) + ("r-s4vectors" ,r-s4vectors) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/MutationalPatterns/") + (synopsis "Extract and visualize mutational patterns in genomic data") + (description "This package provides an extensive toolset for the +characterization and visualization of a wide range of mutational patterns +in SNV base substitution data.") + (license license:expat))) + (define-public r-msnbase (package (name "r-msnbase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e9eebd35b5..2fc46c7978 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8097,51 +8097,6 @@ secondary structure and comparative analysis in R.") @dfn{RNA-centric annotation system} (RCAS).") (license license:agpl3+))) -(define-public r-mutationalpatterns - (package - (name "r-mutationalpatterns") - (version "3.0.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "MutationalPatterns" version)) - (sha256 - (base32 - "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35")))) - (build-system r-build-system) - (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ;; These two packages are suggested packages - ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggalluvial" ,r-ggalluvial) - ("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-magrittr" ,r-magrittr) - ("r-nmf" ,r-nmf) - ("r-pracma" ,r-pracma) - ("r-purrr" ,r-purrr) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-variantannotation" ,r-variantannotation))) - (home-page "https://bioconductor.org/packages/MutationalPatterns/") - (synopsis "Extract and visualize mutational patterns in genomic data") - (description "This package provides an extensive toolset for the -characterization and visualization of a wide range of mutational patterns -in SNV base substitution data.") - (license license:expat))) - (define-public r-chipkernels (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372") (revision "1")) -- cgit 1.4.1 From b6e84d30ebd5b5bd1bb1027a6199601b96580fa9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:15 +0200 Subject: gnu: r-tximport: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-tximport): Move from here... * gnu/packages/bioconductor.scm (r-tximport): ...to here. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 24 ------------------------ 2 files changed, 24 insertions(+), 24 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f66ba6ce5f..f276749abf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4114,6 +4114,30 @@ dependencies between GO terms can be implemented and applied.") ;; Any version of the LGPL applies. (license license:lgpl2.1+))) +(define-public r-tximport + (package + (name "r-tximport") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tximport" version)) + (sha256 + (base32 + "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/tximport") + (synopsis "Import and summarize transcript-level estimates for gene-level analysis") + (description + "This package provides tools to import transcript-level abundance, +estimated counts and transcript lengths, and to summarize them into matrices +for use with downstream gene-level analysis packages. Average transcript +length, weighted by sample-specific transcript abundance estimates, is +provided as a matrix which can be used as an offset for different expression +of gene-level counts.") + (license license:gpl2+))) + (define-public r-variantannotation (package (name "r-variantannotation") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2fc46c7978..fcaed708a6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8164,30 +8164,6 @@ bound and non bound genomic regions to accurately identify transcription factors bound at the specific regions.") (license license:gpl2+))) -(define-public r-tximport - (package - (name "r-tximport") - (version "1.18.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "tximport" version)) - (sha256 - (base32 - "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34")))) - (build-system r-build-system) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/tximport") - (synopsis "Import and summarize transcript-level estimates for gene-level analysis") - (description - "This package provides tools to import transcript-level abundance, -estimated counts and transcript lengths, and to summarize them into matrices -for use with downstream gene-level analysis packages. Average transcript -length, weighted by sample-specific transcript abundance estimates, is -provided as a matrix which can be used as an offset for different expression -of gene-level counts.") - (license license:gpl2+))) - (define-public r-rhdf5filters (package (name "r-rhdf5filters") -- cgit 1.4.1 From 67e99369c1f96b3eda703702de0fdcfa17d34872 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:16 +0200 Subject: gnu: r-rhdf5filters: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-rhdf5filters): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5filters): ...to here. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f276749abf..faa464d5b7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3687,6 +3687,32 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) +(define-public r-rhdf5filters + (package + (name "r-rhdf5filters") + (version "1.2.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "rhdf5filters" version)) + (sha256 + (base32 + "1bjlgc76vx0z81s8vci9ln1d2s3b157qnm32xs36mnyjk31ivasz")))) + (properties `((upstream-name . "rhdf5filters"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rhdf5lib" ,r-rhdf5lib))) + (inputs + `(("zlib" ,zlib))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/grimbough/rhdf5filters") + (synopsis "HDF5 compression filters") + (description + "This package provides a collection of compression filters for use with +HDF5 datasets.") + (license license:bsd-2))) + (define-public r-rsamtools (package (name "r-rsamtools") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fcaed708a6..24973d3cb4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8164,32 +8164,6 @@ bound and non bound genomic regions to accurately identify transcription factors bound at the specific regions.") (license license:gpl2+))) -(define-public r-rhdf5filters - (package - (name "r-rhdf5filters") - (version "1.2.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "rhdf5filters" version)) - (sha256 - (base32 - "1bjlgc76vx0z81s8vci9ln1d2s3b157qnm32xs36mnyjk31ivasz")))) - (properties `((upstream-name . "rhdf5filters"))) - (build-system r-build-system) - (propagated-inputs - `(("r-rhdf5lib" ,r-rhdf5lib))) - (inputs - `(("zlib" ,zlib))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/grimbough/rhdf5filters") - (synopsis "HDF5 compression filters") - (description - "This package provides a collection of compression filters for use with -HDF5 datasets.") - (license license:bsd-2))) - (define-public r-rhdf5 (package (name "r-rhdf5") -- cgit 1.4.1 From cc1dbea883fed7515130144a2413c49c11c5352f Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:17 +0200 Subject: gnu: r-annotationfilter: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-annotationfilter): Move from here... * gnu/packages/bioconductor.scm (r-annotationfilter): ...to here. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index faa464d5b7..a6d0350da9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2009,6 +2009,32 @@ microarrays.") annotation data packages using SQLite data storage.") (license license:artistic2.0))) +(define-public r-annotationfilter + (package + (name "r-annotationfilter") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationFilter" version)) + (sha256 + (base32 + "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9")))) + (properties + `((upstream-name . "AnnotationFilter"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomicranges" ,r-genomicranges) + ("r-lazyeval" ,r-lazyeval))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/Bioconductor/AnnotationFilter") + (synopsis "Facilities for filtering Bioconductor annotation resources") + (description + "This package provides classes and other infrastructure to implement +filters for manipulating Bioconductor annotation resources. The filters are +used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") + (license license:artistic2.0))) + (define-public r-annotationforge (package (name "r-annotationforge") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 24973d3cb4..c144344dc7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8203,32 +8203,6 @@ package, and for letting R applications work on datasets that are larger than the available RAM.") (license license:artistic2.0))) -(define-public r-annotationfilter - (package - (name "r-annotationfilter") - (version "1.14.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "AnnotationFilter" version)) - (sha256 - (base32 - "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9")))) - (properties - `((upstream-name . "AnnotationFilter"))) - (build-system r-build-system) - (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-lazyeval" ,r-lazyeval))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/Bioconductor/AnnotationFilter") - (synopsis "Facilities for filtering Bioconductor annotation resources") - (description - "This package provides classes and other infrastructure to implement -filters for manipulating Bioconductor annotation resources. The filters are -used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") - (license license:artistic2.0))) - (define-public emboss (package (name "emboss") -- cgit 1.4.1 From 0eaa75c8117b4e91475d7c4ad9960b925cef5d56 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:18 +0200 Subject: gnu: r-rhdf5: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-rhdf5): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5): ...to here. --- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 39 --------------------------------------- 2 files changed, 39 insertions(+), 39 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a6d0350da9..5ae045456a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3713,6 +3713,45 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) +(define-public r-rhdf5 + (package + (name "r-rhdf5") + (version "2.34.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "rhdf5" version)) + (sha256 + (base32 + "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-linking + (lambda _ + (substitute* "src/Makevars" + ;; This is to avoid having a plain directory on the list of + ;; libraries to link. + (("\\(RHDF5_LIBS\\)" match) + (string-append match "/libhdf5.a"))) + #t))))) + (propagated-inputs + `(("r-rhdf5filters" ,r-rhdf5filters) + ("r-rhdf5lib" ,r-rhdf5lib))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/rhdf5") + (synopsis "HDF5 interface to R") + (description + "This R/Bioconductor package provides an interface between HDF5 and R. +HDF5's main features are the ability to store and access very large and/or +complex datasets and a wide variety of metadata on mass storage (disk) through +a completely portable file format. The rhdf5 package is thus suited for the +exchange of large and/or complex datasets between R and other software +package, and for letting R applications work on datasets that are larger than +the available RAM.") + (license license:artistic2.0))) + (define-public r-rhdf5filters (package (name "r-rhdf5filters") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c144344dc7..a241a83c80 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8164,45 +8164,6 @@ bound and non bound genomic regions to accurately identify transcription factors bound at the specific regions.") (license license:gpl2+))) -(define-public r-rhdf5 - (package - (name "r-rhdf5") - (version "2.34.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "rhdf5" version)) - (sha256 - (base32 - "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi")))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-linking - (lambda _ - (substitute* "src/Makevars" - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\(RHDF5_LIBS\\)" match) - (string-append match "/libhdf5.a"))) - #t))))) - (propagated-inputs - `(("r-rhdf5filters" ,r-rhdf5filters) - ("r-rhdf5lib" ,r-rhdf5lib))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/rhdf5") - (synopsis "HDF5 interface to R") - (description - "This R/Bioconductor package provides an interface between HDF5 and R. -HDF5's main features are the ability to store and access very large and/or -complex datasets and a wide variety of metadata on mass storage (disk) through -a completely portable file format. The rhdf5 package is thus suited for the -exchange of large and/or complex datasets between R and other software -package, and for letting R applications work on datasets that are larger than -the available RAM.") - (license license:artistic2.0))) - (define-public emboss (package (name "emboss") -- cgit 1.4.1 From 31e50e1f48308a78a04f9aced53f2c2706660b31 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:19 +0200 Subject: gnu: r-chipseq: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-chipseq): Move from here... * gnu/packages/bioconductor.scm (r-chipseq): ...to here. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5ae045456a..2a7872cbd2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2411,6 +2411,32 @@ genome data packages and support for efficient SNP representation.") analysis.") (license license:artistic2.0))) +(define-public r-chipseq + (package + (name "r-chipseq") + (version "1.40.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "chipseq" version)) + (sha256 + (base32 + "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-s4vectors" ,r-s4vectors) + ("r-shortread" ,r-shortread))) + (home-page "https://bioconductor.org/packages/chipseq") + (synopsis "Package for analyzing ChIPseq data") + (description + "This package provides tools for processing short read data from ChIPseq +experiments.") + (license license:artistic2.0))) + (define-public r-complexheatmap (package (name "r-complexheatmap") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a241a83c80..aa92ae3916 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8486,32 +8486,6 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-chipseq - (package - (name "r-chipseq") - (version "1.40.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "chipseq" version)) - (sha256 - (base32 - "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-s4vectors" ,r-s4vectors) - ("r-shortread" ,r-shortread))) - (home-page "https://bioconductor.org/packages/chipseq") - (synopsis "Package for analyzing ChIPseq data") - (description - "This package provides tools for processing short read data from ChIPseq -experiments.") - (license license:artistic2.0))) - (define-public r-copyhelper (package (name "r-copyhelper") -- cgit 1.4.1 From 36cb01066cc03b2d341b55f21ebba2156518a560 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:20 +0200 Subject: gnu: r-copyhelper: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-copyhelper): Move from here... * gnu/packages/bioconductor.scm (r-copyhelper): ...to here. [source]: Repalce 'string-append' by 'bioconductor-uri' with 'experiment. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 24 insertions(+), 26 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2a7872cbd2..9118642e66 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1128,6 +1128,30 @@ average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.") (license license:artistic2.0))) +(define-public r-copyhelper + (package + (name "r-copyhelper") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CopyhelpeR" version 'experiment)) + (sha256 + (base32 + "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq")))) + (properties `((upstream-name . "CopyhelpeR"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/CopyhelpeR/") + (synopsis "Helper files for CopywriteR") + (description + "This package contains the helper files that are required to run the +Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content +and mappability files for the reference genomes hg18, hg19, hg38, mm9 and +mm10. In addition, it contains a blacklist filter to remove regions that +display copy number variation. Files are stored as GRanges objects from the +GenomicRanges Bioconductor package.") + (license license:gpl2))) + (define-public r-genelendatabase (package (name "r-genelendatabase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index aa92ae3916..85e586a174 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8486,32 +8486,6 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-copyhelper - (package - (name "r-copyhelper") - (version "1.6.0") - (source - (origin - (method url-fetch) - (uri (string-append "https://bioconductor.org/packages/release/" - "data/experiment/src/contrib/CopyhelpeR_" - version ".tar.gz")) - (sha256 - (base32 - "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq")))) - (properties `((upstream-name . "CopyhelpeR"))) - (build-system r-build-system) - (home-page "https://bioconductor.org/packages/CopyhelpeR/") - (synopsis "Helper files for CopywriteR") - (description - "This package contains the helper files that are required to run the -Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content -and mappability files for the reference genomes hg18, hg19, hg38, mm9 and -mm10. In addition, it contains a blacklist filter to remove regions that -display copy number variation. Files are stored as GRanges objects from the -GenomicRanges Bioconductor package.") - (license license:gpl2))) - (define-public r-copywriter (package (name "r-copywriter") -- cgit 1.4.1 From 7ab44aeed61b1e0a3a048bf2b991180d76a97aff Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:21 +0200 Subject: gnu: r-copywriter: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-copywriter): Move from here... * gnu/packages/bioconductor.scm (r-copywriter): ...to here. --- gnu/packages/bioconductor.scm | 40 ++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 40 ---------------------------------------- 2 files changed, 40 insertions(+), 40 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9118642e66..fae6073446 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2500,6 +2500,46 @@ provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.") (license license:gpl2+))) +(define-public r-copywriter + (package + (name "r-copywriter") + (version "2.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CopywriteR" version)) + (sha256 + (base32 + "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f")))) + (properties `((upstream-name . "CopywriteR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-chipseq" ,r-chipseq) + ("r-copyhelper" ,r-copyhelper) + ("r-data-table" ,r-data-table) + ("r-dnacopy" ,r-dnacopy) + ("r-futile-logger" ,r-futile-logger) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-gtools" ,r-gtools) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://github.com/PeeperLab/CopywriteR") + (synopsis "Copy number information from targeted sequencing") + (description + "CopywriteR extracts DNA copy number information from targeted sequencing +by utilizing off-target reads. It allows for extracting uniformly distributed +copy number information, can be used without reference, and can be applied to +sequencing data obtained from various techniques including chromatin +immunoprecipitation and target enrichment on small gene panels. Thereby, +CopywriteR constitutes a widely applicable alternative to available copy +number detection tools.") + (license license:gpl2))) + (define-public r-deseq (package (name "r-deseq") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 85e586a174..abfaa3d4af 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8486,46 +8486,6 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-copywriter - (package - (name "r-copywriter") - (version "2.22.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "CopywriteR" version)) - (sha256 - (base32 - "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f")))) - (properties `((upstream-name . "CopywriteR"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-chipseq" ,r-chipseq) - ("r-copyhelper" ,r-copyhelper) - ("r-data-table" ,r-data-table) - ("r-dnacopy" ,r-dnacopy) - ("r-futile-logger" ,r-futile-logger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://github.com/PeeperLab/CopywriteR") - (synopsis "Copy number information from targeted sequencing") - (description - "CopywriteR extracts DNA copy number information from targeted sequencing -by utilizing off-target reads. It allows for extracting uniformly distributed -copy number information, can be used without reference, and can be applied to -sequencing data obtained from various techniques including chromatin -immunoprecipitation and target enrichment on small gene panels. Thereby, -CopywriteR constitutes a widely applicable alternative to available copy -number detection tools.") - (license license:gpl2))) - (define-public r-methylkit (package (name "r-methylkit") -- cgit 1.4.1 From c294c0d782bf36a88e24eb4efcd2fbbf8209ace2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:22 +0200 Subject: gnu: r-methylkit: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-methylkit): Move from here... * gnu/packages/bioconductor.scm (r-methylkit): ...to here. --- gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 47 ----------------------------------------- 2 files changed, 47 insertions(+), 47 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fae6073446..196ee22e25 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3307,6 +3307,53 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-methylkit + (package + (name "r-methylkit") + (version "1.16.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "methylKit" version)) + (sha256 + (base32 + "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3")))) + (properties `((upstream-name . "methylKit"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-emdbook" ,r-emdbook) + ("r-fastseg" ,r-fastseg) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-gtools" ,r-gtools) + ("r-iranges" ,r-iranges) + ("r-kernsmooth" ,r-kernsmooth) + ("r-limma" ,r-limma) + ("r-mclust" ,r-mclust) + ("r-mgcv" ,r-mgcv) + ("r-qvalue" ,r-qvalue) + ("r-r-utils" ,r-r-utils) + ("r-rcpp" ,r-rcpp) + ("r-rhtslib" ,r-rhtslib) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://github.com/al2na/methylKit") + (synopsis + "DNA methylation analysis from high-throughput bisulfite sequencing results") + (description + "MethylKit is an R package for DNA methylation analysis and annotation +from high-throughput bisulfite sequencing. The package is designed to deal +with sequencing data from @dfn{Reduced representation bisulfite +sequencing} (RRBS) and its variants, but also target-capture methods and whole +genome bisulfite sequencing. It also has functions to analyze base-pair +resolution 5hmC data from experimental protocols such as oxBS-Seq and +TAB-Seq.") + (license license:artistic2.0))) + (define-public r-motifrg (package (name "r-motifrg") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index abfaa3d4af..11dbad5a22 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8486,53 +8486,6 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-methylkit - (package - (name "r-methylkit") - (version "1.16.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "methylKit" version)) - (sha256 - (base32 - "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3")))) - (properties `((upstream-name . "methylKit"))) - (build-system r-build-system) - (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-emdbook" ,r-emdbook) - ("r-fastseg" ,r-fastseg) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-limma" ,r-limma) - ("r-mclust" ,r-mclust) - ("r-mgcv" ,r-mgcv) - ("r-qvalue" ,r-qvalue) - ("r-r-utils" ,r-r-utils) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes - (home-page "https://github.com/al2na/methylKit") - (synopsis - "DNA methylation analysis from high-throughput bisulfite sequencing results") - (description - "MethylKit is an R package for DNA methylation analysis and annotation -from high-throughput bisulfite sequencing. The package is designed to deal -with sequencing data from @dfn{Reduced representation bisulfite -sequencing} (RRBS) and its variants, but also target-capture methods and whole -genome bisulfite sequencing. It also has functions to analyze base-pair -resolution 5hmC data from experimental protocols such as oxBS-Seq and -TAB-Seq.") - (license license:artistic2.0))) - (define-public r-raremetals2 (package (name "r-raremetals2") -- cgit 1.4.1 From b0ecd6cea90838018744bfad15662abf8f1b0025 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 15:46:30 +0200 Subject: gnu: r-phantompeakqualtools: Let-bind commit, set revision to 1. * gnu/packages/bioinformatics.scm (r-phantompeakqualtools): Bind the commit outside of the package value. [version]: Use git-version. [source]: Use git-file-name. --- gnu/packages/bioinformatics.scm | 86 +++++++++++++++++++++-------------------- 1 file changed, 44 insertions(+), 42 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 11dbad5a22..a7ff938647 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7977,51 +7977,53 @@ other functional sequencing data.") (license license:gpl2))) (define-public r-phantompeakqualtools - (package - (name "r-phantompeakqualtools") - (version "1.2.2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/kundajelab/phantompeakqualtools") - (commit "8d2b2d18c686d894ef5908b37da7adf72a07ef42"))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 - "00anrvcwsp02d98qhj1xpj85644h2pp4kfzq6dgbmwmdr6jvy7p4")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; There are no tests. - #:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((script (string-append (assoc-ref outputs "out") - "/share/scripts"))) - (install-file "run_spp.R" script))))))) - (inputs - `(("r" ,r-minimal))) - (propagated-inputs - `(("r-catools" ,r-catools) - ("r-snow" ,r-snow) - ("r-snowfall" ,r-snowfall) - ("r-bitops" ,r-bitops) - ("r-rsamtools" ,r-rsamtools) - ("r-spp" ,r-spp) - ("gawk" ,gawk) - ("samtools" ,samtools) - ("boost" ,boost) - ("gzip" ,gzip))) - (home-page "https://github.com/kundajelab/phantompeakqualtools") - (synopsis "Informative enrichment for ChIP-seq data") - (description "This package computes informative enrichment and quality + (let ((commit "8d2b2d18c686d894ef5908b37da7adf72a07ef42") + (revision "1")) + (package + (name "r-phantompeakqualtools") + (version (git-version "1.2.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kundajelab/phantompeakqualtools") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00anrvcwsp02d98qhj1xpj85644h2pp4kfzq6dgbmwmdr6jvy7p4")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests. + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((script (string-append (assoc-ref outputs "out") + "/share/scripts"))) + (install-file "run_spp.R" script))))))) + (inputs + `(("r" ,r-minimal))) + (propagated-inputs + `(("r-catools" ,r-catools) + ("r-snow" ,r-snow) + ("r-snowfall" ,r-snowfall) + ("r-bitops" ,r-bitops) + ("r-rsamtools" ,r-rsamtools) + ("r-spp" ,r-spp) + ("gawk" ,gawk) + ("samtools" ,samtools) + ("boost" ,boost) + ("gzip" ,gzip))) + (home-page "https://github.com/kundajelab/phantompeakqualtools") + (synopsis "Informative enrichment for ChIP-seq data") + (description "This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.") - (license license:bsd-3))) + (license license:bsd-3)))) (define-public r-r4rna (package -- cgit 1.4.1 From 1a6108ce2b85e74306ed5a31f26cbe12c6f0100e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 15:53:09 +0200 Subject: gnu: r-geneoverlap: Move out of experiment section. * gnu/packages/bioconductor.scm (r-geneoverlap): Move the package definition out of the "experiment" section into the section for regular Bioconductor packages. --- gnu/packages/bioconductor.scm | 40 ++++++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 20 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 196ee22e25..ba2bffe23e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1176,26 +1176,6 @@ GenomicRanges Bioconductor package.") genomes and gene ID formats, largely based on the UCSC table browser.") (license license:lgpl2.0+))) -(define-public r-geneoverlap - (package - (name "r-geneoverlap") - (version "1.26.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "GeneOverlap" version)) - (sha256 - (base32 - "0bvh00n4fx0h1m83bypib3jvln1ihcv77ywrrn9xm20y73gymhkh")))) - (build-system r-build-system) - (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-gplots" ,r-gplots))) - (home-page "https://www.bioconductor.org/packages/GeneOverlap/") - (synopsis "Test and visualize gene overlaps") - (description "This package can be used to test two sets of gene lists -and visualize the results.") - (license license:gpl3))) - (define-public r-genomationdata (package (name "r-genomationdata") @@ -2885,6 +2865,26 @@ analysis using other methods.") high-throughput sequencing experiments.") (license license:artistic2.0))) +(define-public r-geneoverlap + (package + (name "r-geneoverlap") + (version "1.26.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GeneOverlap" version)) + (sha256 + (base32 + "0bvh00n4fx0h1m83bypib3jvln1ihcv77ywrrn9xm20y73gymhkh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-gplots" ,r-gplots))) + (home-page "https://www.bioconductor.org/packages/GeneOverlap/") + (synopsis "Test and visualize gene overlaps") + (description "This package can be used to test two sets of gene lists +and visualize the results.") + (license license:gpl3))) + (define-public r-genomation (package (name "r-genomation") -- cgit 1.4.1 From a6e7afd4d55cc790aacbda64a327cb9f38a0d0f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 15:53:20 +0200 Subject: gnu: r-spp: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-spp): Move from here... * gnu/packages/bioconductor.scm (r-spp): ...to here. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 24 ------------------------ 2 files changed, 26 insertions(+), 24 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ba2bffe23e..5f594b85a7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13163,6 +13163,32 @@ network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data.") (license license:gpl2+))) +;; This is a CRAN package, but it depends on r-rsamtools, which is a +;; Bioconductor package. +(define-public r-spp + (package + (name "r-spp") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (cran-uri "spp" version)) + (sha256 + (base32 + "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w")))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-catools" ,r-catools) + ("r-rcpp" ,r-rcpp) + ("r-rsamtools" ,r-rsamtools))) + (home-page "https://cran.r-project.org/web/packages/spp/") + (synopsis "ChIP-Seq processing pipeline") + (description "This package provides tools for analysis of ChIP-seq and +other functional sequencing data.") + (license license:gpl2))) + (define-public r-pathview (package (name "r-pathview") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a7ff938647..27e86b0a3b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7952,30 +7952,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-spp - (package - (name "r-spp") - (version "1.16.0") - (source (origin - (method url-fetch) - (uri (cran-uri "spp" version)) - (sha256 - (base32 - "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w")))) - (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-bh" ,r-bh) - ("r-catools" ,r-catools) - ("r-rcpp" ,r-rcpp) - ("r-rsamtools" ,r-rsamtools))) - (home-page "https://cran.r-project.org/web/packages/spp/") - (synopsis "ChIP-Seq processing pipeline") - (description "This package provides tools for analysis of ChIP-seq and -other functional sequencing data.") - (license license:gpl2))) - (define-public r-phantompeakqualtools (let ((commit "8d2b2d18c686d894ef5908b37da7adf72a07ef42") (revision "1")) -- cgit 1.4.1 From ec543ba6723b1dee4f7f87c48fbcc3f97e273b3e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 15:54:41 +0200 Subject: gnu: r-chipseeker: Move out of experiment section. * gnu/packages/bioconductor.scm (r-chipseeker): Move the package from the "experiment" section to the section for regular Bioconductor packages. --- gnu/packages/bioconductor.scm | 95 +++++++++++++++++++++---------------------- 1 file changed, 47 insertions(+), 48 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5f594b85a7..20e44ca94b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1080,54 +1080,6 @@ from Illumina 450k methylation arrays.") chromstaR package.") (license license:gpl3))) -(define-public r-chipseeker - (package - (name "r-chipseeker") - (version "1.26.2") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "ChIPseeker" version)) - (sha256 - (base32 - "1r197qwsriap6s6nb2p9j3521pjs2f0lgyzvppvlxj1531sa6g6z")))) - (build-system r-build-system) - (inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-boot" ,r-boot) - ("r-enrichplot" ,r-enrichplot) - ("r-iranges" ,r-iranges) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-ggplot2" ,r-ggplot2) - ("r-gplots" ,r-gplots) - ("r-gtools" ,r-gtools) - ("r-dplyr" ,r-dplyr) - ("r-plotrix" ,r-plotrix) - ("r-dplyr" ,r-dplyr) - ("r-magrittr" ,r-magrittr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-txdb-hsapiens-ucsc-hg19-knowngene" - ,r-txdb-hsapiens-ucsc-hg19-knowngene))) - (home-page "https://www.bioconductor.org/packages/ChIPseeker/") - (synopsis - "ChIPseeker for ChIP peak Annotation, Comparison, and Visualization") - (description "This package implements functions to retrieve the nearest -genes around the peak, annotate genomic region of the peak, statstical methods -for estimate the significance of overlap among ChIP peak data sets, and -incorporate GEO database for user to compare the own dataset with those -deposited in database. The comparison can be used to infer cooperative -regulation and thus can be used to generate hypotheses. Several visualization -functions are implemented to summarize the coverage of the peak experiment, -average profile and heatmap of peaks binding to TSS regions, genomic -annotation, distance to TSS, and overlap of peaks or genes.") - (license license:artistic2.0))) - (define-public r-copyhelper (package (name "r-copyhelper") @@ -2415,6 +2367,53 @@ genome data packages and support for efficient SNP representation.") analysis.") (license license:artistic2.0))) +(define-public r-chipseeker + (package + (name "r-chipseeker") + (version "1.26.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ChIPseeker" version)) + (sha256 + (base32 + "1r197qwsriap6s6nb2p9j3521pjs2f0lgyzvppvlxj1531sa6g6z")))) + (build-system r-build-system) + (inputs + `(("r-knitr" ,r-knitr))) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocgenerics" ,r-biocgenerics) + ("r-boot" ,r-boot) + ("r-enrichplot" ,r-enrichplot) + ("r-iranges" ,r-iranges) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-ggplot2" ,r-ggplot2) + ("r-gplots" ,r-gplots) + ("r-gtools" ,r-gtools) + ("r-dplyr" ,r-dplyr) + ("r-plotrix" ,r-plotrix) + ("r-dplyr" ,r-dplyr) + ("r-magrittr" ,r-magrittr) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-txdb-hsapiens-ucsc-hg19-knowngene" + ,r-txdb-hsapiens-ucsc-hg19-knowngene))) + (home-page "https://www.bioconductor.org/packages/ChIPseeker/") + (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization") + (description "This package implements functions to retrieve the nearest +genes around the peak, annotate genomic region of the peak, statstical methods +for estimate the significance of overlap among ChIP peak data sets, and +incorporate GEO database for user to compare the own dataset with those +deposited in database. The comparison can be used to infer cooperative +regulation and thus can be used to generate hypotheses. Several visualization +functions are implemented to summarize the coverage of the peak experiment, +average profile and heatmap of peaks binding to TSS regions, genomic +annotation, distance to TSS, and overlap of peaks or genes.") + (license license:artistic2.0))) + (define-public r-chipseq (package (name "r-chipseq") -- cgit 1.4.1 From f383f9e3111c1708ee85b1acec60a1ff657c0aa6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 16:08:12 +0200 Subject: gnu: filevercmp: Use git-version. * gnu/packages/bioinformatics.scm (filevercmp)[version]: Use git-version; bind "revision" in outer let. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 27e86b0a3b..3ec0d0d301 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8347,10 +8347,11 @@ group or two ChIP groups run under different conditions.") (license license:gpl3+))) (define-public filevercmp - (let ((commit "1a9b779b93d0b244040274794d402106907b71b7")) + (let ((commit "1a9b779b93d0b244040274794d402106907b71b7") + (revision "1")) (package (name "filevercmp") - (version (string-append "0-1." (string-take commit 7))) + (version (git-version "0" revision commit)) (source (origin (method git-fetch) (uri (git-reference -- cgit 1.4.1 From 09b50a6ec25eadfdc60b7f77bb67816123c939df Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 16:08:47 +0200 Subject: gnu: bismark: Use git-file-name. * gnu/packages/bioinformatics.scm (bismark)[source]: Use git-file-name. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3ec0d0d301..92a765c688 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9179,7 +9179,7 @@ Browser.") (uri (git-reference (url "https://github.com/FelixKrueger/Bismark") (commit version))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 "0xchm3rgilj6vfjnyzfzzymfd7djr64sbrmrvs3njbwi66jqbzw9")))) -- cgit 1.4.1 From 3acfbd481117f217e03b596bd234c7b0da9cf18f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 16:09:07 +0200 Subject: gnu: f-seq: Use git-version and git-file-name. * gnu/packages/bioinformatics.scm (f-seq)[version]: Use git-version. [source]: Use git-file-name. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 92a765c688..c0f9c0768b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9115,13 +9115,13 @@ browser.") (revision "1")) (package (name "f-seq") - (version (string-append "1.1-" revision "." (string-take commit 7))) + (version (git-version "1.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/aboyle/F-seq") (commit commit))) - (file-name (string-append name "-" version)) + (file-name (git-file-name name version)) (sha256 (base32 "1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h")) -- cgit 1.4.1 From 8c033085cc61365e7d685687b8d58bb0a2420663 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 16:09:35 +0200 Subject: gnu: r-chipkernels: Use git-version and git-file-name. * gnu/packages/bioinformatics.scm (r-chipkernels)[version]: Use git-version. [source]: Use git-file-name. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c0f9c0768b..f5a652832e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8080,14 +8080,14 @@ secondary structure and comparative analysis in R.") (revision "1")) (package (name "r-chipkernels") - (version (string-append "1.1-" revision "." (string-take commit 9))) + (version (git-version "1.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/ManuSetty/ChIPKernels") (commit commit))) - (file-name (string-append name "-" version)) + (file-name (git-file-name name version)) (sha256 (base32 "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0")))) -- cgit 1.4.1 From d1e1c02e2850a0fd9c06c5884c7853d511948488 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 16:10:00 +0200 Subject: gnu: piranha: Use git-version. * gnu/packages/bioinformatics.scm (piranha)[version]: Use git-version. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f5a652832e..1adcc685e2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8258,7 +8258,7 @@ intervals (e.g. genes, sequence alignments).") (commit "0466d364b71117d01e4471b74c514436cc281233")) (package (name "piranha") - (version (string-append "1.2.1-" revision "." (string-take commit 9))) + (version (git-version "1.2.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference -- cgit 1.4.1 From f463f376e91ccc1fe4ab68d5e822b5d71a1234f5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 16:10:20 +0200 Subject: gnu: bits: Use git-version and git-file-name. * gnu/packages/bioinformatics.scm (bits)[version]: Use git-version. [source]: Use git-file-name. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1adcc685e2..1f018befe6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8212,13 +8212,13 @@ tools for sequence analysis into a seamless whole.") (name "bits") ;; The version is 2.13.0 even though no release archives have been ;; published as yet. - (version (string-append "2.13.0-" revision "." (string-take commit 9))) + (version (git-version "2.13.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/arq5x/bits") (commit commit))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 "17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs")))) -- cgit 1.4.1 From f7825ee85a4b2ea4170f8ad5dbee281704b09371 Mon Sep 17 00:00:00 2001 From: Solene Rapenne via Guix-patches via Date: Fri, 28 May 2021 22:40:02 +0200 Subject: gnu: tome4: Update to 1.7.3. * gnu/packages/games.scm (tome4): Update to 1.7.3. Signed-off-by: Nicolas Goaziou --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 9753f5af47..6b16d5bc8a 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -6900,7 +6900,7 @@ Crowther & Woods, its original authors, in 1995. It has been known as (define-public tome4 (package (name "tome4") - (version "1.7.2") + (version "1.7.3") (synopsis "Single-player, RPG roguelike game set in the world of Eyal") (source (origin @@ -6908,7 +6908,7 @@ Crowther & Woods, its original authors, in 1995. It has been known as (uri (string-append "https://te4.org/dl/t-engine/t-engine4-src-" version ".tar.bz2")) (sha256 - (base32 "1xa0pdn9pggwf7hnqb87ya2qxqhjahkdjwf8cr2y01gixgrkj9lv")) + (base32 "1rik17r01glq3944sdb06xjf0xppgqkjk564wrh22slm4mi3fifz")) (modules '((guix build utils))) (snippet '(begin -- cgit 1.4.1 From dafd3265ad3a83141f45132f1d154964d82f9039 Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Sat, 29 May 2021 10:21:26 +0200 Subject: gnu: Add emacs-evil-paredit. * gnu/packages/emacs-xyz.scm (emacs-evil-paredit): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index efdc1cdac8..bd05408561 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -11035,6 +11035,33 @@ end of a line and increment or decrement it.") a popup window for previewing candidates.") (license license:gpl3+)))) +(define-public emacs-evil-paredit + (let ((commit "e058fbdcf9dbf7ad6cc77f0172d7517ef233d55f")) + (package + (name "emacs-evil-paredit") + (version "0.0.2") ; says 0.0.2 in evil-paredit.el + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/roman/evil-paredit") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0b08y4spapl4g2292j3l4cr84gjlvm3rpma3gqld4yb1sxd7v78p")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-evil" ,emacs-evil) + ("emacs-paredit" ,emacs-paredit))) + (home-page "https://github.com/roman/evil-paredit") + (synopsis "Evil extension to integrate nicely with Paredit") + (description + "This package helps you to not screw up your Paredit setup when using +Evil mode. Whenever you try to use a modifier command like @kbd{d}, @kbd{c}, +@kbd{y} to modify the Paredit buffer, it will stop you to do so in the case +you break the parity of parenthesis.") + (license license:expat)))) + (define-public emacs-evil-args (let ((commit "758ad5ae54ad34202064fec192c88151c08cb387") (revision "1")) -- cgit 1.4.1 From 71854b7dfe034dc47655c6fa885bd255fde3c160 Mon Sep 17 00:00:00 2001 From: Stefan Reichör Date: Sat, 29 May 2021 22:28:37 +0200 Subject: gnu: Add python-easy-ansi. * gnu/packages/python-xyz.scm (python-easy-ansi): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/python-xyz.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b3ed73f04a..886a890049 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16549,6 +16549,30 @@ converting text with ANSI color codes to HTML or LaTeX.") (define-public python2-ansi2html (package-with-python2 python-ansi2html)) +(define-public python-easy-ansi + (package + (name "python-easy-ansi") + (version "0.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/joeysbytes/easy-ansi") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0albh55ynzs98qy9pln4qaxw5qhhh3lk09jy9bx19gycrp1c3lc3")))) + (build-system python-build-system) + (home-page "https://gitlab.com/joeysbytes/easy-ansi") + (synopsis "Terminal framework API") + (description + "Easy ANSI is a terminal framework API to give you an easy way to use +colors, cursor control movements, and line/box drawing. It is not meant as a +replacement to more full-featured frameworks (such as curses or urwid), but as +a tool to quickly create nice-looking screens in your terminal window. You +can even create animations with the cursor controls.") + (license license:expat))) + (define-public python-ddt (package (name "python-ddt") -- cgit 1.4.1 From d16ddafcc78ddbf179573d523fe652a634fa57ce Mon Sep 17 00:00:00 2001 From: Stefan Reichör Date: Sat, 29 May 2021 23:39:18 +0200 Subject: gnu: Add emacs-eyebrowse. * gnu/packages/emacs-xyz.scm (emacs-eyebrowse): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index bd05408561..80da75388c 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -7979,6 +7979,35 @@ perspective only its buffers are available by default.") can be saved to and restored from a file.") (license license:gpl2+))) +(define-public emacs-eyebrowse + ;; XXX: Upstream has no tagged release. Version is extracted from keyword + ;; in main file. + (let ((commit "88c7b59aa7c5c93bc23812217213adfa238f977b") + (revision "0")) + (package + (name "emacs-eyebrowse") + (version (git-version "0.7.8" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://depp.brause.cc/eyebrowse.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "09s07mvg5bz3dm9sxgn40c7z6d6ry1sdjzsxwgmy825f3xm66avs")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-dash" ,emacs-dash))) + (home-page "https://depp.brause.cc/eyebrowse/") + (synopsis "Simple-minded way to manage window configs in Emacs") + (description + "Eyebrowse is a global minor mode for Emacs that allows you to manage +your window configurations in a simple manner, just like tiling window +managers like i3wm with their workspaces do. It displays their current state +in the modeline by default.") + (license license:gpl3+)))) + (define-public emacs-test-simple (package (name "emacs-test-simple") -- cgit 1.4.1 From 4092813037f9fadb2c1da805dc9117277efc7910 Mon Sep 17 00:00:00 2001 From: Solene Rapenne via Guix-patches via Date: Sun, 30 May 2021 15:49:32 +0200 Subject: gnu: lagrange: Update to 1.5.0. * gnu/packages/web-browsers.scm (lagrange): Update to 1.5.0. Signed-off-by: Nicolas Goaziou --- gnu/packages/web-browsers.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index 214320d2a1..d2cda59540 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -722,7 +722,7 @@ key-bindings (Emacs, vi, CUA), and is fully configurable in Common Lisp.") (define-public lagrange (package (name "lagrange") - (version "1.4.2") + (version "1.5.0") (source (origin (method url-fetch) @@ -730,7 +730,7 @@ key-bindings (Emacs, vi, CUA), and is fully configurable in Common Lisp.") (string-append "https://git.skyjake.fi/skyjake/lagrange/releases/" "download/v" version "/lagrange-" version ".tar.gz")) (sha256 - (base32 "1gnivksxxw2k0kx7fsyrwrxffl67dph2b9w9hsv9id6x89k6dwh2")))) + (base32 "0ziidk1qv7gaj2pvbla09vznjgslgqwr9ljfd9hskrv6nc68wafs")))) (build-system cmake-build-system) (arguments `(#:tests? #false)) ;no tests -- cgit 1.4.1 From 6cdc1c72f1b45c502ce4bbbec27eee900d812db1 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 31 May 2021 21:24:15 +0200 Subject: gnu: emacs-posframe: Update to 1.0.3. * gnu/packages/emacs-xyz.scm (emacs-posframe): Update to 1.0.3. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 80da75388c..60a7e05372 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13054,14 +13054,14 @@ shuangpin, wubi and cangjie.") (define-public emacs-posframe (package (name "emacs-posframe") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "posframe-" version ".tar")) (sha256 - (base32 "19a1dkjyw9m74aamyqrsvzrdwshngqpmjzdngx6v5nifvcilrlnk")))) + (base32 "0c3lnrydsysv8j25brgc0cckf1hz54yhkginncmw81y1ia43rqmx")))) (build-system emacs-build-system) ;; emacs-minimal does not include the function font-info. (arguments -- cgit 1.4.1 From 5af640b6d7ced5b040821d4da332a94cb6302646 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 31 May 2021 21:25:28 +0200 Subject: gnu: emacs-moody: Update to 0.5.5. * gnu/packages/emacs-xyz.scm (emacs-moody): Update to 0.5.5. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 60a7e05372..d2276c104a 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -851,7 +851,7 @@ Alternatively the menu can be bound globally, for example: (define-public emacs-moody (package (name "emacs-moody") - (version "0.5.4") + (version "0.5.5") (source (origin (method git-fetch) @@ -860,7 +860,7 @@ Alternatively the menu can be bound globally, for example: (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0n8p864yj5m3n7f9qiq9hy24dwfvv0a0wchx2818rppff6vfq3hf")))) + (base32 "0b4kg4dxy4ywwin96vz6x3rpvgr718y5rgrdarmwym9wv1qz0a0c")))) (build-system emacs-build-system) (home-page "https://github.com/tarsius/moody") (synopsis "Tabs and ribbons for Emacs mode-line") -- cgit 1.4.1 From 4e74d25d853bec403f64af159463b1176ae5b623 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 31 May 2021 21:35:53 +0200 Subject: gnu: texmacs: Update to 1.99.21. * gnu/packages/text-editors.scm (texmacs): Update to 1.99.21. --- gnu/packages/text-editors.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm index 30747057f8..eb557cb80a 100644 --- a/gnu/packages/text-editors.scm +++ b/gnu/packages/text-editors.scm @@ -806,14 +806,14 @@ editors.") (define-public texmacs (package (name "texmacs") - (version "1.99.20") + (version "1.99.21") (source (origin (method url-fetch) (uri (string-append "https://www.texmacs.org/Download/ftp/tmftp/" "source/TeXmacs-" version "-src.tar.gz")) (sha256 - (base32 "0wny36qsgzpp084h2i85rd3l8fq1q69sglc266prb06ygcb0iyia")))) + (base32 "0zmm8212cha22dp1xablj1h4anlnyhjh09n13ckqf6ppb1bkf4gm")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config) -- cgit 1.4.1 From 93744e470b26a88e6167d3a1a8d3fc1a7c34d4aa Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 31 May 2021 21:37:15 +0200 Subject: gnu: emacs-solaire-mode: Update to 2.0.0. * gnu/packages/emacs-xyz.scm (emacs-solaire-mode): Update to 2.0.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index d2276c104a..a93e83c089 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -7624,7 +7624,7 @@ single theme but a set of guidelines with numerous implementations.") (define-public emacs-solaire-mode (package (name "emacs-solaire-mode") - (version "1.1.5") + (version "2.0.0") (source (origin (method git-fetch) @@ -7633,7 +7633,7 @@ single theme but a set of guidelines with numerous implementations.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1l2w06w8b904h55xchs3dnjm4ry7xnpmyc4fg2vvrw1hr69q6mda")))) + (base32 "0aigavrqfi2dy4q5vrfs48n5k7839gqnafq7mp14cmcbrzcwadrd")))) (build-system emacs-build-system) (home-page "https://github.com/hlissner/emacs-solaire-mode") (synopsis "Change background of file-visiting buffers in Emacs") -- cgit 1.4.1 From eb8928eebab3c00dc2835564da383639ca3539b7 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 31 May 2021 21:37:53 +0200 Subject: gnu: emacs-tramp: Update to 2.5.0.5. * gnu/packages/emacs-xyz.scm (emacs-tramp): Update to 2.5.0.5. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a93e83c089..a1083f999b 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -24137,14 +24137,14 @@ well as an option for visually flashing evaluated s-expressions.") (define-public emacs-tramp (package (name "emacs-tramp") - (version "2.5.0.4") + (version "2.5.0.5") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "tramp-" version ".tar")) (sha256 - (base32 "0yk4ckk45gkjp24nfywz49j8pazq33m6pga3lirb5h6zc8an5z24")))) + (base32 "1dclxffynfacvwi2scpda35sxjb42603yyf2p0477qa9b0i4xha0")))) (build-system emacs-build-system) (arguments `(#:emacs ,emacs ;need D-Bus -- cgit 1.4.1 From 8a0dc5f1bfba4493d2460bf05be9aff200a9bd04 Mon Sep 17 00:00:00 2001 From: Brice Waegeneire Date: Mon, 31 May 2021 21:44:02 +0200 Subject: tests: Fix loadable-kernel-modules-service tests. * gnu/tests/linux-modules.scm (run-loadable-kernel-modules-service-test): Actually load the modules with kernel-module-loader-service-type. Use a singleton service instead of defining a custom one. * doc/guix.texi (Service Reference): To give an example of linux-loadable-module-service-type use a singleton instead of defining a new service. --- doc/guix.texi | 13 +++++-------- gnu/tests/linux-modules.scm | 13 +++++-------- 2 files changed, 10 insertions(+), 16 deletions(-) (limited to 'gnu') diff --git a/doc/guix.texi b/doc/guix.texi index 0126099d68..39dc2446ef 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -76,7 +76,7 @@ Copyright @copyright{} 2020 Damien Cassou@* Copyright @copyright{} 2020 Jakub Kądziołka@* Copyright @copyright{} 2020 Jack Hill@* Copyright @copyright{} 2020 Naga Malleswari@* -Copyright @copyright{} 2020 Brice Waegeneire@* +Copyright @copyright{} 2020, 2021 Brice Waegeneire@* Copyright @copyright{} 2020 R Veera Kumar@* Copyright @copyright{} 2020 Pierre Langlois@* Copyright @copyright{} 2020 pinoaffe@* @@ -34379,13 +34379,10 @@ This service type is intended to be extended by other service types, such as below: @lisp -(define module-installing-service-type - (service-type - (name 'module-installing-service) - (extensions (list (service-extension linux-loadable-module-service-type - (const (list module-to-install-1 - module-to-install-2))))) - (default-value #f))) +(simple-service 'installing-module + linux-loadable-module-service-type + (list module-to-install-1 + module-to-install-2)) @end lisp This does not actually load modules at bootup, only adds it to the diff --git a/gnu/tests/linux-modules.scm b/gnu/tests/linux-modules.scm index 30d8eae03b..fc8945b77f 100644 --- a/gnu/tests/linux-modules.scm +++ b/gnu/tests/linux-modules.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2019 Jakob L. Kreuze ;;; Copyright © 2020 Danny Milosavljevic -;;; Copyright © 2020 Brice Waegeneire +;;; Copyright © 2020, 2021 Brice Waegeneire ;;; Copyright © 2021 raid5atemyhomework ;;; ;;; This file is part of GNU Guix. @@ -112,16 +112,13 @@ are loaded in memory." "Run a test of an OS having MODULE-PACKAGES, which are loaded by creating a service that extends LINUXL-LOADABLE-MODULE-SERVICE-TYPE. Then verify that MODULE-NAMES are loaded in memory." - (define module-installing-service-type - (service-type - (name 'module-installing-service) - (extensions (list (service-extension linux-loadable-module-service-type - (const module-packages)))) - (default-value #f))) (run-loadable-kernel-modules-test-base (operating-system (inherit (simple-operating-system)) - (services (cons* (service module-installing-service-type) + (services (cons* (simple-service 'installing-module + linux-loadable-module-service-type + module-packages) + (service kernel-module-loader-service-type module-names) (operating-system-user-services (simple-operating-system))))) module-names)) -- cgit 1.4.1 From 62a8d487d61513d214b9aa72e7efaefde215cd9b Mon Sep 17 00:00:00 2001 From: Brice Waegeneire Date: Wed, 27 May 2020 18:07:14 +0200 Subject: services: hostapd: Use package from configuration. * gnu/services/networking.scm (hostapd-shepherd-services): Replace 'hostapd' by the package specified in the configuration. --- gnu/services/networking.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm index b78c8ceacc..87b3d754a3 100644 --- a/gnu/services/networking.scm +++ b/gnu/services/networking.scm @@ -1591,7 +1591,8 @@ extra-settings "\n")))) (requirement `(user-processes ,@requirement)) (documentation "Run the hostapd WiFi access point daemon.") (start #~(make-forkexec-constructor - (list #$(file-append hostapd "/sbin/hostapd") + (list #$(file-append (hostapd-configuration-package config) + "/sbin/hostapd") #$(hostapd-configuration-file config)) #:log-file "/var/log/hostapd.log")) (stop #~(make-kill-destructor))))) -- cgit 1.4.1 From ea55e1355bb3d45d5f04e7cb390d2c6afa8e68e6 Mon Sep 17 00:00:00 2001 From: Brice Waegeneire Date: Thu, 4 Jun 2020 16:14:01 +0200 Subject: services: dnsmasq: Extend 'activation-service'. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/services/dns.scm (dnsmasq-activation): New procedure … (dnsmasq-service-type): … use it. --- gnu/services/dns.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/services/dns.scm b/gnu/services/dns.scm index 55211cb08f..aeb2bfdc86 100644 --- a/gnu/services/dns.scm +++ b/gnu/services/dns.scm @@ -861,12 +861,20 @@ cache.size = 100 * MB #:pid-file "/run/dnsmasq.pid")) (stop #~(make-kill-destructor)))))) +(define (dnsmasq-activation config) + #~(begin + (use-modules (guix build utils)) + ;; create directory to store dnsmasq lease file + (mkdir-p "/var/lib/misc"))) + (define dnsmasq-service-type (service-type (name 'dnsmasq) (extensions (list (service-extension shepherd-root-service-type - (compose list dnsmasq-shepherd-service)))) + (compose list dnsmasq-shepherd-service)) + (service-extension activation-service-type + dnsmasq-activation))) (default-value (dnsmasq-configuration)) (description "Run the dnsmasq DNS server."))) -- cgit 1.4.1 From a6a193925151656804c97c11708796d17ba07d44 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 1 Jun 2021 09:01:58 +0100 Subject: gnu: guix-build-coordinator: Update to 0-30.f9af463. * gnu/packages/package-management.scm (guix-build-coordinator): Update to 0-30.f9af463. --- gnu/packages/package-management.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index efafbb704b..6a3ef66d32 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -1061,8 +1061,8 @@ environments.") (license (list license:gpl3+ license:agpl3+ license:silofl1.1)))) (define-public guix-build-coordinator - (let ((commit "8c98f47714fb1c1898ffa7b54966eaf913a0ae1d") - (revision "29")) + (let ((commit "f9af463e81d9fcc712d7c58a491101d8d17457e8") + (revision "30")) (package (name "guix-build-coordinator") (version (git-version "0" revision commit)) @@ -1073,7 +1073,7 @@ environments.") (commit commit))) (sha256 (base32 - "09llhpv3ni8m24i4v37mgjcmaabaj6cy9fxgci7pch6dsi3rkc1r")) + "08ysa7a33fsm069gxqnvbf1yzqcsky6gk2pifamkq0wq1dls661r")) (file-name (string-append name "-" version "-checkout")))) (build-system gnu-build-system) (arguments -- cgit 1.4.1 From b346a7c7db6b3d6e5a2bdd964fc99038f99f29a7 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 1 Jun 2021 10:13:38 +0200 Subject: gnu: Add python-stdlib-list. * gnu/packages/python-xyz.scm (python-stdlib-list): New variable. --- gnu/packages/python-xyz.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 886a890049..05c1b6d8d6 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9692,6 +9692,26 @@ output.") "Python library that makes exceptions handling and inspection easier.") (license license:expat))) +(define-public python-stdlib-list + (package + (name "python-stdlib-list") + (version "0.8.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "stdlib-list" version)) + (sha256 + (base32 + "17vdn4q0sdlndc2fr9svapxx6366hnrhkn0fswp1xmr0jxqh7rd1")))) + (build-system python-build-system) + (arguments + `(#:tests? #f)) ; Tests require more dependencies. + (native-inputs + `(("python-sphinx" ,python-sphinx))) + (home-page "https://github.com/jackmaney/python-stdlib-list") + (synopsis "Python Standard Libraries") + (description "This package contains a list of Python Standard Libraries.") + (license license:expat))) + (define-public python-straight-plugin (package (name "python-straight-plugin") -- cgit 1.4.1 From 50dfbbf8ef52111067071c788e19fc21d54c40d6 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 1 Jun 2021 10:18:00 +0200 Subject: gnu: Add python-sinfo. * gnu/packages/python-xyz.scm (python-sinfo): New variable. --- gnu/packages/python-xyz.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 05c1b6d8d6..a5cc04edaf 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2189,6 +2189,25 @@ The event dispatch is implicit, which means you can easily use @code{Eventlet} from the Python interpreter, or as a small part of a larger application.") (license license:expat))) +(define-public python-sinfo + (package + (name "python-sinfo") + (version "0.3.4") + (source (origin + (method url-fetch) + (uri (pypi-uri "sinfo" version)) + (sha256 + (base32 + "0kdsp883mx0lfyykv0p12bvs203kdm3skb8bw5wf2pc7kb393sl1")))) + (build-system python-build-system) + (propagated-inputs + `(("python-stdlib-list" ,python-stdlib-list))) + (home-page "https://gitlab.com/joelostblom/session_info") + (synopsis "Output module version information loaded in a Python session") + (description "This package outputs version information for modules loaded +in the current session, Python, and the OS.") + (license license:bsd-3))) + (define-public python-six (package (name "python-six") -- cgit 1.4.1 From fd0650eebe33d2ffcded9cd4a66f5e80232d8cd6 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Tue, 1 Jun 2021 11:03:45 +0200 Subject: gnu: guix: Update to 1.3.0-3.50dfbbf. * gnu/packages/package-management.scm (guix): Update to 1.3.0-3.50dfbbf. --- gnu/packages/package-management.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 6a3ef66d32..d3d9f87be4 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -132,8 +132,8 @@ ;; Note: the 'update-guix-package.scm' script expects this definition to ;; start precisely like this. (let ((version "1.3.0") - (commit "9f2b2c432b834c8057ce2f4119599d36197bc063") - (revision 2)) + (commit "50dfbbf8ef52111067071c788e19fc21d54c40d6") + (revision 3)) (package (name "guix") @@ -149,7 +149,7 @@ (commit commit))) (sha256 (base32 - "09w6b4hqcxaj6x1q6m1q8vlp4dyk6anfv8p6mfwmpqis81cspphn")) + "128608qyza3p769h7awp183c2mi9gdx2b1xidvmjilfkphlg1lyi")) (file-name (string-append "guix-" version "-checkout")))) (build-system gnu-build-system) (arguments -- cgit 1.4.1 From d769fcd683edd8f93fa549dd0d60ec7d073e0839 Mon Sep 17 00:00:00 2001 From: Paul Garlick Date: Tue, 1 Jun 2021 10:12:08 +0100 Subject: gnu: vtk: Wrap python modules. * gnu/packages/image-processing.scm (vtk)[inputs]: Add python. [arguments]: Add VTK_WRAP_PYTHON and VTK_PYTHON_VERSION flags. --- gnu/packages/image-processing.scm | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index ed21b26812..da2653c546 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -16,6 +16,7 @@ ;;; Copyright © 2021 Felix Gruber ;;; Copyright © 2021 Andy Tai ;;; Copyright © 2021 Ekaitz Zarraga +;;; Copyright © 2021 Paul Garlick ;;; ;;; This file is part of GNU Guix. ;;; @@ -298,6 +299,8 @@ many popular formats.") "-DVTK_MODULE_USE_EXTERNAL_VTK_theora=ON" "-DVTK_MODULE_USE_EXTERNAL_VTK_tiff=ON" "-DVTK_MODULE_USE_EXTERNAL_VTK_zlib=ON" + "-DVTK_WRAP_PYTHON=ON" + "-DVTK_PYTHON_VERSION:STRING=3" ) #:phases (modify-phases %standard-phases @@ -328,6 +331,7 @@ many popular formats.") ("netcdf" ,netcdf) ("png" ,libpng) ("proj" ,proj.4) + ("python", python) ;("pugixml" ,pugixml) ("sqlite" ,sqlite) ("tiff" ,libtiff) @@ -871,6 +875,7 @@ libraries designed for computer vision research and implementation.") ;; variable in the installed CMake files. This is necessary as other ;; packages using insight-toolkit could not be configured otherwise. "-DGTEST_ROOT=gtest") + #:phases (modify-phases %standard-phases (add-after 'unpack 'do-not-tune -- cgit 1.4.1 From 641a88e8c8c3fe160e8d4a4cf76c685440698fb6 Mon Sep 17 00:00:00 2001 From: Paul Garlick Date: Tue, 1 Jun 2021 10:15:56 +0100 Subject: gnu: Add python-vedo. * gnu/packages/python-science.scm (python-vedo): New variable. --- gnu/packages/python-science.scm | 63 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index fdfd03d424..428452909a 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -12,6 +12,7 @@ ;;; Copyright © 2020, 2021 Vinicius Monego ;;; Copyright © 2021 Greg Hogan ;;; Copyright © 2021 Roel Janssen +;;; Copyright © 2021 Paul Garlick ;;; ;;; This file is part of GNU Guix. ;;; @@ -34,13 +35,17 @@ #:use-module (gnu packages base) #:use-module (gnu packages check) #:use-module (gnu packages gcc) + #:use-module (gnu packages image-processing) #:use-module (gnu packages maths) + #:use-module (gnu packages mpi) #:use-module (gnu packages perl) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages simulation) #:use-module (gnu packages sphinx) #:use-module (gnu packages time) #:use-module (gnu packages xdisorg) @@ -48,6 +53,7 @@ #:use-module (gnu packages xorg) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix utils) #:use-module (guix build-system python)) @@ -639,3 +645,60 @@ annotations on an existing boxplots and barplots generated by seaborn.") UpSet plots are used to visualize set overlaps; like Venn diagrams but more readable.") (license license:bsd-3))) + +(define-public python-vedo + (package + (name "python-vedo") + (version "2021.0.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/marcomusy/vedo") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "18i3ajh5jzhpc86di15lwh4jv97jhm627ii877sa4yhv6abzjfpn")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'mpi-setup + ,%openmpi-setup) + (replace 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (setenv "HOME" (getcwd)) + (add-installed-pythonpath inputs outputs) + (with-directory-excursion "tests" + (for-each (lambda (dir) + (with-directory-excursion dir + (invoke "./run_all.sh"))) + '("common" "dolfin"))) + #t))))) + (inputs ; for the check phase + `(("dolfin" ,fenics) + ("pkgconfig" ,python-pkgconfig) + ("pkg-config" ,pkg-config) + ("matplotlib" ,python-matplotlib))) + (propagated-inputs + `(("numpy" ,python-numpy) + ("vtk" ,vtk))) + (home-page "https://github.com/marcomusy/vedo") + (synopsis + "Analysis and visualization of 3D objects and point clouds") + (description + "@code{vedo} is a fast and lightweight python module for +scientific analysis and visualization. The package provides a wide +range of functionalities for working with three-dimensional meshes and +point clouds. It can also be used to generate high quality +two-dimensional renderings such as scatter plots and histograms. +@code{vedo} is based on @code{vtk} and @code{numpy}, with no other +dependencies.") + ;; vedo is released under the Expat license. Included fonts are + ;; covered by the OFL license and textures by the CC0 license. + ;; The earth images are in the public domain. + (license (list license:expat + license:silofl1.1 + license:cc0 + license:public-domain)))) -- cgit 1.4.1 From b4e3b77270be9d6ff579429d5ced84b467f0f6a3 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Tue, 1 Jun 2021 12:00:57 +0200 Subject: gnu: sbcl: Update to 2.1.5. * gnu/packages/lisp.scm (sbcl): Update to 2.1.5. --- gnu/packages/lisp.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index 082eb920be..55da4b061e 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -400,14 +400,14 @@ an interpreter, a compiler, a debugger, and much more.") (define-public sbcl (package (name "sbcl") - (version "2.1.4") + (version "2.1.5") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/sbcl/sbcl/" version "/sbcl-" version "-source.tar.bz2")) (sha256 - (base32 "04dxxycqhds9r1ycqx3cbavv7p4r13svl5bfakjjmlpw8qihw9lr")))) + (base32 "1id8r2y8hiz34lmvszikdqgrmr778jshim0fibb915assvn0fn4n")))) (build-system gnu-build-system) (outputs '("out" "doc")) (native-inputs -- cgit 1.4.1 From 7ae2b1f2dcc35b1cb670cfa8c87b2d0a5779f5b9 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 1 Jun 2021 13:14:38 +0200 Subject: gnu: Add bamutils. * gnu/packages/bioinformatics.scm (bamutils): New variable. --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1f018befe6..66e790367d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -326,6 +326,37 @@ instance, it implements several methods to assess contig-wise read coverage.") BAM files.") (license license:expat))) +(define-public bamutils + (package + (name "bamutils") + (version "1.0.13") + (source (origin + (method url-fetch) + (uri + (string-append + "https://genome.sph.umich.edu/w/images/7/70/" + "BamUtilLibStatGen." version ".tgz")) + (sha256 + (base32 + "0asr1kmjbr3cyf4hkg865y8c2s30v87xvws4q6c8pyfi6wfd1h8n")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests. + #:make-flags `("USER_WARNINGS=-std=gnu++98" + ,(string-append "INSTALLDIR=" + (assoc-ref %outputs "out") "/bin")) + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://genome.sph.umich.edu/wiki/BamUtil") + (synopsis "Programs for working on SAM/BAM files") + (description "This package provides several programs that perform +operations on SAM/BAM files. All of these programs are built into a +single executable called @code{bam}.") + (license license:gpl3+))) + (define-public bcftools (package (name "bcftools") -- cgit 1.4.1 From 0b76b25a0eff7a422f8ebcc8c095d7ede82c8863 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Tue, 1 Jun 2021 11:14:04 +0200 Subject: tests: hpcguix-web: Fix it. * gnu/tests/web.scm (run-hpcguix-web-server-test): Increase the VM memory size and add retries for the http-get test. --- gnu/tests/web.scm | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/tests/web.scm b/gnu/tests/web.scm index 61575f497d..518c9c1ff3 100644 --- a/gnu/tests/web.scm +++ b/gnu/tests/web.scm @@ -378,12 +378,14 @@ HTTP-PORT, along with php-fpm." (define vm (virtual-machine (operating-system os) - (port-forwardings '((8080 . 5000))))) + (port-forwardings '((8080 . 5000))) + (memory-size 1024))) (define test (with-imported-modules '((gnu build marionette)) #~(begin (use-modules (srfi srfi-11) (srfi srfi-64) + (ice-9 match) (gnu build marionette) (web uri) (web client) @@ -412,9 +414,13 @@ HTTP-PORT, along with php-fpm." 200 (begin (wait-for-tcp-port 5000 marionette) - (let-values (((response text) - (http-get "http://localhost:8080"))) - (response-code response)))) + (#$retry-on-error + (lambda () + (let-values (((response text) + (http-get "http://localhost:8080"))) + (response-code response))) + #:times 10 + #:delay 5))) (test-end) (exit (= (test-runner-fail-count (test-runner-current)) 0))))) -- cgit 1.4.1 From 776a21a0967b13192953d66fe7791d63737c843a Mon Sep 17 00:00:00 2001 From: Jonathan Brielmaier Date: Tue, 1 Jun 2021 17:59:34 +0200 Subject: gnu: rust-cbindgen@0.17: Update to 0.19.0. * gnu/packages/rust-apps.scm (rust-cbindgen-0.17): Update to 0.19.0 and rename to rust-cbindgen-0.19. --- gnu/packages/rust-apps.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm index b74e09c534..0219c4053d 100644 --- a/gnu/packages/rust-apps.scm +++ b/gnu/packages/rust-apps.scm @@ -464,11 +464,11 @@ gitignore rules.") "This package provides a tool for generating C/C++ bindings to Rust code.") (license license:mpl2.0))) -(define-public rust-cbindgen-0.17 +(define-public rust-cbindgen-0.19 (package (inherit rust-cbindgen) (name "rust-cbindgen") - (version "0.17.0") + (version "0.19.0") (source (origin (method url-fetch) @@ -477,7 +477,7 @@ gitignore rules.") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1f40hxj6h7wqmsj8dzxjm3m421hjqpz2m5zxasbn8kgnr6scykvl")))) + "1yld9fni9g9mzg4r42zfk79aq9mzm2sfzzjrrx4vir4lp4qqqwiq")))) (arguments `(#:cargo-inputs (("rust-clap" ,rust-clap-2) -- cgit 1.4.1 From cb821238ed2344d550255c93b41267d8481eefd2 Mon Sep 17 00:00:00 2001 From: Leo Prikler Date: Tue, 1 Jun 2021 18:40:10 +0200 Subject: gnu: musescore: Add missing QML imports. This fixes an issue wherein the palettes sidebar would turn up empty. * gnu/packages/music.scm (musescore)[build-system]: Use qt-build-systems. [inputs]: Add qtgraphicaleffects. --- gnu/packages/music.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index ed64d70a0b..cc9076e763 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -69,6 +69,7 @@ #:use-module (guix build-system python) #:use-module (guix build-system scons) #:use-module (guix build-system glib-or-gtk) + #:use-module (guix build-system qt) #:use-module (guix build-system waf) #:use-module (guix build-system trivial) #:use-module (guix build-system go) @@ -4756,7 +4757,7 @@ standalone JACK client and an LV2 plugin is also available.") "thirdparty/portmidi" "thirdparty/qt-google-analytics")) #t)))) - (build-system cmake-build-system) + (build-system qt-build-system) (arguments `(#:configure-flags `("-DBUILD_TELEMETRY_MODULE=OFF" ;don't phone home @@ -4787,6 +4788,7 @@ standalone JACK client and an LV2 plugin is also available.") ("pulseaudio" ,pulseaudio) ("qtbase" ,qtbase) ("qtdeclarative" ,qtdeclarative) + ("qtgraphicaleffects" ,qtgraphicaleffects) ("qtquickcontrols2" ,qtquickcontrols2) ("qtscript" ,qtscript) ("qtsvg" ,qtsvg) -- cgit 1.4.1 From 9ea6e3f4d86a70f6c1bcfd0579582120dce3b98b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 1 Jun 2021 20:54:01 +0300 Subject: gnu: gcc-9: Update to 9.4.0. * gnu/packages/gcc.scm (gcc-9): Update to 9.4.0. --- gnu/packages/gcc.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm index ad3706359d..1fd5710e57 100644 --- a/gnu/packages/gcc.scm +++ b/gnu/packages/gcc.scm @@ -568,14 +568,14 @@ It also includes runtime support libraries for these languages."))) (define-public gcc-9 (package (inherit gcc-8) - (version "9.3.0") + (version "9.4.0") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/gcc/gcc-" version "/gcc-" version ".tar.xz")) (sha256 (base32 - "1la2yy27ziasyf0jvzk58y1i5b5bq2h176qil550bxhifs39gqbi")) + "13l3p6g2krilaawbapmn9zmmrh3zdwc36mfr3msxfy038hps6pf9")) (patches (search-patches "gcc-9-strmov-store-file-names.patch" "gcc-9-asan-fix-limits-include.patch" "gcc-5.0-libvtv-runpath.patch")))))) -- cgit 1.4.1 From e54c03c1f569220c1939a7ddc917b0daec989dea Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 1 Jun 2021 18:17:03 +0200 Subject: gnu: icu4c: Add 69.1. * gnu/packages/icu4c.scm (icu4c-69): New public variable. --- gnu/packages/icu4c.scm | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/icu4c.scm b/gnu/packages/icu4c.scm index bf98fc3a40..12f8393900 100644 --- a/gnu/packages/icu4c.scm +++ b/gnu/packages/icu4c.scm @@ -130,6 +130,22 @@ C/C++ part.") (base32 "09fng7a80xj8d5r1cgbgq8r47dsw5jsr6si9p2cj2ylhwgg974f7")))))) +(define-public icu4c-69 + (package + (inherit icu4c) + (version "69.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/unicode-org/icu/releases/download/release-" + (string-map (lambda (x) (if (char=? x #\.) #\- x)) version) + "/icu4c-" + (string-map (lambda (x) (if (char=? x #\.) #\_ x)) version) + "-src.tgz")) + (sha256 + (base32 + "0icps0avkwy5df3wwc5kybxcg63hcgk4phdh9g244g0xrmx7pfjc")))))) + (define-public icu4c-build-root (package (inherit icu4c) -- cgit 1.4.1 From 304895d5e04d6f09a29b3fe233e3a8f6b62fbd8b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 1 Jun 2021 18:17:49 +0200 Subject: gnu: ungoogled-chromium: Update to 91.0.4472.77-0.6802c88. * gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for 91. (%chromium-version): Set to 91.0.4472.77. (%ungoogled-revision): Set to 91.0.4472.77-1-0-g6802c88. (%debian-patches): Remove obsolete patch. (%ungoogled-origin): Update hash. (ungoogled-chromium-snippet): Add substitution for an unbundling file. (ungoogled-chromium): Update hash. [arguments]: Add a substitution previously provided by a Debian patch. [inputs]: Change from ICU-68 to ICU-69. --- gnu/packages/chromium.scm | 31 ++++++++++++++++++++++--------- 1 file changed, 22 insertions(+), 9 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm index f06767f305..6a98867cc8 100644 --- a/gnu/packages/chromium.scm +++ b/gnu/packages/chromium.scm @@ -163,6 +163,7 @@ "third_party/google_input_tools/third_party/closure_library/third_party/closure" ;Expat "third_party/googletest" ;BSD-3 "third_party/harfbuzz-ng" ;Expat + "third_party/highway" ;ASL2.0 "third_party/hunspell" ;MPL1.1/GPL2+/LGPL2.1+ "third_party/iccjpeg" ;IJG "third_party/inspector_protocol" ;BSD-3 @@ -179,6 +180,7 @@ "third_party/libaom/source/libaom/third_party/fastfeat" ;BSD-3 "third_party/libaom/source/libaom/third_party/vector" ;Expat "third_party/libaom/source/libaom/third_party/x86inc" ;ISC + "third_party/libjxl" ;ASL2.0 "third_party/libgav1" ;ASL2.0 "third_party/libgifcodec" ;MPL1.1/GPL2+/LGPL2.1+, BSD-3, BSD-2 "third_party/libjingle_xmpp" ;BSD-3 @@ -239,7 +241,6 @@ "third_party/rnnoise" ;BSD-3 "third_party/ruy" ;ASL2.0 "third_party/s2cellid" ;ASL2.0 - "third_party/schema_org" ;CC-BY-SA3.0 "third_party/securemessage" ;ASL2.0 "third_party/shell-encryption" ;ASL2.0 "third_party/skia" ;BSD-3 @@ -274,6 +275,7 @@ "third_party/wayland-protocols" ;Expat "third_party/web-animations-js" ;ASL2.0 "third_party/webdriver" ;ASL2.0 + "third_party/webgpu-cts" ;BSD-3 "third_party/webrtc" ;BSD-3 "third_party/webrtc/common_audio/third_party/ooura" ;Non-copyleft "third_party/webrtc/common_audio/third_party/spl_sqrt_floor" ;Public domain @@ -320,14 +322,14 @@ (string-append "ungoogled-chromium-" category "-" name)))) (sha256 (base32 hash)))) -(define %chromium-version "90.0.4430.212") +(define %chromium-version "91.0.4472.77") (define %debian-revision "debian/90.0.4430.85-1") -(define %ungoogled-revision "90.0.4430.85-1-11-g3184907") +;; Note: use 'git describe --long' even for exact tags to placate the +;; custom version format for ungoogled-chromium. +(define %ungoogled-revision "91.0.4472.77-1-0-g6802c88") (define %debian-patches - (list (debian-patch "fixes/missing-includes.patch" - "1f0drxp1cy76g71rkkzxxbwixn03yn9b0q22vb0mb6h2qk6cw92q") - (debian-patch "fixes/nomerge.patch" + (list (debian-patch "fixes/nomerge.patch" "0lybs2b5gk08j8cr6vjrs9d3drd7qfw013z2r0y00by8dnpm74i3") (debian-patch "system/nspr.patch" "1gdirn1k1i841l8zp8xgr95kl16b5nx827am9rcxj8sfkm8hgkn3") @@ -344,7 +346,7 @@ (file-name (git-file-name "ungoogled-chromium" %ungoogled-revision)) (sha256 (base32 - "18xfwgkw3xarxcgnzvyv70h4icyqh3k8lfx6fvhp7fsr6x20sai0")))) + "1jfmmkw1y4rcjfgsm7b4v2lrgd3sks5qpajvq0djflbhkpsqxfk0")))) (define %guix-patches (list (local-file @@ -399,6 +401,11 @@ (format #t "Replacing GN files...~%") (force-output) + ;; XXX: Chromium no longer relies on overriding ICU's UCHAR_TYPE, + ;; but the unbundling code was not updated. Remove for M92. + (substitute* "build/linux/unbundle/icu.gn" + (("\"UCHAR_TYPE=uint16_t\",") + "")) (substitute* "tools/generate_shim_headers/generate_shim_headers.py" ;; The "is_official_build" configure option enables certain ;; release optimizations like those used in the commercial @@ -481,7 +488,7 @@ %chromium-version ".tar.xz")) (sha256 (base32 - "17nmhrkl81qqvzbh861k2mmifncx4wg1mv1fmn52f8gzn461vqdb")) + "0c8vj3gq3nmb7ssiwj6875g0a8hcprss1a4gqw9h7llqywza9ma5")) (modules '((guix build utils))) (snippet (force ungoogled-chromium-snippet)))) (build-system gnu-build-system) @@ -630,6 +637,12 @@ (("include \"third_party/lcms/include/lcms2\\.h\"") "include \"lcms2.h\"")) + ;; Add missing include statement. + (substitute* "third_party/pdfium/core/fxcodec/png/png_decoder.cpp" + (("#include \"core/fxcodec/fx_codec.h\"" all) + (string-append all + "\n#include \"core/fxcodec/fx_codec_def.h\""))) + (substitute* "third_party/breakpad/breakpad/src/common/linux/libcurl_wrapper.h" (("include \"third_party/curl") @@ -852,7 +865,7 @@ ("glib" ,glib) ("gtk+" ,gtk+) ("harfbuzz" ,harfbuzz) - ("icu4c" ,icu4c-68) + ("icu4c" ,icu4c-69) ("lcms" ,lcms) ("libevent" ,libevent) ("libffi" ,libffi) -- cgit 1.4.1 From 8d14d602ea00a048401472387f282c7cf995d144 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 1 Jun 2021 18:18:17 +0200 Subject: gnu: unbound: Enable DoH support. * gnu/packages/dns.scm (unbound)[inputs]: Add NGHTTP2:LIB. [arguments]: Add "--with-libnghttp2" to #:configure-flags. --- gnu/packages/dns.scm | 3 +++ 1 file changed, 3 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index 86185373c4..a0388a1419 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -625,12 +625,15 @@ to result in system-wide compromise.") (inputs `(("expat" ,expat) ("libevent" ,libevent) + ("nghttp2" ,nghttp2 "lib") ("protobuf" ,protobuf) ("python-wrapper" ,python-wrapper) ("openssl" ,openssl))) (arguments `(#:configure-flags (list "--disable-static" ; save space and non-determinism in libunbound.a + (string-append + "--with-libnghttp2=" (assoc-ref %build-inputs "nghttp2")) (string-append "--with-ssl=" (assoc-ref %build-inputs "openssl")) (string-append -- cgit 1.4.1 From 49b15701adb758f89bdf4f36f3220851d744c817 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 1 Jun 2021 22:50:01 +0300 Subject: gnu: llvm-7: Update to 7.1.0. * gnu/packages/llvm.scm (llvm-7): Update to 7.1.0. --- gnu/packages/llvm.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index b510f319f9..575c63c713 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2017 Roel Janssen ;;; Copyright © 2018, 2019, 2020 Marius Bakke ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice -;;; Copyright © 2018 Efraim Flashner +;;; Copyright © 2018, 2021 Efraim Flashner ;;; Copyright © 2018 Tim Gesthuizen ;;; Copyright © 2018 Pierre Neidhardt ;;; Copyright © 2019 Rutger Helling @@ -690,23 +690,23 @@ of programming tools as well as libraries with equivalent functionality.") (define-public llvm-7 (package (inherit llvm-8) - (version "7.0.1") + (version "7.1.0") (source (origin (method url-fetch) (uri (llvm-uri "llvm" version)) (sha256 (base32 - "16s196wqzdw4pmri15hadzqgdi926zln3an2viwyq0kini6zr3d3")))))) + "0r1p5didv4rkgxyvbkyz671xddg6i3dxvbpsi1xxipkla0l9pk0v")))))) (define-public clang-runtime-7 (clang-runtime-from-llvm llvm-7 - "065ybd8fsc4h2hikbdyricj6pyv4r7r7kpcikhb2y5zf370xybkq" + "1n48p8gjarihkws0i2bay5w9bdwyxyxxbpwyng7ba58jb30dlyq5" '("clang-runtime-9-libsanitizer-mode-field.patch"))) (define-public clang-7 (clang-from-llvm llvm-7 clang-runtime-7 - "067lwggnbg0w1dfrps790r5l6k8n5zwhlsw7zb6zvmfpwpfn4nx4" + "0vc4i87qwxnw9lci4ayws9spakg0z6w5w670snj9f8g5m9rc8zg9" #:patches '("clang-7.0-libc-search-path.patch"))) (define-public clang-toolchain-7 -- cgit 1.4.1 From 82d8ab01f5cb6d479e3b82c08067e2442ee7cad8 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 26 May 2021 22:30:31 +0200 Subject: maint: Require Guile 3.0. * configure.ac: Require Guile 3.0. * doc/guix.texi (Requirements): Adjust accordingly. * gnu/packages/package-management.scm (guile2.2-guix): Remove. * guix/lint.scm (exception-with-kind-and-args?): Remove 'cond-expand'. * guix/scripts/deploy.scm (deploy-machine*): Likewise. * guix/store.scm (call-with-store): Likewise. * guix/swh.scm (http-get*, http-post*): Likewise. * guix/ui.scm (without-compiler-optimizations, guard*) (call-with-error-handling): Likewise. --- configure.ac | 6 +---- doc/guix.texi | 3 +-- gnu/packages/package-management.scm | 34 --------------------------- guix/lint.scm | 11 +++------ guix/scripts/deploy.scm | 5 +--- guix/store.scm | 16 ++++--------- guix/swh.scm | 20 +++++----------- guix/ui.scm | 46 +++++++++++++------------------------ 8 files changed, 32 insertions(+), 109 deletions(-) (limited to 'gnu') diff --git a/configure.ac b/configure.ac index 583b902361..84592f6041 100644 --- a/configure.ac +++ b/configure.ac @@ -96,16 +96,12 @@ m4_pattern_forbid([^GUIX_]) dnl Search for 'guile' and 'guild'. This macro defines dnl 'GUILE_EFFECTIVE_VERSION'. -GUILE_PKG([3.0 2.2]) +GUILE_PKG([3.0]) GUILE_PROGS if test "x$GUILD" = "x"; then AC_MSG_ERROR(['guild' binary not found; please check your Guile installation.]) fi -if test "x$GUILE_EFFECTIVE_VERSION" = "x2.2"; then - PKG_CHECK_MODULES([GUILE], [guile-2.2 >= 2.2.6]) -fi - dnl Get CFLAGS and LDFLAGS for libguile. GUILE_FLAGS diff --git a/doc/guix.texi b/doc/guix.texi index 39dc2446ef..43198a0af1 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -840,8 +840,7 @@ GNU Guix is available for download from its website at GNU Guix depends on the following packages: @itemize -@item @url{https://gnu.org/software/guile/, GNU Guile}, version 3.0.x or -2.2.x; +@item @url{https://gnu.org/software/guile/, GNU Guile}, version 3.0.x; @item @url{https://notabug.org/cwebber/guile-gcrypt, Guile-Gcrypt}, version 0.1.0 or later; @item diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index d3d9f87be4..7229723ab8 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -518,40 +518,6 @@ the Nix package manager.") (invoke "make" "install-binPROGRAMS"))) (delete 'wrap-program))))))) - -(define-public guile2.2-guix - (package - (inherit guix) - (name "guile2.2-guix") - (native-inputs - `(("guile" ,guile-2.2) - ("gnutls" ,guile2.2-gnutls) - ("guile-gcrypt" ,guile2.2-gcrypt) - ("guile-json" ,guile2.2-json) - ("guile-lib" ,guile2.2-lib) - ("guile-sqlite3" ,guile2.2-sqlite3) - ("guile-ssh" ,guile2.2-ssh) - ("guile-git" ,guile2.2-git) - ("guile-zlib" ,guile2.2-zlib) - ("guile-lzlib" ,guile2.2-lzlib) - ,@(fold alist-delete (package-native-inputs guix) - '("guile" "gnutls" "guile-gcrypt" "guile-json" - "guile-lib" "guile-sqlite3" "guile-ssh" "guile-git" - "guile-zlib" "guile-lzlib")))) - (inputs - `(("guile" ,guile-2.2) - ,@(alist-delete "guile" (package-inputs guix)))) - (propagated-inputs - `(("gnutls" ,gnutls) - ("guile-gcrypt" ,guile2.2-gcrypt) - ("guile-json" ,guile2.2-json) - ("guile-lib" ,guile2.2-lib) - ("guile-sqlite3" ,guile2.2-sqlite3) - ("guile-ssh" ,guile2.2-ssh) - ("guile-git" ,guile2.2-git) - ("guile-zlib" ,guile2.2-zlib) - ("guile-lzlib" ,guile2.2-lzlib))))) - (define-public guile3.0-guix (deprecated-package "guile3.0-guix" guix)) diff --git a/guix/lint.scm b/guix/lint.scm index a2d6418b85..023a179ea6 100644 --- a/guix/lint.scm +++ b/guix/lint.scm @@ -1003,14 +1003,9 @@ descriptions maintained upstream." (origin-uris origin)) '()))) -(cond-expand - (guile-3 - ;; Guile 3.0.0 does not export this predicate. - (define exception-with-kind-and-args? - (exception-predicate &exception-with-kind-and-args))) - (else ;Guile 2 - (define exception-with-kind-and-args? - (const #f)))) +;; Guile 3.0.0 does not export this predicate. +(define exception-with-kind-and-args? + (exception-predicate &exception-with-kind-and-args)) (define* (check-derivation package #:key store) "Emit a warning if we fail to compile PACKAGE to a derivation." diff --git a/guix/scripts/deploy.scm b/guix/scripts/deploy.scm index bf2e8afa7f..7c62b05d12 100644 --- a/guix/scripts/deploy.scm +++ b/guix/scripts/deploy.scm @@ -125,10 +125,7 @@ Perform the deployment specified by FILE.\n")) ;; and include a '&message'. However, that message only contains ;; the format string. Thus, special-case it here to avoid ;; displaying a bare format string. - ((cond-expand - (guile-3 - ((exception-predicate &exception-with-kind-and-args) c)) - (else #f)) + (((exception-predicate &exception-with-kind-and-args) c) (raise c)) ((message-condition? c) diff --git a/guix/store.scm b/guix/store.scm index 9d706ae590..cf5d5eeccc 100644 --- a/guix/store.scm +++ b/guix/store.scm @@ -648,18 +648,10 @@ connection. Use with care." (close-connection store) (apply values results))))) - (cond-expand - (guile-3 - (with-exception-handler (lambda (exception) - (close-connection store) - (raise-exception exception)) - thunk)) - (else ;Guile 2.2 - (catch #t - thunk - (lambda (key . args) - (close-connection store) - (apply throw key args))))))) + (with-exception-handler (lambda (exception) + (close-connection store) + (raise-exception exception)) + thunk))) (define-syntax-rule (with-store store exp ...) "Bind STORE to an open connection to the store and evaluate EXPs; diff --git a/guix/swh.scm b/guix/swh.scm index 06d2957252..f6d5241e06 100644 --- a/guix/swh.scm +++ b/guix/swh.scm @@ -148,20 +148,12 @@ url (string-append url "/"))) -(cond-expand - (guile-3 - ;; XXX: Work around a bug in Guile 3.0.2 where #:verify-certificate? would - ;; be ignored (). - (define* (http-get* uri #:rest rest) - (apply http-request uri #:method 'GET rest)) - (define* (http-post* uri #:rest rest) - (apply http-request uri #:method 'POST rest))) - (else ;Guile 2.2 - ;; Guile 2.2 did not have #:verify-certificate? so ignore it. - (define* (http-get* uri #:key verify-certificate? streaming?) - (http-request uri #:method 'GET #:streaming? streaming?)) - (define* (http-post* uri #:key verify-certificate? streaming?) - (http-request uri #:method 'POST #:streaming? streaming?)))) +;; XXX: Work around a bug in Guile 3.0.2 where #:verify-certificate? would +;; be ignored (). +(define* (http-get* uri #:rest rest) + (apply http-request uri #:method 'GET rest)) +(define* (http-post* uri #:rest rest) + (apply http-request uri #:method 'POST rest)) (define %date-regexp ;; Match strings like "2014-11-17T22:09:38+01:00" or diff --git a/guix/ui.scm b/guix/ui.scm index 05b3f5f84c..6b0155f563 100644 --- a/guix/ui.scm +++ b/guix/ui.scm @@ -196,17 +196,11 @@ information, or #f if it could not be found." (stack-ref stack 1) ;skip the 'throw' frame last)))) -(cond-expand - (guile-3 - (define-syntax-rule (without-compiler-optimizations exp) - ;; Compile with the baseline compiler (-O1), which is much less expensive - ;; than -O2. - (parameterize (((@ (system base compile) default-optimization-level) 1)) - exp))) - (else - (define-syntax-rule (without-compiler-optimizations exp) - ;; No easy way to turn off optimizations on Guile 2.2. - exp))) +(define-syntax-rule (without-compiler-optimizations exp) + ;; Compile with the baseline compiler (-O1), which is much less expensive + ;; than -O2. + (parameterize (((@ (system base compile) default-optimization-level) 1)) + exp)) (define* (load* file user-module #:key (on-error 'nothing-special)) @@ -674,22 +668,17 @@ or variants of @code{~a} in the same profile.") or remove one of them from the profile.") name1 name2))))) -(cond-expand - (guile-3 - ;; On Guile 3.0, in 'call-with-error-handling' we need to re-raise. To - ;; preserve useful backtraces in case of unhandled errors, we want that to - ;; happen before the stack has been unwound, hence 'guard*'. - (define-syntax-rule (guard* (var clauses ...) exp ...) - "This variant of SRFI-34 'guard' does not unwind the stack before +;; On Guile 3.0, in 'call-with-error-handling' we need to re-raise. To +;; preserve useful backtraces in case of unhandled errors, we want that to +;; happen before the stack has been unwound, hence 'guard*'. +(define-syntax-rule (guard* (var clauses ...) exp ...) + "This variant of SRFI-34 'guard' does not unwind the stack before evaluating the tests and bodies of CLAUSES." - (with-exception-handler - (lambda (var) - (cond clauses ... (else (raise var)))) - (lambda () exp ...) - #:unwind? #f))) - (else - (define-syntax-rule (guard* (var clauses ...) exp ...) - (guard (var clauses ...) exp ...)))) + (with-exception-handler + (lambda (var) + (cond clauses ... (else (raise var)))) + (lambda () exp ...) + #:unwind? #f)) (define (call-with-error-handling thunk) "Call THUNK within a user-friendly error handler." @@ -822,10 +811,7 @@ directories:~{ ~a~}~%") ;; Furthermore, use of 'guard*' ensures that the stack has not ;; been unwound when we re-raise, since that would otherwise show ;; useless backtraces. - ((cond-expand - (guile-3 - ((exception-predicate &exception-with-kind-and-args) c)) - (else #f)) + (((exception-predicate &exception-with-kind-and-args) c) (raise c)) ((message-condition? c) -- cgit 1.4.1 From ec9307ea079fa6b25c51f7fde3114f1d9183f497 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 1 Jun 2021 21:33:16 +0200 Subject: services: cuirass: Create the profile and GC root directory. * gnu/services/cuirass.scm (cuirass-activation): Create /var/guix/profiles/per-user/cuirass/cuirass or similar. --- gnu/services/cuirass.scm | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/services/cuirass.scm b/gnu/services/cuirass.scm index 5b4e24d794..2daf3082df 100644 --- a/gnu/services/cuirass.scm +++ b/gnu/services/cuirass.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016 Mathieu Lirzin -;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ludovic Courtès +;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès ;;; Copyright © 2017, 2020 Mathieu Othacehe ;;; Copyright © 2017 Jan Nieuwenhuizen ;;; Copyright © 2018, 2019 Ricardo Wurmus @@ -272,6 +272,8 @@ remote-server))) (user (cuirass-configuration-user config)) (log "/var/log/cuirass") + (profile (string-append "/var/guix/profiles/per-user/" user)) + (roots (string-append profile "/cuirass")) (group (cuirass-configuration-group config))) (with-imported-modules '((guix build utils)) #~(begin @@ -279,6 +281,7 @@ (mkdir-p #$cache) (mkdir-p #$log) + (mkdir-p #$roots) (when #$remote-cache (mkdir-p #$remote-cache)) @@ -287,6 +290,8 @@ (gid (group:gid (getgr #$group)))) (chown #$cache uid gid) (chown #$log uid gid) + (chown #$roots uid gid) + (chown #$profile uid gid) (when #$remote-cache (chown #$remote-cache uid gid))))))) -- cgit 1.4.1 From 0db906c52ca329adfbafd6677a7045232e5fdd48 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 1 Jun 2021 21:36:15 +0200 Subject: services: cuirass: Do not export record type descriptors. * gnu/services/cuirass.scm () (, ): Do not export. --- gnu/services/cuirass.scm | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/services/cuirass.scm b/gnu/services/cuirass.scm index 2daf3082df..99b137e05e 100644 --- a/gnu/services/cuirass.scm +++ b/gnu/services/cuirass.scm @@ -38,16 +38,13 @@ #:use-module (gnu system shadow) #:use-module (srfi srfi-1) #:use-module (ice-9 match) - #:export ( - cuirass-remote-server-configuration + #:export (cuirass-remote-server-configuration cuirass-remote-server-configuration? - cuirass-configuration cuirass-configuration? cuirass-service-type - cuirass-remote-worker-configuration cuirass-remote-worker-configuration? cuirass-remote-worker-service-type)) -- cgit 1.4.1 From 2885c3568edec35086f8feeae5b60259cbea407c Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 1 Jun 2021 22:35:28 +0200 Subject: machine: ssh: Gracefully handle failure of the effectful bits. Previously, '&inferior-exception' raised by 'upgrade-shepherd-services' and co. would go through as-is, leaving users with an ugly backtrace. * gnu/machine/ssh.scm (deploy-managed-host): Define 'eval/error-handling' and use it in lieu of EVAL as arguments to 'switch-to-system', 'upgrade-shepherd-services', and 'install-bootloader'. --- gnu/machine/ssh.scm | 40 +++++++++++++++++++++++++++++++++++++--- 1 file changed, 37 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/machine/ssh.scm b/gnu/machine/ssh.scm index fa942169c4..93b0a007da 100644 --- a/gnu/machine/ssh.scm +++ b/gnu/machine/ssh.scm @@ -38,6 +38,9 @@ #:use-module (guix store) #:use-module (guix utils) #:use-module ((guix self) #:select (make-config.scm)) + #:use-module ((guix inferior) + #:select (inferior-exception? + inferior-exception-arguments)) #:use-module (gcrypt pk-crypto) #:use-module (ice-9 format) #:use-module (ice-9 match) @@ -443,17 +446,46 @@ have you run 'guix archive --generate-key?'") (mlet %store-monad ((_ (check-deployment-sanity machine)) (boot-parameters (machine-boot-parameters machine))) (let* ((os (machine-operating-system machine)) + (host (machine-ssh-configuration-host-name + (machine-configuration machine))) (eval (cut machine-remote-eval machine <>)) (menu-entries (map boot-parameters->menu-entry boot-parameters)) (bootloader-configuration (operating-system-bootloader os)) (bootcfg (operating-system-bootcfg os menu-entries))) + (define-syntax-rule (eval/error-handling condition handler ...) + ;; Return a wrapper around EVAL such that HANDLER is evaluated if an + ;; exception is raised. + (lambda (exp) + (lambda (store) + (guard (condition ((inferior-exception? condition) + (values (begin handler ...) store))) + (run-with-store store (eval exp)))))) + (mbegin %store-monad (with-roll-back #f - (switch-to-system eval os)) + (switch-to-system (eval/error-handling c + (raise (formatted-message + (G_ "\ +failed to switch systems while deploying '~a':~%~{~s ~}") + host + (inferior-exception-arguments c)))) + os)) (with-roll-back #t (mbegin %store-monad - (upgrade-shepherd-services eval os) - (install-bootloader eval bootloader-configuration bootcfg))))))) + (upgrade-shepherd-services (eval/error-handling c + (warning (G_ "\ +an error occurred while upgrading services on '~a':~%~{~s ~}~%") + host + (inferior-exception-arguments + c))) + os) + (install-bootloader (eval/error-handling c + (raise (formatted-message + (G_ "\ +failed to install bootloader on '~a':~%~{~s ~}~%") + host + (inferior-exception-arguments c)))) + bootloader-configuration bootcfg))))))) ;;; @@ -540,4 +572,6 @@ for environment of type '~a'") ;; Local Variables: ;; eval: (put 'remote-let 'scheme-indent-function 1) +;; eval: (put 'with-roll-back 'scheme-indent-function 1) +;; eval: (put 'eval/error-handling 'scheme-indent-function 1) ;; End: -- cgit 1.4.1 From 2df1c4f134454ce812439691b40cad285ef808ae Mon Sep 17 00:00:00 2001 From: Zhu Zihao Date: Thu, 27 May 2021 16:35:56 +0800 Subject: gnu: rtl8821ce-linux-module: Update to 0.0.0-3.897e7c4. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fix the broken build with linux-libre 5.12. * gnu/packages/linux.scm (rtl8821ce-linux-module): Update to 0.0.0-3.897e7c4. Signed-off-by: Ludovic Courtès --- gnu/packages/linux.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index b803426b74..8d93e9e19c 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1229,8 +1229,8 @@ RTL8812AU, RTL8821AU, and RTL8814AU chips.") (license license:gpl2+)))) (define-public rtl8821ce-linux-module - (let ((commit "14b536f0c9ad2d0abbdab8afc7ade684900ca9cf") - (revision "2")) + (let ((commit "897e7c4c15dd5a0a569745dc223d969a26ff5bfc") + (revision "3")) (package (name "rtl8821ce-linux-module") (version (git-version "0.0.0" revision commit)) @@ -1243,7 +1243,7 @@ RTL8812AU, RTL8821AU, and RTL8814AU chips.") (file-name (git-file-name name version)) (sha256 (base32 - "0z7r7spsgn22gwv9pcmkdjn9ingi8jj7xkxasph8118h46fw8ip2")))) + "0935dzz0njxh78wfd17yqah1dxn6b3kaszvzclwwrwwhwcrdp80j")))) (build-system linux-module-build-system) (arguments `(#:make-flags -- cgit 1.4.1 From c9b3627d566bde6b60841185f147589df45e65eb Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Mon, 16 Dec 2019 12:09:16 +0100 Subject: gnu: Add why3. * gnu/packages/maths.scm (why3): New variable. --- gnu/packages/maths.scm | 67 +++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 66 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 747ad1ddfd..22cd62e2f5 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -28,7 +28,7 @@ ;;; Copyright © 2018 Adam Massmann ;;; Copyright © 2018, 2020 Marius Bakke ;;; Copyright © 2018 Eric Brown -;;; Copyright © 2018 Julien Lepiller +;;; Copyright © 2018, 2021 Julien Lepiller ;;; Copyright © 2018 Amin Bandali ;;; Copyright © 2019, 2021 Nicolas Goaziou ;;; Copyright © 2019 Steve Sprang @@ -75,6 +75,7 @@ #:use-module (guix build-system cmake) #:use-module (guix build-system glib-or-gtk) #:use-module (guix build-system gnu) + #:use-module (guix build-system ocaml) #:use-module (guix build-system python) #:use-module (guix build-system ruby) #:use-module (gnu packages algebra) @@ -86,11 +87,13 @@ #:use-module (gnu packages check) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) + #:use-module (gnu packages coq) #:use-module (gnu packages curl) #:use-module (gnu packages cyrus-sasl) #:use-module (gnu packages dbm) #:use-module (gnu packages documentation) #:use-module (gnu packages elf) + #:use-module (gnu packages emacs) #:use-module (gnu packages file) #:use-module (gnu packages flex) #:use-module (gnu packages fltk) @@ -120,6 +123,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages netpbm) + #:use-module (gnu packages ocaml) #:use-module (gnu packages onc-rpc) #:use-module (gnu packages pcre) #:use-module (gnu packages popt) @@ -6290,3 +6294,64 @@ interval arithmetic, plotting.") "Numdiff compares files line by line and field by field, ignoring small numeric differences and differences in numeric formats.") (license license:gpl3+))) + +(define-public why3 + (package + (name "why3") + (version "1.3.1") + (source (origin + (method url-fetch) + (uri (string-append "https://gforge.inria.fr/frs/download.php/file" + "/38291/why3-" version ".tar.gz")) + (sha256 + (base32 + "16zcrc60zz2j3gd3ww93z2z9x2jkxb3kr57y8i5rcgmacy7mw3bv")))) + (build-system ocaml-build-system) + (native-inputs + `(("coq" ,coq) + ("ocaml" ,ocaml) + ("which" ,which))) + (propagated-inputs + `(("camlzip" ,camlzip) + ("ocaml-graph" ,ocaml-graph) + ("ocaml-menhir" ,ocaml-menhir) + ("ocaml-num" ,ocaml-num) + ("ocaml-zarith" ,ocaml-zarith))) + (inputs + `(("coq-flocq" ,coq-flocq) + ("emacs-minimal" ,emacs-minimal) + ("zlib" ,zlib))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'configure 'fix-configure + (lambda _ + (setenv "CONFIG_SHELL" (which "sh")) + (substitute* "configure" + ;; find ocaml-num in the correct directory + (("\\$DIR/nums.cma") "$DIR/../nums.cma") + (("\\$DIR/num.cmi") "$DIR/../num.cmi")) + #t)) + (add-after 'configure 'fix-makefile + (lambda _ + (substitute* "Makefile" + ;; find ocaml-num in the correct directory + (("site-lib/num") "site-lib")) + #t)) + (add-after 'install 'install-lib + (lambda _ + (invoke "make" "byte") + (invoke "make" "install-lib") + #t))))) + (home-page "http://why3.lri.fr") + (synopsis "Deductive program verification") + (description "Why3 provides a language for specification and programming, +called WhyML, and relies on external theorem provers, both automated and +interactive, to discharge verification conditions. Why3 comes with a standard +library of logical theories (integer and real arithmetic, Boolean operations, +sets and maps, etc.) and basic programming data structures (arrays, queues, +hash tables, etc.). A user can write WhyML programs directly and get +correct-by-construction OCaml programs through an automated extraction +mechanism. WhyML is also used as an intermediate language for the verification +of C, Java, or Ada programs.") + (license license:lgpl2.1))) -- cgit 1.4.1 From b94bc3ea30a9451f9019cca66ac20f585870eecd Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Mon, 16 Dec 2019 12:40:18 +0100 Subject: gnu: Add frama-c. * gnu/packages/maths.scm (frama-c): New variable. --- gnu/packages/maths.scm | 47 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 22cd62e2f5..e78c5dfb93 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -6355,3 +6355,50 @@ correct-by-construction OCaml programs through an automated extraction mechanism. WhyML is also used as an intermediate language for the verification of C, Java, or Ada programs.") (license license:lgpl2.1))) + +(define-public frama-c + (package + (name "frama-c") + (version "22.0") + (source (origin + (method url-fetch) + (uri (string-append "http://frama-c.com/download/frama-c-" + version "-Titanium.tar.gz")) + (sha256 + (base32 + "1mq1fijka95ydrla486yr4w6wdl9l7vmp512s1q00b0p6lmfwmkh")))) + (build-system ocaml-build-system) + (arguments + `(#:tests? #f; no test target in Makefile + #:phases + (modify-phases %standard-phases + (add-before 'configure 'export-shell + (lambda* (#:key inputs #:allow-other-keys) + (setenv "CONFIG_SHELL" (string-append (assoc-ref inputs "bash") + "/bin/sh")) + #t))))) + (inputs + `(("gmp" ,gmp))) + (propagated-inputs + `(("ocaml-biniou" ,ocaml-biniou) + ("ocaml-easy-format" ,ocaml-easy-format) + ("ocaml-graph" ,ocaml-graph) + ("ocaml-yojson" ,ocaml-yojson) + ("ocaml-zarith" ,ocaml-zarith) + ("why3" ,why3))) + (native-search-paths + (list (search-path-specification + (variable "FRAMAC_SHARE") + (files '("share/frama-c")) + (separator #f)) + (search-path-specification + (variable "FRAMAC_LIB") + (files '("lib/frama-c")) + (separator #f)))) + (home-page "http://frama-c.com") + (synopsis "C source code analysis platform") + (description "Frama-C is an extensible and collaborative platform dedicated +to source-code analysis of C software. The Frama-C analyzers assist you in +various source-code-related activities, from the navigation through unfamiliar +projects up to the certification of critical software.") + (license license:lgpl2.1+))) -- cgit 1.4.1 From 841edfa49119c63eade4930751ac4ff5c012bfe5 Mon Sep 17 00:00:00 2001 From: Simon Streit Date: Wed, 2 Jun 2021 01:11:31 +0200 Subject: gnu: redis: Update to 6.2.4 [security fixes]. Fixes CVE-2021-29477. * gnu/packages/databases.scm (redis): Update to 6.2.4. [arguments]: Disable the 'integration/failover' test. Signed-off-by: Leo Famulari --- gnu/packages/databases.scm | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index cead8c0e5a..cd760ee5ef 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -51,6 +51,7 @@ ;;; Copyright © 2021 David Larsson ;;; Copyright © 2021 Pjotr Prins ;;; Copyright © 2021 Bonface Munyoki Kilyungi +;;; Copyright © 2021 Simon Streit ;;; ;;; This file is part of GNU Guix. ;;; @@ -2135,14 +2136,14 @@ similar to BerkeleyDB, LevelDB, etc.") (define-public redis (package (name "redis") - (version "6.0.11") + (version "6.2.4") (source (origin (method url-fetch) (uri (string-append "http://download.redis.io/releases/redis-" version".tar.gz")) (sha256 (base32 - "0prwqap452m581nyc3cz642d1z3x9nd81896hlqdm3z8238z49y9")) + "0vp1d9mlfsppry3nsj9f7bmh9wjgsy3jggp24sac1hhgl43c8cms")) (modules '((guix build utils))) (snippet ;; Delete bundled jemalloc, as the package will use the libc one @@ -2150,8 +2151,8 @@ similar to BerkeleyDB, LevelDB, etc.") #t)))) (build-system gnu-build-system) (native-inputs - `(("procps" ,procps) ; for tests - ("tcl" ,tcl))) ; for tests + `(("procps" ,procps) ; for tests + ("tcl" ,tcl))) ; for tests (arguments '(#:phases (modify-phases %standard-phases @@ -2168,9 +2169,10 @@ similar to BerkeleyDB, LevelDB, etc.") (lambda _ ;; Disable failing tests (substitute* "tests/test_helper.tcl" - ((" integration/replication[^-]") "") - ((" integration/replication-4") "") - ((" integration/replication-psync") "")) + (("integration/failover") "") + (("integration/replication-4") "") + (("integration/replication-psync") "") + (("integration/replication[^-]") "")) #t))) #:make-flags `("CC=gcc" "MALLOC=libc" -- cgit 1.4.1 From 51e853956645e5db46941ba49fe99364ce145115 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sun, 30 May 2021 04:05:16 +0000 Subject: gnu: python-sphinx-gallery: Update to 0.9.0. * gnu/packages/sphinx.scm (python-sphinx-gallery): Update to 0.9.0. [source]: Build from PyPI. [arguments]: Enable tests. Add custom 'check phase and phase to make test files writable. [native-inputs]: Add python-joblib, python-matplotlib, python-numpy, python-pillow, python-pytest, python-pytest-cov, python-sphinx. Remove python-pytest-runner. [home-page]: Follow redirect. (python2-sphinx-gallery): Remove package. Signed-off-by: Efraim Flashner --- gnu/packages/sphinx.scm | 51 +++++++++++++++++++++++++++++++------------------ 1 file changed, 32 insertions(+), 19 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm index 14bc3f5a79..428a701d87 100644 --- a/gnu/packages/sphinx.scm +++ b/gnu/packages/sphinx.scm @@ -15,6 +15,7 @@ ;;; Copyright © 2019 Brett Gilio ;;; Copyright © 2020 Giacomo Leidi ;;; Copyright © 2021 Eric Bavier +;;; Copyright © 2021 Vinicius Monego ;;; ;;; This file is part of GNU Guix. ;;; @@ -409,34 +410,46 @@ integrate Sphinx documents in web templates and to handle searches.") (define-public python-sphinx-gallery (package (name "python-sphinx-gallery") - (version "0.1.13") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/sphinx-gallery/sphinx-gallery") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "14nbqh9krx2l2y2ylbln6l6w8iak3wac1lngvaf278y1cx7685kg")))) + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "sphinx-gallery" version)) + (sha256 + (base32 "14zyhr7m92nafhhnzfvnbgkf5m91krd9mjyi24zn59bjq6zyr8hl")))) (build-system python-build-system) (arguments - ;; FIXME: Tests attempt to download , - ;; , and - ;; . - `(#:tests? #f)) + `(#:phases + (modify-phases %standard-phases + (add-before 'check 'writable-files-for-tests + (lambda _ + (for-each make-file-writable (find-files ".")))) + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "python" "-m" "pytest" "--pyargs" "sphinx_gallery" "-k" + (string-append + ;; These tests require online data. + "not test_embed_code_links_get_data" + " and not test_run_sphinx" + ;; AssertionError. + " and not test_embed_links_and_styles")))))))) (native-inputs - `(("python-pytest-runner" ,python-pytest-runner))) - (home-page "https://sphinx-gallery.github.io/") + `(("python-joblib" ,python-joblib) + ("python-matplotlib" ,python-matplotlib) + ("python-numpy" ,python-numpy) + ("python-pillow" ,python-pillow) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-sphinx" ,python-sphinx))) + (home-page "https://sphinx-gallery.github.io/stable/index.html") (synopsis "Generate an examples gallery automatically") (description "@code{sphinx_gallery} is a Sphinx extension that builds an HTML version from any set of Python scripts and puts it into an examples gallery.") (license license:bsd-3))) -(define-public python2-sphinx-gallery - (package-with-python2 python-sphinx-gallery)) - (define-public python-sphinx-me (package (name "python-sphinx-me") -- cgit 1.4.1 From 49e40006f6eab32c25ed4e2bccd876f1e411634b Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Thu, 27 May 2021 20:59:01 +0200 Subject: gnu: python-hg-evolve: Update to 10.3.1. * gnu/packages/version-control.scm (python-hg-evolve): Update to 10.3.1. Signed-off-by: Efraim Flashner --- gnu/packages/version-control.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 80842ecf0c..cd262402c1 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -1701,7 +1701,7 @@ interface.") (define-public python-hg-evolve (package (name "python-hg-evolve") - (version "10.0.1") + (version "10.3.1") (source (origin (method hg-fetch) @@ -1711,7 +1711,7 @@ interface.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1lz407373lfam9n02gq0l0rc2sjvn0m96kbzy93ipia3ika8fa68")))) + "0msnp5fp8sz4q2r5xpcmm60h82kwkyg23y212v1xfp7ixkq9f4qa")))) (build-system python-build-system) (arguments ;; Tests need mercurial source code. -- cgit 1.4.1 From 873c6b4f21ebc63a10d659f2b3363ea82549e9f8 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Tue, 1 Jun 2021 22:38:18 -0400 Subject: gnu: icecat: Update to 78.11.0-guix0-preview1 [fixes CVE-2021-29967]. * gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update. (icecat-source): Update upstream source hash. --- gnu/packages/gnuzilla.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index dc3ed4d3fd..cc65b1ccfb 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -694,8 +694,8 @@ from forcing GEXP-PROMISE." #:system system #:guile-for-build guile))) -(define %icecat-version "78.10.0-guix0-preview1") -(define %icecat-build-id "20210419000000") ;must be of the form YYYYMMDDhhmmss +(define %icecat-version "78.11.0-guix0-preview1") +(define %icecat-build-id "20210601000000") ;must be of the form YYYYMMDDhhmmss ;; 'icecat-source' is a "computed" origin that generates an IceCat tarball ;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat' @@ -717,7 +717,7 @@ from forcing GEXP-PROMISE." "firefox-" upstream-firefox-version ".source.tar.xz")) (sha256 (base32 - "0h6zl87czbhyhy3597bxqzwy4p1vsaqimkg92lw31gjbv6k434cp")))) + "0zjpzkxx3wc2840d7q4b9lnkj1kwk1qps29s9c83jf5y6xclnf9q")))) (upstream-icecat-base-version "78.7.0") ; maybe older than base-version ;;(gnuzilla-commit (string-append "v" upstream-icecat-base-version)) -- cgit 1.4.1 From da340369ac35dc4db008d0b3997a51e72b941a18 Mon Sep 17 00:00:00 2001 From: Paul Garlick Date: Wed, 2 Jun 2021 10:23:09 +0100 Subject: gnu: python-vedo: Make pkg-config a native input. * gnu/packages/python-science.scm (python-vedo)[inputs]: Move pkg-config to... [native-inputs]: ...here. --- gnu/packages/python-science.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 428452909a..39f52f1d64 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -676,11 +676,12 @@ readable.") (invoke "./run_all.sh"))) '("common" "dolfin"))) #t))))) - (inputs ; for the check phase + (inputs ; for the check phase `(("dolfin" ,fenics) ("pkgconfig" ,python-pkgconfig) - ("pkg-config" ,pkg-config) ("matplotlib" ,python-matplotlib))) + (native-inputs ; for python-pkgconfig + `(("pkg-config" ,pkg-config))) (propagated-inputs `(("numpy" ,python-numpy) ("vtk" ,vtk))) -- cgit 1.4.1 From 57278dc214bcd699217614efa885da35e4b9c31b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 2 Jun 2021 12:52:44 +0200 Subject: gnu: libavif: Update to 0.9.1. * gnu/packages/image.scm (libavif): Update to 0.9.1. --- gnu/packages/image.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 64863cd3b3..55fdf18e7e 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -2126,7 +2126,7 @@ This package can be used to create @code{favicon.ico} files for web sites.") (define-public libavif (package (name "libavif") - (version "0.9.0") + (version "0.9.1") (source (origin (method git-fetch) (uri (git-reference @@ -2135,7 +2135,7 @@ This package can be used to create @code{favicon.ico} files for web sites.") (file-name (git-file-name name version)) (sha256 (base32 - "1aw41m8ddrckq375w0lv2zd4ybhccsy1hw4f9kipppwxhgvk17gf")))) + "1h1gf4cbrff73f8s4avkph2sbr4d3s71kifipskzcmrqjbjc2qsx")))) (build-system cmake-build-system) (arguments `(#:configure-flags '("-DAVIF_CODEC_AOM=ON" "-DAVIF_CODEC_DAV1D=ON" -- cgit 1.4.1 From 6c0a09b34105471b4a5a08e09d868f6048d0e019 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 1 Jun 2021 15:27:40 +0200 Subject: gnu: retroarch: Update to 1.9.4. * gnu/packages/emulators.scm (retroarch): Update to 1.9.4. --- gnu/packages/emulators.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index 1b401e66c9..716d1174ad 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -1314,7 +1314,7 @@ as RetroArch.") (define-public retroarch (package (name "retroarch") - (version "1.9.3") + (version "1.9.4") (source (origin (method git-fetch) @@ -1323,7 +1323,7 @@ as RetroArch.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "01ssacnq5sl9221476df95dgry5m1z5mnlk3l3dh3rrg0qr4nvv3")) + (base32 "1wky28y52nsjmannks3y1hbjgw0dvqh85gxrllr98f9y7kvk1cvf")) (patches (search-patches "retroarch-LIBRETRO_DIRECTORY.patch")))) (build-system gnu-build-system) -- cgit 1.4.1 From fa26ca54f9220d8dd568b0e3c6891adcfe50575f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 1 Jun 2021 15:27:50 +0200 Subject: gnu: osip: Update to 5.2.1. * gnu/packages/telephony.scm (osip): Update to 5.2.1. --- gnu/packages/telephony.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/telephony.scm b/gnu/packages/telephony.scm index af7148bf84..9d8184801c 100644 --- a/gnu/packages/telephony.scm +++ b/gnu/packages/telephony.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2016 Francesco Frassinelli ;;; Copyright © 2016, 2017 Nikita ;;; Copyright © 2017, 2018 Ricardo Wurmus -;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018, 2021 Tobias Geerinckx-Rice ;;; Copyright © 2017 Adonay Felipe Nogueira ;;; Copyright © 2018 Jovany Leandro G.C ;;; Copyright © 2018 Tim Gesthuizen @@ -324,14 +324,14 @@ GNU ccRTP stack and serves as library for other RTP stacks (define-public osip (package (name "osip") - (version "5.2.0") + (version "5.2.1") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/osip/libosip2-" version ".tar.gz")) (patches (search-patches "osip-CVE-2017-7853.patch")) (sha256 (base32 - "0xdk3cszkzb8nb757gl47slrr13mf6xz43ab4k343fv8llp8pd2g")))) + "1wibs2zs035ay7qvl5ai8drv6f0xw7iscb0frmpgax3pisy88dzf")))) (build-system gnu-build-system) (synopsis "Library implementing SIP (RFC-3261)") -- cgit 1.4.1 From 6fee3239b36503e9a20ed07619e9b79012291417 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 2 Jun 2021 01:37:45 +0200 Subject: gnu: memtester: Update to 4.5.1. * gnu/packages/hardware.scm (memtester): Update to 4.5.1. --- gnu/packages/hardware.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/hardware.scm b/gnu/packages/hardware.scm index d5941b6c0f..ecbcca79b1 100644 --- a/gnu/packages/hardware.scm +++ b/gnu/packages/hardware.scm @@ -240,7 +240,7 @@ Memtest86+ cannot currently be used on computers booted with UEFI.") (define-public memtester (package (name "memtester") - (version "4.5.0") + (version "4.5.1") (source (origin (method url-fetch) @@ -248,7 +248,7 @@ Memtest86+ cannot currently be used on computers booted with UEFI.") (uri (string-append "http://pyropus.ca/software/memtester/old-versions/" "memtester-" version ".tar.gz")) (sha256 - (base32 "0dxfwayns3hjjplkxkpkm1409lmjlpi4chcrahcvdbnl0q6jpmcf")))) + (base32 "0issrasdihav8jgsqb49cfyj0v564z8k9lyg2jrq9h3n4lwc4pqw")))) (build-system gnu-build-system) (arguments `(#:make-flags -- cgit 1.4.1 From f01215635a7ee69b4008904f00b0554bd127ce7c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 10:52:24 +0200 Subject: gnu: r-with-tests: Update to 4.1.0. * gnu/packages/statistics.scm (r-with-tests): Update to 4.1.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 90103ce91a..f267ef7588 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -185,7 +185,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (define r-with-tests (package (name "r-with-tests") - (version "4.0.4") + (version "4.1.0") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -193,7 +193,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") version ".tar.gz")) (sha256 (base32 - "0bl098xcv8v316kqnf43v6gb4kcsv31ydqfm1f7qr824jzb2fgsj")))) + "109732arm6dq6d6v3fl1nyx63lcvv9569j8g6r3s2b18sxcqkrp8")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) -- cgit 1.4.1 From 18e0081045703f599aaf1789a206578a2854bdf2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 12:12:00 +0200 Subject: gnu: Add libmaus2. * gnu/packages/bioinformatics.scm (libmaus2): New variable. --- gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 66e790367d..ece59e982e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10969,6 +10969,46 @@ contigs alone.") (license (list license:gpl2+ ; bundled ogdf license:gpl3+)))) +(define-public libmaus2 + (package + (name "libmaus2") + (version "2.0.786") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/german.tischler/libmaus2") + (commit (string-append version "-release-20210531143054")))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1rxakmwjcx2yq5sjh3v849f7dfw4xzc2fyzf6s28s3p95z84w564")))) + (build-system gnu-build-system) + ;; The test suite attempts to execute ../test-driver, which does not exist. + (arguments '(#:tests? #false)) + (propagated-inputs + `(("zlib" ,zlib))) + (native-inputs + `(("gcc" ,gcc-10) ;Code has C++17 requirements + ("pkg-config" ,pkg-config))) + (home-page "https://gitlab.com/german.tischler/libmaus2") + (synopsis "Collection of data structures and algorithms useful for bioinformatics") + (description "libmaus2 is a collection of data structures and +algorithms. It contains: + +@itemize +@item I/O classes (single byte and UTF-8); +@item @code{bitio} classes (input, output and various forms of bit level + manipulation); +@item text indexing classes (suffix and LCP array, fulltext and minute (FM), + etc.); +@item BAM sequence alignment files input/output (simple and collating); +and many lower level support classes. +@end itemize\n") + ;; The code is explicitly available under the terms of either GPLv2 or + ;; GPLv3 according to the AUTHORS file, though most files have a GPLv3+ + ;; license header. + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-circus (package (name "r-circus") -- cgit 1.4.1 From 011d586c2c6c748fa203456d307d72447ed6b54e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 13:45:54 +0200 Subject: gnu: Add biobambam2. * gnu/packages/bioinformatics.scm (biobambam2): New variable. --- gnu/packages/bioinformatics.scm | 50 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ece59e982e..94d15cc4c0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11009,6 +11009,56 @@ and many lower level support classes. ;; license header. (license (list license:gpl2+ license:gpl3+)))) +(define-public biobambam2 + (package + (name "biobambam2") + (version "2.0.182") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/german.tischler/biobambam2") + (commit (string-append version "-release-20210412001032")))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0b7w7a2a7hpkgrdn0n7hy4pilzrj82zqrh7q4bg1l0cd6bqr60m5")))) + (build-system gnu-build-system) + (arguments + ;; The test suite attempts to execute ../test-driver, which does not exist. + `(#:tests? #false + #:configure-flags + (list (string-append "--with-libmaus2=" + (assoc-ref %build-inputs "libmaus2"))))) + (inputs + `(("libmaus2" ,libmaus2) + ("xerces-c" ,xerces-c))) + (native-inputs + `(("gcc" ,gcc-10) ;Code has C++17 requirements + ("pkg-config" ,pkg-config))) + (home-page "https://gitlab.com/german.tischler/biobambam2") + (synopsis "Tools for processing BAM files") + (description "This package contains some tools for processing BAM files +including: + +@itemize +@item bamsormadup: parallel sorting and duplicate marking +@item bamcollate2: reads BAM and writes BAM reordered such that alignment or + collated by query name +@item bammarkduplicates: reads BAM and writes BAM with duplicate alignments + marked using the BAM flags field +@item bammaskflags: reads BAM and writes BAM while masking (removing) bits + from the flags column +@item bamrecompress: reads BAM and writes BAM with a defined compression + setting. This tool is capable of multi-threading. +@item bamsort: reads BAM and writes BAM resorted by coordinates or query name +@item bamtofastq: reads BAM and writes FastQ; output can be collated or + uncollated by query name. +@end itemize +") + ;; The COPYING file states that the code is distributed under version 3 of + ;; the GPL, but the license headers include the "or later" clause. + (license license:gpl3+))) + (define-public r-circus (package (name "r-circus") -- cgit 1.4.1 From 1bd85824c7a04e8c77bb2ba31c310975664c7a53 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 2 Jun 2021 13:40:01 +0200 Subject: gnu: ispell: Update to 3.4.03. * gnu/packages/aspell.scm (ispell): Update to 3.4.03. --- gnu/packages/aspell.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/aspell.scm b/gnu/packages/aspell.scm index e19c369517..4821e08432 100644 --- a/gnu/packages/aspell.scm +++ b/gnu/packages/aspell.scm @@ -489,14 +489,14 @@ under permissive licensing terms. See the 'Copyright' file.")))) (define-public ispell (package (name "ispell") - (version "3.4.02") + (version "3.4.03") (source (origin (method url-fetch) (uri (string-append "https://www.cs.hmc.edu/~geoff/tars/ispell-" version ".tar.gz")) (sha256 - (base32 "0b6rqzqjdhwf323sf1dv8qzx5pxa5asz618922r59zjp65660yb6")))) + (base32 "040wvf81ihq2sdacvi4kk1n6f19fjdn44hb1ydz0l5lj1sz6mrxs")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f -- cgit 1.4.1 From 10343994dc562f68771207bf4da313a7d531d2b3 Mon Sep 17 00:00:00 2001 From: Ron Nazarov via Guix-patches via Date: Wed, 2 Jun 2021 13:32:45 +0100 Subject: gnu: Add udftools. * gnu/packages/file-systems.scm (udftools): New variable. Signed-off-by: Tobias Geerinckx-Rice --- gnu/packages/file-systems.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm index c64c0df727..4d6dc89fd9 100644 --- a/gnu/packages/file-systems.scm +++ b/gnu/packages/file-systems.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2020 Morgan Smith ;;; Copyright © 2021 raid5atemyhomework ;;; Copyright © 2021 Stefan Reichör +;;; Copyright © 2021 Noisytoot ;;; ;;; This file is part of GNU Guix. ;;; @@ -1526,3 +1527,35 @@ your put them. TMSU maintains its own database and you simply gain an additional view, which you can mount where you like, based upon the tags you set up.") (license license:gpl3+))) + +(define-public udftools + (package + (name "udftools") + (version "2.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pali/udftools") + (commit version))) + (sha256 + (base32 + "1nl2s61znyzaap23zhbdg3znj6l6akr313fchn5wwvjzj8k70is9")) + (file-name (git-file-name name version)))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags + (list (string-append "--docdir=" (assoc-ref %outputs "out") + "/share/doc/" ,name "-" ,version)))) + (native-inputs + `(("automake" ,automake) + ("autoconf" ,autoconf) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (home-page "https://github.com/pali/udftools") + (synopsis "Tools to manage UDF file systems and DVD/CD-R(W) drives") + (description "@code{udftools} is a set of programs for reading +and modifying @acronym{UDF, Universal Disk Format} file systems. +@acronym{UDF, Universal Disk Format} is a file system mostly used for DVDs +and other optical media. It supports read-only media (DVD/CD-R) +and rewritable media that wears out (DVD/CD-RW).") + (license license:gpl2+))) -- cgit 1.4.1 From e17b8d5e3f1fc21babd64e99b74f884a7b0bb802 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 2 Jun 2021 14:39:06 +0200 Subject: gnu: python-django: Update to 3.2.4 [fixes CVE-2021-33203, CVE-2021-33571]. * gnu/packages/django.scm (python-django): Update to 3.2.4. --- gnu/packages/django.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index fa67e7412a..e736b7d258 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -47,13 +47,13 @@ (define-public python-django (package (name "python-django") - (version "3.2.2") + (version "3.2.4") (source (origin (method url-fetch) (uri (pypi-uri "Django" version)) (sha256 (base32 - "0gffaabnnpzj0sl3jl7mllvi3gc0jvab6xw2bckvyljwsrd1j78a")))) + "15pjwyvrx4n8gi8n51b14wp54bg4jqapr25p52597zn6ikdxijb6")))) (build-system python-build-system) (arguments '(#:phases -- cgit 1.4.1 From 882ec50ca184b74519e8f2315a3922587da36ba6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 2 Jun 2021 14:41:29 +0200 Subject: gnu: python-django@2.2: Update to 2.2.24 [fixes CVE-2021-33203, CVE-2021-33571]. * gnu/packages/django.scm (python-django-2.2): Update to 2.2.24. --- gnu/packages/django.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index e736b7d258..f157db9ba2 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -142,13 +142,13 @@ to the @dfn{don't repeat yourself} (DRY) principle.") (define-public python-django-2.2 (package (inherit python-django) - (version "2.2.22") + (version "2.2.24") (source (origin (method url-fetch) (uri (pypi-uri "Django" version)) (sha256 (base32 - "0q30zjcmnvwp1v1syn739wapahs2dx784n0yjyypq0cr3kdi88nv")))) + "1dvx3x85lggm91x7mpvaf9nmpxyz7r97pbpnmr2k1qfy0c7gyf9k")))) (native-inputs `(;; XXX: In 2.2 and 3.0, selenium is required for the test suite. ("python-selenium" ,python-selenium) -- cgit 1.4.1 From 8cc146b24a8c85c302c6b5498bd4549544af2c35 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:22:57 +0200 Subject: gnu: r-bisquerna: Update to 1.0.5. * gnu/packages/bioconductor.scm (r-bisquerna): Update to 1.0.5. [native-inputs]: Add r-knitr. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 20e44ca94b..7a584e4211 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1618,18 +1618,20 @@ absolute GSEA.") (define-public r-bisquerna (package (name "r-bisquerna") - (version "1.0.4") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "BisqueRNA" version)) (sha256 (base32 - "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2")))) + "0p3p5lp69gri7vs6qfpm7br4ksbs4l7clm4nj8ki99wpqiqni23n")))) (properties `((upstream-name . "BisqueRNA"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-limsolve" ,r-limsolve))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://www.biorxiv.org/content/10.1101/669911v1") (synopsis "Decomposition of bulk expression with single-cell sequencing") (description "This package provides tools to accurately estimate cell type -- cgit 1.4.1 From 375fea067daadee4470aab816a54978c032015cc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:01 +0200 Subject: gnu: r-extremes: Update to 2.1-1. * gnu/packages/cran.scm (r-extremes): Update to 2.1-1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 711792958c..439c3103f6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3811,14 +3811,14 @@ which should be seen for details.") (define-public r-extremes (package (name "r-extremes") - (version "2.1") + (version "2.1-1") (source (origin (method url-fetch) (uri (cran-uri "extRemes" version)) (sha256 (base32 - "1b69r3mzl6hp3g3rqxyc77m8r40jyq7c2d87q85af7xqkn6hnxid")))) + "00ps7yggp89sx1j0w6c8dk0la3k95rwjv1iz7rdfqy7i46xjf6as")))) (properties `((upstream-name . "extRemes"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 05ee34f0de25ba7e80eb5800ae5b910aeb544e42 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:01 +0200 Subject: gnu: r-inline: Update to 0.3.19. * gnu/packages/cran.scm (r-inline): Update to 0.3.19. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 439c3103f6..ad40e7f741 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3880,13 +3880,13 @@ by Li, Brown, Huang, and Bickel") (define-public r-inline (package (name "r-inline") - (version "0.3.18") + (version "0.3.19") (source (origin (method url-fetch) (uri (cran-uri "inline" version)) (sha256 (base32 - "0fpcfwbhfg1lhkqc0gdqv2sq64r3ljld7piy34vv0nimq30xi2fc")))) + "1mcr9hgq6kkq03n7pkcccxa7vg8jma0q7lfxc5vvkc6snydk1s8f")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/inline") (synopsis "Functions to inline C, C++, Fortran function calls from R") -- cgit 1.4.1 From 52eaf9d864b4735828e1c4149e1dc8d454e8f55e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:01 +0200 Subject: gnu: r-fitdistrplus: Update to 1.1-5. * gnu/packages/cran.scm (r-fitdistrplus): Update to 1.1-5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ad40e7f741..5c8757a19c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4070,14 +4070,14 @@ functions from LINPACK.") (define-public r-fitdistrplus (package (name "r-fitdistrplus") - (version "1.1-3") + (version "1.1-5") (source (origin (method url-fetch) (uri (cran-uri "fitdistrplus" version)) (sha256 (base32 - "1pjnqx0j26dai2fa4ip56wspmfsrcm9dpmxkg15y9623w5b58vbp")))) + "1p9rvvh05zqb9vzhcyzdh7i8lbmb53nj8nyn0gqcmp7wafg9cd1f")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) -- cgit 1.4.1 From c4ca93cec9c6deb5d9e82190f33c6a4667f08154 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:01 +0200 Subject: gnu: r-tinytex: Update to 0.32. * gnu/packages/cran.scm (r-tinytex): Update to 0.32. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5c8757a19c..abf4c52a10 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5841,14 +5841,14 @@ packages that work with genomic data.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.31") + (version "0.32") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "04a3ncaxix30n9m73slpsn1idxv7j1f7fy3nhxpvkk514x9rgg0p")))) + "17y20kb5xgmz77n4rrkqmcm0cnjwfi4mn84h6zabij76b8cjiykh")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) -- cgit 1.4.1 From ec1666550de8735ffb5f10dda4ffcfc2de605f0c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:01 +0200 Subject: gnu: r-signal: Update to 0.7-7. * gnu/packages/cran.scm (r-signal): Update to 0.7-7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index abf4c52a10..72041ed8fa 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6869,14 +6869,14 @@ and within plot factors interact.") (define-public r-signal (package (name "r-signal") - (version "0.7-6") + (version "0.7-7") (source (origin (method url-fetch) (uri (cran-uri "signal" version)) (sha256 (base32 - "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b")))) + "0qaf39vfmhn3d0bdjqd805ayfkaj48dkmf5dqd47bpk7dp21b837")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) (native-inputs `(("gfortran" ,gfortran))) -- cgit 1.4.1 From e6068fe40128bbc877dc5cd17a245a39b30bceff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:02 +0200 Subject: gnu: r-zip: Update to 2.2.0. * gnu/packages/cran.scm (r-zip): Update to 2.2.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 72041ed8fa..6b457f444d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7256,14 +7256,14 @@ misclassification probabilities of different models.") (define-public r-zip (package (name "r-zip") - (version "2.1.1") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "zip" version)) (sha256 (base32 - "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i")))) + "1n5ryjdj3i16b4mdp29wapgaklz3yzas5k8ffx7q6fa0jry9i5cz")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/zip") (synopsis "Cross-platform Zip compression") -- cgit 1.4.1 From 27bff67ea9883fd8e9a42db061bffdcfed53ea27 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:02 +0200 Subject: gnu: r-fansi: Update to 0.5.0. * gnu/packages/cran.scm (r-fansi): Update to 0.5.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6b457f444d..6a8c8b2f94 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8190,14 +8190,14 @@ steps and provides ggplot2-based elegant data visualization.") (define-public r-fansi (package (name "r-fansi") - (version "0.4.2") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "fansi" version)) (sha256 (base32 - "0i7wmaflkjzdbggqv31wnsj3m9imvc6db429vyjk64xrz1ng1vd2")))) + "0kx5kjhr8dvqz1mq1zkijkgp29jv8b0irm1xplx1d74n2v1zh6wx")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes -- cgit 1.4.1 From 6c5543d1d7e3dff08c5e58de96c31988dd7ed740 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:02 +0200 Subject: gnu: r-rdpack: Update to 2.1.2. * gnu/packages/cran.scm (r-rdpack): Update to 2.1.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6a8c8b2f94..fba5ba1e44 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8372,14 +8372,14 @@ implemented in bibutils.") (define-public r-rdpack (package (name "r-rdpack") - (version "2.1.1") + (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 - "11psw5yiamq0g7jc6fqn2wis565i60qgda4a5d09qi8fyzd6mnfb")))) + "0s51c5fw1ka75b8cxk5bh27h6wcy5169yl93sjlxji2k27n9fj3i")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 8b459409a96894007a4daf212e3a97228b05bf1e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:02 +0200 Subject: gnu: r-insight: Update to 0.14.1. * gnu/packages/cran.scm (r-insight): Update to 0.14.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fba5ba1e44..494af6384e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8624,14 +8624,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.14.0") + (version "0.14.1") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "1zkifkj2qg9vdv26z4qvi81qv9l1cqyrq3ihdpacpax80plkgdln")))) + "0af15kqz4kiyi5p4qi748hvdw462vdwigzyykh1k7vj6gacn2xqf")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From 304d9c5dd357b52bae776e569235e14363b40c95 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:03 +0200 Subject: gnu: r-manipulatewidget: Update to 0.11.0. * gnu/packages/cran.scm (r-manipulatewidget): Update to 0.11.0. [propagated-inputs]: Add r-shinyjs. [native-inputs]: Add r-knitr. --- gnu/packages/cran.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 494af6384e..4305180b9a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9221,13 +9221,13 @@ based on index arrays and simple triplet representations, respectively.") (define-public r-manipulatewidget (package (name "r-manipulatewidget") - (version "0.10.1") + (version "0.11.0") (source (origin (method url-fetch) (uri (cran-uri "manipulateWidget" version)) (sha256 - (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx")))) + (base32 "0iysgl6ab8fvg1xxdx6hr3swqwbkfqzjkk4x5sbvmawbl2a395gj")))) (properties `((upstream-name . "manipulateWidget"))) (build-system r-build-system) @@ -9239,7 +9239,10 @@ based on index arrays and simple triplet representations, respectively.") ("r-knitr" ,r-knitr) ("r-miniui" ,r-miniui) ("r-shiny" ,r-shiny) + ("r-shinyjs" ,r-shinyjs) ("r-webshot" ,r-webshot))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/") (synopsis "Add even more interactivity to interactive charts") (description -- cgit 1.4.1 From 0d813e0275671beb9f1886b97a596599fff1b9c7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:03 +0200 Subject: gnu: r-emmeans: Update to 1.6.1. * gnu/packages/cran.scm (r-emmeans): Update to 1.6.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4305180b9a..6ec36c67d0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10572,14 +10572,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.6.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "07iw3faprf98mncymbjbmfm2yi294yiwdg30xlql5sfx12qbf6r0")))) + "02sh1q6f2ik56w348pfkg4a8jvdn3a31r7d8mzg7zq3sv7lmvqwl")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) -- cgit 1.4.1 From 3a5b90d0ab9459fb223ff6401683cb3353a00e72 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:03 +0200 Subject: gnu: r-bayestestr: Update to 0.10.0. * gnu/packages/cran.scm (r-bayestestr): Update to 0.10.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6ec36c67d0..4acd7e1dfb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10808,14 +10808,14 @@ differentiation.") (define-public r-bayestestr (package (name "r-bayestestr") - (version "0.9.0") + (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 - "0msr24ymnazpaz8s9qs5v3xn1i9984p98lr9x4qq9cxgx34rm9h0")))) + "1qr51mag5wf44h4sygkn5arsirpqdanf039cg6fxmyw83k51fi2v")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 0bc5c20756f228795c6a18546c94d6442adca884 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:03 +0200 Subject: gnu: r-effectsize: Update to 0.4.5. * gnu/packages/cran.scm (r-effectsize): Update to 0.4.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4acd7e1dfb..7f707ccfd0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10892,14 +10892,14 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.4.4-1") + (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "02rwf3lxnzgc8yh0wridsc6lqr9s6v0cqzbk4biwnr494rvs46zb")))) + "0rp0r75p8q467lmrsr1gl9wjpib9jz7ksx5rm6c7q2lfg9b9zrjf")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a9ecb3cf20acd8263165fbdfcbc7c9d4c3906016 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:03 +0200 Subject: gnu: r-sjplot: Update to 2.8.8. * gnu/packages/cran.scm (r-sjplot): Update to 2.8.8. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7f707ccfd0..c0c2f9218c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10919,13 +10919,13 @@ conversion of indices such as Cohen's d, r, odds, etc.") (define-public r-sjplot (package (name "r-sjplot") - (version "2.8.7") + (version "2.8.8") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 - (base32 "1g4qabg654kwdm09ihp4h3mg64a1d7a7gsn6w56rwsidqqaxilq0")))) + (base32 "050aarycgzy1n8ad67pj09s8k7s7xk6dicg0kjg0ivlkyyq0shqz")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From eb991f31681c7774d52d3ac769c5937eb78eba16 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:04 +0200 Subject: gnu: r-mvabund: Update to 4.1.12. * gnu/packages/cran.scm (r-mvabund): Update to 4.1.12. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c0c2f9218c..1c268c492c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11498,14 +11498,14 @@ the interfaces between R and C++.") (define-public r-mvabund (package (name "r-mvabund") - (version "4.1.9") + (version "4.1.12") (source (origin (method url-fetch) (uri (cran-uri "mvabund" version)) (sha256 (base32 - "19kyg0agjk7gxipa5kmklz4cqh97xrdbibmmy1g99r1gp3s9ml30")))) + "107pwv2bwird1a98chcnbld2wqj9prkf4pkncyrrp304zpdkkby1")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) -- cgit 1.4.1 From caeed0e512f3cfca3147232c38a60c3278360f00 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:04 +0200 Subject: gnu: r-weights: Update to 1.0.2. * gnu/packages/cran.scm (r-weights): Update to 1.0.2. [propagated-inputs]: Add r-lme4. --- gnu/packages/cran.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1c268c492c..66ee09f76c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11612,21 +11612,21 @@ al. (2016)).") (define-public r-weights (package (name "r-weights") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "weights" version)) (sha256 (base32 - "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5")))) + "1sq8ls5idspddn8m2c8n2107lgx53kbach8vgjrhqx1mc6xfvrvw")))) (build-system r-build-system) (propagated-inputs `(("r-gdata" ,r-gdata) ("r-hmisc" ,r-hmisc) + ("r-lme4" ,r-lme4) ("r-mice" ,r-mice))) - (home-page - "https://cran.r-project.org/web/packages/weights/") + (home-page "https://cran.r-project.org/web/packages/weights/") (synopsis "Weighting and weighted statistics") (description "This package Provides a variety of functions for producing simple weighted statistics, such as weighted Pearson's correlations, partial -- cgit 1.4.1 From ee285cb4ce5d0ca830a728c70404bb99f6baf455 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:04 +0200 Subject: gnu: r-ks: Update to 1.13.1. * gnu/packages/cran.scm (r-ks): Update to 1.13.1. [propagated-inputs]: Add r-pracma. --- gnu/packages/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 66ee09f76c..8765de104a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11842,13 +11842,13 @@ isosurfaces.") (define-public r-ks (package (name "r-ks") - (version "1.12.0") + (version "1.13.1") (source (origin (method url-fetch) (uri (cran-uri "ks" version)) (sha256 - (base32 "1sff6rlpq64lqyvwgral9zbcan30wpgmfb26hw9y6wzypd9gxbz6")))) + (base32 "0zi7yixz3hvqvb5fxipkxprk5p4irr61csd3k6scsxqyhrb5ffls")))) (build-system r-build-system) (propagated-inputs `(("r-fnn" ,r-fnn) @@ -11859,7 +11859,8 @@ isosurfaces.") ("r-mgcv" ,r-mgcv) ("r-multicool" ,r-multicool) ("r-mvtnorm" ,r-mvtnorm) - ("r-plot3d" ,r-plot3d))) + ("r-plot3d" ,r-plot3d) + ("r-pracma" ,r-pracma))) (home-page "https://www.mvstat.net/tduong/") (synopsis "Kernel smoothing") (description -- cgit 1.4.1 From 0a6526ebfdf67cae972011958039d423be35e56e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:04 +0200 Subject: gnu: r-tidytree: Update to 0.3.4. * gnu/packages/cran.scm (r-tidytree): Update to 0.3.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8765de104a..758dfcfdb6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12309,13 +12309,13 @@ maps.") (define-public r-tidytree (package (name "r-tidytree") - (version "0.3.3") + (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 - (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6")))) + (base32 "0bqsb0zplkqkx2mp8kpanadkds4kwwvdrc07lp0qzwqqzaxq5xa3")))) (build-system r-build-system) (propagated-inputs `(("r-ape" ,r-ape) -- cgit 1.4.1 From 37fc760ef13ea410e361ac2a584a9ac440050d6d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:04 +0200 Subject: gnu: r-spdep: Update to 1.1-8. * gnu/packages/cran.scm (r-spdep): Update to 1.1-8. [source]: Remove generated files, including Rmarkdown files whose outputs conflict with the main Rmarkdown file. --- gnu/packages/cran.scm | 28 ++++++++++++++++++++-------- 1 file changed, 20 insertions(+), 8 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 758dfcfdb6..a20e10b9d9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15905,14 +15905,26 @@ datum transformations.") (define-public r-spdep (package (name "r-spdep") - (version "1.1-7") - (source - (origin - (method url-fetch) - (uri (cran-uri "spdep" version)) - (sha256 - (base32 - "0sg417d95paww625663lgmk6jwhs88djqzc96gbs1hxazlf77qb1")))) + (version "1.1-8") + (source (origin + (method url-fetch) + (uri (cran-uri "spdep" version)) + (sha256 + (base32 + "1k82vx58kpn0fwgcpxq2jc3qfffl8wzbgr4cdkxihrfk28kkqh7l")) + (snippet + '(for-each delete-file '("inst/doc/nb_igraph.html" + "inst/doc/nb_igraph.R" + "inst/doc/nb_igraph.Rmd" + "inst/doc/sids.html" + "inst/doc/sids.R" + "inst/doc/nb.html" + "inst/doc/nb.R" + "inst/doc/CO69.html" + "inst/doc/CO69.R" + "inst/doc/nb_sf.html" + "inst/doc/nb_sf.R" + "inst/doc/nb_sf.Rmd"))))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) -- cgit 1.4.1 From 509eea0f5d2e94f1b7b4910769f4bad0f4481c6a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:05 +0200 Subject: gnu: r-dalex: Update to 2.2.1. * gnu/packages/cran.scm (r-dalex): Update to 2.2.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a20e10b9d9..6fe7ead054 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18133,14 +18133,14 @@ been used in the call to @code{aov}.") (define-public r-dalex (package (name "r-dalex") - (version "2.2.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 - "1qnjbhilv4jfmwqxfi9xc5ysrh8gr84a2a5imjfci7d1n3zcnryn")))) + "184mzby1giismhx4brvrdfl5n5kialyvv8ik18blhchvpy145cwf")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 81bb987e7eaa2ce645051a3b74678d598508b069 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:05 +0200 Subject: gnu: r-plot3d: Update to 1.4. * gnu/packages/cran.scm (r-plot3d): Update to 1.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6fe7ead054..e08c80cd9f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18189,14 +18189,14 @@ annotated biological functions.") (define-public r-plot3d (package (name "r-plot3d") - (version "1.3") + (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "plot3D" version)) (sha256 (base32 - "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r")))) + "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh")))) (properties `((upstream-name . "plot3D"))) (build-system r-build-system) (propagated-inputs `(("r-misc3d" ,r-misc3d))) -- cgit 1.4.1 From 8998ed1d8eaa7cdb4e77a1469aedc7b5c88c2c47 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:05 +0200 Subject: gnu: r-leiden: Update to 0.3.8. * gnu/packages/cran.scm (r-leiden): Update to 0.3.8. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e08c80cd9f..a0cb3333ff 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18527,14 +18527,14 @@ computed using the L1 (Manhattan, taxicab) metric.") (define-public r-leiden (package (name "r-leiden") - (version "0.3.7") + (version "0.3.8") (source (origin (method url-fetch) (uri (cran-uri "leiden" version)) (sha256 (base32 - "14iqn5iqcya6bqbjvjivpd7q9gwc323sj29y7ssrbhb3sz9982bp")))) + "0sv0j4sgpz8z65vhbpmaglg878jhq52srzf5rpw4vbsbys2807w1")))) (properties `((upstream-name . "leiden"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 47cdb9c9a8781534a44329adbcb38c6979de5cec Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:05 +0200 Subject: gnu: r-parameters: Update to 0.14.0. * gnu/packages/cran.scm (r-parameters): Update to 0.14.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a0cb3333ff..24d862ba06 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18915,14 +18915,14 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.13.0") + (version "0.14.0") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "17dlwx9hrl6z2il14nxji0snwsf4sfbp3mv33jbpcw13sani1q81")))) + "03x2h8izbpz9cq25i0a6dh99m26a9isgpv4kxsfkx97qzlh9cd67")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 184b3c500c671be06489bd671bf6e19f7c4d6bd8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:05 +0200 Subject: gnu: r-gdina: Update to 2.8.7. * gnu/packages/cran.scm (r-gdina): Update to 2.8.7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 24d862ba06..53f960ad10 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21029,14 +21029,14 @@ allowed.") (define-public r-gdina (package (name "r-gdina") - (version "2.8.0") + (version "2.8.7") (source (origin (method url-fetch) (uri (cran-uri "GDINA" version)) (sha256 (base32 - "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7")))) + "08cdjp4mqn81j3wa770v7n8zkslys9jqqb3d3c09dkfmgdk6hga4")))) (properties `((upstream-name . "GDINA"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 83fa31438df01b389e0aa1d807b6e26ea0645bb4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:05 +0200 Subject: gnu: r-actuar: Update to 3.1-4. * gnu/packages/cran.scm (r-actuar): Update to 3.1-4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 53f960ad10..34543cff44 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21492,14 +21492,14 @@ API; see the package vignette for details.") (define-public r-actuar (package (name "r-actuar") - (version "3.1-2") + (version "3.1-4") (source (origin (method url-fetch) (uri (cran-uri "actuar" version)) (sha256 (base32 - "0gaqm8bkjly2b1jkr1nqnxlp5vqvfpj0a4jd70jv4f9ndlif676y")))) + "0m9b4787a866cddf1skjz6634237dvg1i5qyqss4sgvcrbmx3hw0")))) (properties `((upstream-name . "actuar"))) (build-system r-build-system) (propagated-inputs `(("r-expint" ,r-expint))) -- cgit 1.4.1 From b3aad04bed2f2e3829943f2b4c7dfa1c1ab394bb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:06 +0200 Subject: gnu: r-biclust: Update to 2.0.3. * gnu/packages/cran.scm (r-biclust): Update to 2.0.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 34543cff44..ad88f41e5d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21826,14 +21826,14 @@ cluster stability.") (define-public r-biclust (package (name "r-biclust") - (version "2.0.2") + (version "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "biclust" version)) (sha256 (base32 - "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b")))) + "0lgyc2f04dhr65cwga78pradxsdzgjrpp8vphchqn60ab1z95dlp")))) (properties `((upstream-name . "biclust"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 317267c460dc7d3fa654770bd5ca471bce6c5fe3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:06 +0200 Subject: gnu: r-archivist: Update to 2.3.6. * gnu/packages/cran.scm (r-archivist): Update to 2.3.6. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ad88f41e5d..5bed543762 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22388,14 +22388,14 @@ both exclusive and shared locking.") (define-public r-archivist (package (name "r-archivist") - (version "2.3.5") + (version "2.3.6") (source (origin (method url-fetch) (uri (cran-uri "archivist" version)) (sha256 (base32 - "0sk16bcafgswrvwh39ysbgm6jvsg20yil4pdsg3wsp81nnsrb43k")))) + "0q1qysack30xzxdbvvi56rk7r85hsj4ghls9r70ki7bl3rqwr4c9")))) (properties `((upstream-name . "archivist"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 318808dcdd968de6b6ff5308f19fb28c9a355486 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:06 +0200 Subject: gnu: r-forecast: Update to 8.15. * gnu/packages/cran.scm (r-forecast): Update to 8.15. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5bed543762..8304b6d41f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22560,14 +22560,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.") (define-public r-forecast (package (name "r-forecast") - (version "8.14") + (version "8.15") (source (origin (method url-fetch) (uri (cran-uri "forecast" version)) (sha256 (base32 - "12bfw029xb1dndcjyn2r7a51i7hnkkbdilp69k97sz2v8b7v1y3s")))) + "0x4ij55sb45qnwba3bybs50vsvv82q3j8p47xmbv959h13nsnfn7")))) (properties `((upstream-name . "forecast"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 17bd981986a37a4d310f0e23539de9da77e2dda6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:06 +0200 Subject: gnu: r-rsconnect: Update to 0.8.18. * gnu/packages/cran.scm (r-rsconnect): Update to 0.8.18. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8304b6d41f..4d28e10f0f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23542,14 +23542,14 @@ and reproducible way.") (define-public r-rsconnect (package (name "r-rsconnect") - (version "0.8.17") + (version "0.8.18") (source (origin (method url-fetch) (uri (cran-uri "rsconnect" version)) (sha256 (base32 - "0cd2bpc22jam1qxn6yg7yr7xdhsm0jgnm5bm2f3vg5b3c96plxk4")))) + "01bj16iggj5fggfa7n312458p8xg30zx2vzfkd8jqcchnbrphfvl")))) (properties `((upstream-name . "rsconnect"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From f6ae19fedcb9a35bfad2c758be28512f63efb0e1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:06 +0200 Subject: gnu: r-clusterr: Update to 1.2.5. * gnu/packages/cran.scm (r-clusterr): Update to 1.2.5. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4d28e10f0f..04bade5588 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25799,14 +25799,14 @@ model.") (define-public r-clusterr (package (name "r-clusterr") - (version "1.2.4") + (version "1.2.5") (source (origin (method url-fetch) (uri (cran-uri "ClusterR" version)) (sha256 (base32 - "01vgr1mpm7l1lyhril5hm1l72aicqc4iwb0b15ypijb6hwkv7g47")))) + "1fsb9pzs1paw1cbyr5a56lfh8h2d50232p6isk0xg5sl110ql7kx")))) (properties `((upstream-name . "ClusterR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From d9d8a1cdc08b3baa8ff3802f3d205794a08d2b9b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:06 +0200 Subject: gnu: r-parsnip: Update to 0.1.6. * gnu/packages/cran.scm (r-parsnip): Update to 0.1.6. [propagated-inputs]: Add r-lifecycle. --- gnu/packages/cran.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 04bade5588..4388901e75 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26875,14 +26875,14 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.") (define-public r-parsnip (package (name "r-parsnip") - (version "0.1.5") + (version "0.1.6") (source (origin (method url-fetch) (uri (cran-uri "parsnip" version)) (sha256 (base32 - "0c12lyfxqsdprqlcmgy421py38z28h88d68pxb1c4fw14v1c2d06")))) + "0qhdh2xdswqy94f4gkdxi1iqm0k794p9y8sdh6mgbd1a86c8ngfs")))) (properties `((upstream-name . "parsnip"))) (build-system r-build-system) (propagated-inputs @@ -26890,6 +26890,7 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.") ("r-generics" ,r-generics) ("r-globals" ,r-globals) ("r-glue" ,r-glue) + ("r-lifecycle" ,r-lifecycle) ("r-magrittr" ,r-magrittr) ("r-prettyunits" ,r-prettyunits) ("r-purrr" ,r-purrr) -- cgit 1.4.1 From 9b9bb2b73269c5e3b7326c7a1a00ec4c195452c3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:07 +0200 Subject: gnu: r-seurat: Update to 4.0.2. * gnu/packages/cran.scm (r-seurat): Update to 4.0.2. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4388901e75..c662ec5b2b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27335,13 +27335,13 @@ other R users.") (define-public r-seurat (package (name "r-seurat") - (version "4.0.1") + (version "4.0.2") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "17cmp9mimvykb8ny796dn1zwmvg0pwwjw1zcixyamc5q1lwnxi3p")))) + "1b1wyj4dxjn0hfg09l8z282grdgwgah0czs7pn2ian455x0dphng")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 0af6a92695f5c1d31bbc66578c0ecf0b1e9bac32 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:07 +0200 Subject: gnu: r-calculus: Update to 0.3.1. * gnu/packages/cran.scm (r-calculus): Update to 0.3.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c662ec5b2b..bedc0114aa 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27463,14 +27463,14 @@ rate speciation and extinction.") (define-public r-calculus (package (name "r-calculus") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "calculus" version)) (sha256 (base32 - "1wa5ap89cfcp0ancj9ivx5s2y0wqr2vmp9y115g7f6g772jwhscj")))) + "0m9cjc3bqv88vrrj51kd7c7xnczka5w9q0ln4l4nk514gvlr79bn")))) (properties `((upstream-name . "calculus"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 72e8eabc3a7dff5b1bd9251ad936bdc42d2b1953 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:07 +0200 Subject: gnu: r-textshape: Update to 1.7.3. * gnu/packages/cran.scm (r-textshape): Update to 1.7.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index bedc0114aa..ab21707d92 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -28377,14 +28377,14 @@ in same length matches).") (define-public r-textshape (package (name "r-textshape") - (version "1.7.1") + (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "textshape" version)) (sha256 (base32 - "02111kj3kka84mpx7s19bjna9cas8diw5fxz51v5ggz0ldswa5pa")))) + "0k9injxykgj2qprc7dygd7gafvcbh3r9x84qzaa1al21pk0dz7ds")))) (properties `((upstream-name . "textshape"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From fdc6bfa2aa10483830bb114e6b611c89dd16f69c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:07 +0200 Subject: gnu: r-matrix: Update to 1.3-4. * gnu/packages/statistics.scm (r-matrix): Update to 1.3-4. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index f267ef7588..3b6929ddfa 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -586,14 +586,14 @@ also flexible enough to handle most nonstandard requirements.") (define-public r-matrix (package (name "r-matrix") - (version "1.3-3") + (version "1.3-4") (source (origin (method url-fetch) (uri (cran-uri "Matrix" version)) (sha256 (base32 - "0fvayd6b8w6yzhil85xw7lib68dvxyzpcznwvwczlyxf8ggchzpp")))) + "0fbcbysp3vaivmp1yasmp8mdsldhr826vfs4vyxrjpjl8jfifhmb")))) (properties `((upstream-name . "Matrix"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 61d7869e8988d78a29b9856d9ebdf00467d04acb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:07 +0200 Subject: gnu: r-mgcv: Update to 1.8-36. * gnu/packages/statistics.scm (r-mgcv): Update to 1.8-36. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 3b6929ddfa..d35ef70ce7 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -630,13 +630,13 @@ nonlinear mixed-effects models.") (define-public r-mgcv (package (name "r-mgcv") - (version "1.8-35") + (version "1.8-36") (source (origin (method url-fetch) (uri (cran-uri "mgcv" version)) (sha256 - (base32 "1dyphss1bw5rd8apgxsb364rcrkdbc9pcbsa0jy95mg9g5434wvk")))) + (base32 "002n4572sxslz9zfqvs5ys59m8q8wkcc5ks2m0yqs4p7l88xzca2")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) -- cgit 1.4.1 From 80f2d363b8ea163c1b97f61b46ec8d607e1ba49e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:07 +0200 Subject: gnu: r-formatr: Update to 1.11. * gnu/packages/statistics.scm (r-formatr): Update to 1.11. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index d35ef70ce7..4ebe4758a3 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1330,13 +1330,13 @@ adapted for other output formats, such as HTML or LaTeX.") (define-public r-formatr (package (name "r-formatr") - (version "1.9") + (version "1.11") (source (origin (method url-fetch) (uri (cran-uri "formatR" version)) (sha256 (base32 - "0vbzvb91y5cxjbnwpww0r40r6m1l9w1qa979sv7ghhalzr7bib3i")))) + "0353aj975mj0yjc91z76bbfy86y7d5cvlqqyfr93cdng14nnd0dx")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From a8313bfbae71fee44719dd7f40b9bd0fd721a900 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:07 +0200 Subject: gnu: r-rversions: Update to 2.1.1. * gnu/packages/statistics.scm (r-rversions): Update to 2.1.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 4ebe4758a3..45678a88f3 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2098,13 +2098,13 @@ jackknifed confidence intervals are available for most estimates.") (define-public r-rversions (package (name "r-rversions") - (version "2.0.2") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "rversions" version)) (sha256 (base32 - "0ghpla5r3d6zh5dn6d6ii5p0a952lcdv004m88fk8r9k76vz88rm")))) + "1cbwwbz8lqx2n33xr4q904whvld22s63rpyy1nn93395l7ssrakr")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) -- cgit 1.4.1 From a3268eb59869f8f8d0103eb3cf31958b2aa603c9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:08 +0200 Subject: gnu: r-rcpparmadillo: Update to 0.10.5.0.0. * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.10.5.0.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 45678a88f3..a6a05d83cf 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2643,13 +2643,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.10.4.0.0") + (version "0.10.5.0.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "00nc7wfrra645mp7dl4j451m3pk3a0b3lrhgf8ydnw862avr9s6v")))) + "059qi872f9h40ns65166qsq1i1jq1mvizm29a0xmqlyn7a5y9ca3")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 3319e97c40dc4547941abb019f4828a89e8323c7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:08 +0200 Subject: gnu: r-e1071: Update to 1.7-7. * gnu/packages/statistics.scm (r-e1071): Update to 1.7-7. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index a6a05d83cf..7934358ec1 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3409,14 +3409,14 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.") (define-public r-e1071 (package (name "r-e1071") - (version "1.7-6") + (version "1.7-7") (source (origin (method url-fetch) (uri (cran-uri "e1071" version)) (sha256 (base32 - "0blfnv3m5k5xm9bfx1v5awvagqlhqaqpabrvzplf4244c3j259qa")))) + "1phqrx787fkiamgx56sjjmzl9nh5wgpffah0mlwd7ijrf446qz3r")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class) -- cgit 1.4.1 From 350489b33191fb0b6c1ae56dd4051db7eddfdbad Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:08 +0200 Subject: gnu: r-matrixstats: Update to 0.59.0. * gnu/packages/statistics.scm (r-matrixstats): Update to 0.59.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7934358ec1..747d795cc8 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3657,13 +3657,13 @@ t-probabilities, quantiles, random deviates and densities.") (define-public r-matrixstats (package (name "r-matrixstats") - (version "0.58.0") + (version "0.59.0") (source (origin (method url-fetch) (uri (cran-uri "matrixStats" version)) (sha256 (base32 - "0jab3xk56vqqzgz8jbsvxvsvr83sj0gb3cic0906wjyjijwv8rw3")))) + "178baqrd7rbin3l10zyrkps5sda0q9mdqil9r12b3n99mlk8fhh7")))) (properties `((upstream-name . "matrixStats"))) (build-system r-build-system) (arguments -- cgit 1.4.1 From c6be262b78b0602b92352936e6b0d4a231072534 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:08 +0200 Subject: gnu: r-fastcluster: Update to 1.2.3. * gnu/packages/statistics.scm (r-fastcluster): Update to 1.2.3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 747d795cc8..2f891c1adb 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4140,14 +4140,14 @@ hierarchical clustering dendrograms.") (define-public r-fastcluster (package (name "r-fastcluster") - (version "1.1.25") + (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "fastcluster" version)) (sha256 (base32 - "01a2xnhhvv1swd4g8p4lzyn7ww7kg49jlnzc7kfz60jqjzpisrpk")))) + "009amz7i5yndqw2008fgd3p11n4fsb291k2ypg3pip6dw4lr28hz")))) (build-system r-build-system) (home-page "http://danifold.net/fastcluster.html") (synopsis "Fast hierarchical clustering routines") -- cgit 1.4.1 From 08de5b0689c3ffcbf3e69ddc4dd63c023a354b81 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:08 +0200 Subject: gnu: r-beeswarm: Update to 0.4.0. * gnu/packages/statistics.scm (r-beeswarm): Update to 0.4.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 2f891c1adb..bf22c278da 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4377,13 +4377,13 @@ within a category based on their density using quasirandom noise.") (define-public r-beeswarm (package (name "r-beeswarm") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "beeswarm" version)) (sha256 (base32 - "1jsggypyww77hkcic03kdb3fp8h938qs142xi0lapzh62bkn2pjj")))) + "016mqcbdksialkmap56rprzna9b6cd6896ml9gl2n2h8yjdk7x2i")))) (build-system r-build-system) (home-page "https://www.cbs.dtu.dk/~eklund/beeswarm/") (synopsis "Implementation of bee swarm plots") -- cgit 1.4.1 From 02efdd3abfacf57f99a6f86b789a3cdb63804dab Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:08 +0200 Subject: gnu: r-deoptimr: Update to 1.0-9. * gnu/packages/statistics.scm (r-deoptimr): Update to 1.0-9. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index bf22c278da..e4491a700a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4794,14 +4794,14 @@ data for species delimitation, nearest neighbor based noise detection.") (define-public r-deoptimr (package (name "r-deoptimr") - (version "1.0-8") + (version "1.0-9") (source (origin (method url-fetch) (uri (cran-uri "DEoptimR" version)) (sha256 (base32 - "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4")))) + "04k5gi0a5hbm6znzvjaipbmkacp694krkqs38dkbxx1gymsallb1")))) (properties `((upstream-name . "DEoptimR"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/DEoptimR") -- cgit 1.4.1 From b851f38a2f2a7bd10b8e25736c4e0e59d0bb3c45 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 17:23:08 +0200 Subject: gnu: r-robustbase: Update to 0.93-8. * gnu/packages/statistics.scm (r-robustbase): Update to 0.93-8. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index e4491a700a..a6c9c9d558 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4817,14 +4817,14 @@ can be efficiently implemented directly in the R language.") (define-public r-robustbase (package (name "r-robustbase") - (version "0.93-7") + (version "0.93-8") (source (origin (method url-fetch) (uri (cran-uri "robustbase" version)) (sha256 (base32 - "0mh9d114p3jdrjf8yn4dx5ff41niz5wn411y0ckjcpnazp8d44c9")))) + "16fmnk3p32mi70rkx89l1v4pry3gnrpy9jicnlfnk6lg1pwz5j8w")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit 1.4.1 From 5be7870a8d4a0b27628e9eb6add61ddc5c05f186 Mon Sep 17 00:00:00 2001 From: Diego Nicola Barbato Date: Thu, 25 Feb 2021 10:00:13 +0100 Subject: gnu: pioneer: Build with model files. Fixes . * gnu/packages/games.scm (pioneer)[arguments]: Add make-flags for building with model files. Signed-off-by: Nicolas Goaziou --- gnu/packages/games.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 6b16d5bc8a..2eaea5868e 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -7293,7 +7293,8 @@ elements to achieve a simple goal in the most complex way possible.") `(#:tests? #f ;tests are broken #:configure-flags (list "-DUSE_SYSTEM_LIBLUA:BOOL=YES" (string-append "-DPIONEER_DATA_DIR=" - %output "/share/games/pioneer")))) + %output "/share/games/pioneer")) + #:make-flags (list "all" "build-data"))) (home-page "https://pioneerspacesim.net") (synopsis "Game of lonely space adventure") (description -- cgit 1.4.1 From f32e6e1e2cab0dea2947c1c1475e870f631e1bf6 Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Wed, 26 May 2021 16:16:04 +0200 Subject: gnu: Add emacs-org-pandoc-import. * gnu/packages/emacs-xyz.scm (emacs-org-pandoc-import): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a1083f999b..81aec3097d 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -7147,6 +7147,43 @@ It also prettifies Org plain list bullets by: Features degrade gracefully when viewed from terminal.") (license license:gpl3+))) +(define-public emacs-org-pandoc-import + (package + (name "emacs-org-pandoc-import") + (version "1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tecosaur/org-pandoc-import/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "00z9bpm975mlyqlxbyib3j547br6kvcam04b70qkmq22vh8yf341")))) + (build-system emacs-build-system) + (arguments + `(#:include + (cons* "^filters\\/" "^preprocessors" %default-include) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-exec-paths + (lambda* (#:key inputs #:allow-other-keys) + (let ((pandoc (assoc-ref inputs "pandoc"))) + (substitute* "org-pandoc-import.el" + (("\"pandoc\"") (string-append "\"" pandoc "/bin/pandoc\""))))))))) + (inputs + `(("pandoc" ,pandoc))) + (home-page "https://github.com/tecosaur/org-pandoc-import/") + (synopsis "Read and edit non-Org file types in Org") + (description + "This package uses Pandoc to convert selected file types to Org. It can +convert supported non-Org files to an Org file with Pandoc. + +It can also intercept requests for non-Org files it knows it can convert, +convert the file to a temporary Org file, and open this file instead. On +save, it exports back to the original non-Org file.") + (license license:gpl3+))) + (define-public emacs-org-pomodoro ;; Last release version was from 2016. (let ((commit "aa07c11318f91219336197e62c47bc7a3d090479") -- cgit 1.4.1 From 6d71f6a73cd27d61d3302b9658893428af6314d2 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 23 May 2021 14:22:16 +0200 Subject: gnu: expat: Replace with 2.4.1 [fixes CVE-2013-0340]. * gnu/packages/xml.scm (expat-2.4.1): New variable. (expat)[replacement]: New field. Co-authored-by: Leo Famulari --- gnu/packages/xml.scm | 21 ++++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index ad2e3ec6c9..9743086b1e 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -13,7 +13,7 @@ ;;; Copyright © 2016 Jan Nieuwenhuizen ;;; Copyright © 2016, 2017 Nikita ;;; Copyright © 2016–2021 Tobias Geerinckx-Rice -;;; Copyright © 2016, 2017, 2018, 2019, 2020 Marius Bakke +;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Marius Bakke ;;; Copyright © 2017 Adriano Peluso ;;; Copyright © 2017 Gregor Giesen ;;; Copyright © 2017 Alex Vong @@ -121,6 +121,7 @@ the entire document.") (package (name "expat") (version "2.2.9") + (replacement expat-2.4.1) (source (let ((dot->underscore (lambda (c) (if (char=? #\. c) #\_ c)))) (origin (method url-fetch) @@ -144,6 +145,24 @@ stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags).") (license license:expat))) +;; Replacement package to fix CVE-2013-0340. +(define expat-2.4.1 + (package + (inherit expat) + (version "2.4.1") + (source (let ((dot->underscore (lambda (c) (if (char=? #\. c) #\_ c)))) + (origin + (method url-fetch) + (uri (list (string-append "mirror://sourceforge/expat/expat/" + version "/expat-" version ".tar.xz") + (string-append + "https://github.com/libexpat/libexpat/releases/download/R_" + (string-map dot->underscore version) + "/expat-" version ".tar.xz"))) + (sha256 + (base32 + "0spvyb9d3hijs4ys3x64cfmilsynl8kv6clfahv8d4lvp86js0yg"))))))) + (define-public libebml (package (name "libebml") -- cgit 1.4.1 From 9e7d93f67566d52a2dc9006f02a4c2ad2be14442 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 31 May 2021 20:08:40 -0400 Subject: gnu: curl: Update to 7.77.0 [fixes CVE-2021-{22897,22898,22901}]. * gnu/packages/curl.scm (curl/fixed): Replace with ... (curl-7.77.0): ... new variable. (curl)[replacement]: Use curl-7.77.0. --- gnu/packages/curl.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm index 94dc51cfc5..76b9b9840c 100644 --- a/gnu/packages/curl.scm +++ b/gnu/packages/curl.scm @@ -53,6 +53,7 @@ (define-public curl (package (name "curl") + (replacement curl-7.77.0) (version "7.74.0") (source (origin (method url-fetch) @@ -62,7 +63,6 @@ (base32 "12w7gskrglg6qrmp822j37fmbr0icrcxv7rib1fy5xiw80n5z7cr")) (patches (search-patches "curl-use-ssl-cert-env.patch")))) - (replacement curl/fixed) (build-system gnu-build-system) (outputs '("out" "doc")) ;1.2 MiB of man3 pages @@ -152,10 +152,10 @@ tunneling, and so on.") (name "curl-minimal") (inputs (alist-delete "openldap" (package-inputs curl)))))) -(define-public curl/fixed +(define-public curl-7.77.0 (package (inherit curl) - (version "7.76.0") + (version "7.77.0") (source (origin (inherit (package-source curl)) @@ -164,7 +164,7 @@ tunneling, and so on.") (patches (search-patches "curl-7.76-use-ssl-cert-env.patch")) (sha256 (base32 - "1j2g04m6als6hmqzvddv84c31m0x90bfgyz3bjrwdkarbkby40k3")))))) + "0jsrc97vbghvljic997r9nypc9qqddcil2lzvv032br8ahn5hr0g")))))) (define-public kurly (package -- cgit 1.4.1 From 929b72dd58b03f7dff08564cc8bba004721bf83e Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Thu, 3 Jun 2021 08:23:13 +0200 Subject: gnu: Add simple-inferiors. * gnu/packages/lisp-xyz.scm (cl-simple-inferiors, ecl-simple-inferiors, sbcl-simple-inferiors): New variables. --- gnu/packages/lisp-xyz.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 3bf1552d66..5beebdf311 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -17178,3 +17178,37 @@ any existing or future application.") (define-public cl-flare (sbcl-package->cl-source-package sbcl-flare)) + +(define-public sbcl-simple-inferiors + (let ((commit "deac886354e03f8a9502ce96f12a0459ce3be671")) + (package + (name "sbcl-simple-inferiors") + (version (git-version "1.1.0" "1" commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Shinmera/simple-inferiors") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "08vsvqv3768bwb2y8mwxbw5wyqzzwqr7rd004r6gafdgf9p9mcx3")))) + (build-system asdf-build-system/sbcl) + (inputs + `(("bordeaux-threads" ,sbcl-bordeaux-threads) + ("documentation-utils" ,sbcl-documentation-utils))) + (home-page "https://shinmera.github.io/simple-inferiors/") + (synopsis "Common Lisp library to use inferior processes") + (description + "This is a library to allow easy handling of external processes, and +primarily to get their output. It handles proper copying of the standard and +error outputs of the process simultaneously, both in a sequential and parallel +fashion. It also features a lazy directory switching mechanism, to avoid +running into parallelism problems when having to change directory.") + (license license:zlib)))) + +(define-public ecl-simple-inferiors + (sbcl-package->ecl-package sbcl-simple-inferiors)) + +(define-public cl-simple-inferiors + (sbcl-package->cl-source-package sbcl-simple-inferiors)) -- cgit 1.4.1 From 80a6de6b3ae2cdedb1b7fedc7d14e0ae67a2f8f2 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Thu, 3 Jun 2021 08:23:23 +0200 Subject: gnu: Add legit. * gnu/packages/lisp-xyz.scm (cl-legit, ecl-legit, sbcl-legit): New variables. --- gnu/packages/lisp-xyz.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 5beebdf311..a692a373eb 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -17212,3 +17212,38 @@ running into parallelism problems when having to change directory.") (define-public cl-simple-inferiors (sbcl-package->cl-source-package sbcl-simple-inferiors)) + +(define-public sbcl-legit + (let ((commit "48d50a20d8dcbd941d119683463b7c8257ba6458")) + (package + (name "sbcl-legit") + (version (git-version "1.0.0" "1" commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Shinmera/legit") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "181aqpj4zkfk1aavj5jw8rym6gw4ma3gd64z2h5fpryabgmwk236")))) + (build-system asdf-build-system/sbcl) + (inputs + `(("simple-inferiors" ,sbcl-simple-inferiors) + ("lambda-fiddle" ,sbcl-lambda-fiddle) + ("cl-ppcre" ,sbcl-cl-ppcre) + ("documentation-utils" ,sbcl-documentation-utils))) + (home-page "https://shinmera.github.io/legit/") + (synopsis "Interface to the git binary") + (description + "This is an interface to the @code{git} binary to make controlling it +from within Common Lisp much easier. It might not ever reach full coverage of +all features given git's immense size, but features will be added as they are +needed. The low-level command API is fully mapped however.") + (license license:zlib)))) + +(define-public ecl-legit + (sbcl-package->ecl-package sbcl-legit)) + +(define-public cl-legit + (sbcl-package->cl-source-package sbcl-legit)) -- cgit 1.4.1 From a923127d3051841e4187ee5e817f6c85e6387c3e Mon Sep 17 00:00:00 2001 From: Leo Prikler Date: Thu, 3 Jun 2021 08:26:23 +0200 Subject: gnu: Remove font-ubuntu. The Ubuntu Font License has not been approved by the FSF and is considered non-free by Debian and Fedora, see . * gnu/packages/fonts.scm (font-ubuntu): Removed variable. --- gnu/packages/fonts.scm | 24 ------------------------ 1 file changed, 24 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index c2280565ab..973393acc4 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -119,30 +119,6 @@ well as other mediums.") in print. With attention to detail for high resolution rendering.") (license license:silofl1.1))) -(define-public font-ubuntu - (package - (name "font-ubuntu") - (version "0.83") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://salsa.debian.org/fonts-team/fonts-ubuntu") - (commit (string-append "upstream/" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1d2xrjpxy70f3nsgqiggwv6pj06qglf5vj2847pqx60w3ygi903g")))) - (build-system font-build-system) - (home-page "http://font.ubuntu.com/") - (synopsis "The Ubuntu Font Family") - (description "The Ubuntu Font Family is a unique, custom designed font -that has a very distinctive look and feel. This package provides the -TrueType (TTF) files.") - (license - (license:non-copyleft - "http://font.ubuntu.com/ufl/ubuntu-font-licence-1.0.txt" - "Ubuntu Font License v1.0")))) - (define-public font-dejavu (package (name "font-dejavu") -- cgit 1.4.1 From f6a979860c4550e35b595d3ecdfc5be490c40836 Mon Sep 17 00:00:00 2001 From: Leo Prikler Date: Thu, 3 Jun 2021 08:49:18 +0200 Subject: gnu: openshot: Use free font. * gnu/packages/video.scm (openshot)[inputs]: Use font-dejavu. [patch-font-location]: Adjust accordingly. --- gnu/packages/video.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 2e9f9e3267..d85a4045f1 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -4535,7 +4535,7 @@ API. It includes bindings for Python, Ruby, and other languages.") (build-system python-build-system) (inputs `(("ffmpeg" ,ffmpeg) - ("font-ubuntu" ,font-ubuntu) + ("font-dejavu" ,font-dejavu) ("libopenshot" ,libopenshot) ("python" ,python) ("python-pyqt" ,python-pyqt) @@ -4556,10 +4556,11 @@ API. It includes bindings for Python, Ruby, and other languages.") (invoke "python" "src/tests/query_tests.py"))) (add-after 'unpack 'patch-font-location (lambda* (#:key inputs #:allow-other-keys) - (let ((font (assoc-ref inputs "font-ubuntu"))) + (let ((font (assoc-ref inputs "font-dejavu"))) (substitute* "src/classes/app.py" (("info.IMAGES_PATH") (string-append "\"" font "\"")) - (("fonts") "share/fonts/truetype"))) + (("fonts") "share/fonts/truetype") + (("[A-Za-z_-]+.ttf") "DejaVuSans.ttf"))) #t)) (add-before 'install 'set-tmp-home (lambda _ -- cgit 1.4.1 From 13b737f132b16bf26793ae05fc0d1f2f7180b25d Mon Sep 17 00:00:00 2001 From: Lars-Dominik Braun Date: Thu, 3 Jun 2021 11:18:03 +0200 Subject: gnu: r-with-tests: Use patched texlive-amsfonts. See commit 75af43162e58a0b3fdc804963809ecb801fb81b7. * gnu/packages/statistics.scm (r-with-tests)[native-inputs]: Replace texlive-amsfonts with texlive-amsfonts/patched. --- gnu/packages/statistics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index a6c9c9d558..1292ac6898 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -340,7 +340,7 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ ("texlive" ,(texlive-union (list texlive-ae texlive-inconsolata texlive-fonts-ec - texlive-amsfonts + texlive-amsfonts/patched texlive-latex-base texlive-latex-fancyvrb texlive-latex-graphics -- cgit 1.4.1 From 0928e552662965f5a18fbc831e6c9758744bd042 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Jun 2021 12:18:35 +0200 Subject: gnu: Add fit-sne. * gnu/packages/bioinformatics.scm (fit-sne): New variable. --- gnu/packages/bioinformatics.scm | 63 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 94d15cc4c0..408c93bd34 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11214,6 +11214,69 @@ spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA) in RNA-seq data.") (license license:gpl3)))) +(define-public fit-sne + (package + (name "fit-sne") + (version "1.2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/KlugerLab/FIt-SNE") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1imq4577awc226wvygf94kpz156qdfw8xl0w0f7ss4w10lhmpmf5")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #false ; there are none + #:phases + ;; There is no build system. + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (invoke "g++" "-std=c++11" "-O3" + "src/sptree.cpp" + "src/tsne.cpp" + "src/nbodyfft.cpp" + "-o" "bin/fast_tsne" + "-pthread" "-lfftw3" "-lm" + "-Wno-address-of-packed-member"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (share (string-append out "/share/fit-sne"))) + (for-each (lambda (file) (install-file file bin)) + (find-files "bin")) + + (substitute* "fast_tsne.R" + (("^FAST_TSNE_SCRIPT_DIR.*") + (string-append "FAST_TSNE_SCRIPT_DIR = \"" out "\"\n"))) + (install-file "fast_tsne.R" share))))))) + (inputs + `(("fftw" ,fftw))) + (home-page "https://github.com/KlugerLab/FIt-SNE") + (synopsis "Fast Fourier Transform-accelerated interpolation-based t-SNE") + (description "@dfn{t-Stochastic Neighborhood Embedding} (t-SNE) is a +method for dimensionality reduction and visualization of high dimensional +datasets. A popular implementation of t-SNE uses the Barnes-Hut algorithm to +approximate the gradient at each iteration of gradient descent. This +implementation differs in these ways: + +@itemize +@item Instead of approximating the N-body simulation using Barnes-Hut, we + interpolate onto an equispaced grid and use FFT to perform the convolution. +@item Instead of computing nearest neighbors using vantage-point trees, we + approximate nearest neighbors using the Annoy library. The neighbor lookups + are multithreaded to take advantage of machines with multiple cores. +@end itemize +") + ;; See LICENSE.txt for details on what license applies to what files. + (license (list license:bsd-4 license:expat license:asl2.0)))) + (define-public python-scanpy (package (name "python-scanpy") -- cgit 1.4.1 From fe509e017fa1c0e3d0b057784b081def3aa621ad Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Thu, 3 Jun 2021 12:33:08 +0200 Subject: machine: ssh: Respect calling convention for monadic procedures. Fixes a regression introduced in 2885c3568edec35086f8feeae5b60259cbea407c. Reported by Mathieu Othacehe. * gnu/machine/ssh.scm (deploy-managed-host)[eval/error-handling]: Return two values in the standard case. --- gnu/machine/ssh.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/machine/ssh.scm b/gnu/machine/ssh.scm index 93b0a007da..ecd02e336c 100644 --- a/gnu/machine/ssh.scm +++ b/gnu/machine/ssh.scm @@ -459,7 +459,8 @@ have you run 'guix archive --generate-key?'") (lambda (store) (guard (condition ((inferior-exception? condition) (values (begin handler ...) store))) - (run-with-store store (eval exp)))))) + (values (run-with-store store (eval exp)) + store))))) (mbegin %store-monad (with-roll-back #f -- cgit 1.4.1 From e4283e03a3004ab27266e195c4c57128d5c91b23 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 2 Jun 2021 22:31:25 +0200 Subject: gnu: rust-assert-cmd-1: Update to 1.0.4. * gnu/packages/crates-io.scm (rust-assert-cmd-1): Update to 1.0.4. --- gnu/packages/crates-io.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 58ff4ca431..ae9ea6337e 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -2429,7 +2429,7 @@ standard library.") (define-public rust-assert-cmd-1 (package (name "rust-assert-cmd") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) @@ -2438,7 +2438,7 @@ standard library.") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "15h3wfxn1q7sfcrin4z35x9hgf539f2dhkwz2mq4zswlrmc5nizj")))) + "127mhhjbclg63rfhmy0jc382w5x7y6aig0b9rhnyfkbymk0zwmwg")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs -- cgit 1.4.1 From 11d84f4b7f5d59bf2e1dc15b28b116c8385c1a25 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 2 Jun 2021 22:32:08 +0200 Subject: gnu: rust-url-2: Update to 2.2.2. * gnu/packages/crates-io.scm (rust-url-2): Update to 2.2.2. --- gnu/packages/crates-io.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index ae9ea6337e..cae8bfc5ea 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -47443,7 +47443,7 @@ untrusted inputs in Rust.") (define-public rust-url-2 (package (name "rust-url") - (version "2.2.1") + (version "2.2.2") (source (origin (method url-fetch) @@ -47452,7 +47452,7 @@ untrusted inputs in Rust.") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "12qzdzgcvmc5l1fk4psldiipx80423mikb6g4a9qwb322d0rdkcw")))) + "132pzpvfvpw33gjlzqd55n5iag9qddzffq8qbp1myfykna1w61x5")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t -- cgit 1.4.1 From 558db7b6e5e8467d1cd82f598f1f8dc8ad9227f1 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 2 Jun 2021 22:33:50 +0200 Subject: gnu: Add rust-sha2-asm-0.6. * gnu/packages/crates-io.scm (rust-sha2-asm-0.6): New variable. (rust-sha2-asm-0.5): Inherit from above. --- gnu/packages/crates-io.scm | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index cae8bfc5ea..eecabf4fa0 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -38444,27 +38444,40 @@ function family including SHA-224, SHA-256, SHA-384, and SHA-512.") ("rust-generic-array" ,rust-generic-array-0.8) ("rust-sha2-asm" ,rust-sha2-asm-0.3)))))) -(define-public rust-sha2-asm-0.5 +(define-public rust-sha2-asm-0.6 (package (name "rust-sha2-asm") - (version "0.5.4") + (version "0.6.1") (source (origin (method url-fetch) (uri (crate-uri "sha2-asm" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0y4n8r4362y2fa6p2j0dgny4zfi194gdf01l6j850n9vf8ha3kwj")))) + (base32 "08rp21zv96n8cnwcix177xkdw43zx8dqgfjfwd0gly9hvrl7lfaw")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-cc" ,rust-cc-1)))) ;; build dependency + (("rust-cc" ,rust-cc-1)))) ;build dependency (home-page "https://github.com/RustCrypto/asm-hashes") (synopsis "Assembly implementation of SHA-2") (description "This package provides an assembly implementations of hash functions core functionality.") (license license:expat))) +(define-public rust-sha2-asm-0.5 + (package + (inherit rust-sha2-asm-0.6) + (name "rust-sha2-asm") + (version "0.5.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "sha2-asm" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0y4n8r4362y2fa6p2j0dgny4zfi194gdf01l6j850n9vf8ha3kwj")))))) + (define-public rust-sha2-asm-0.3 (package (inherit rust-sha2-asm-0.5) -- cgit 1.4.1 From adc7fc093e26c1cf858a42ef31f4aca3a842d062 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 2 Jun 2021 22:37:04 +0200 Subject: gnu: Add rust-cpufeatures-0.1. * gnu/packages/crates-io.scm (rust-cpufeatures-0.1): New variable. --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index eecabf4fa0..0a2768aacc 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -8979,6 +8979,29 @@ intrinsics.") (("rust-clap" ,rust-clap-2) ("rust-diff" ,rust-diff-0.1)))))) +(define-public rust-cpufeatures-0.1 + (package + (name "rust-cpufeatures") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "cpufeatures" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1j0i97325c2grndsfgnm3lqk0xbyvdl2dbgn8i5dd9yhnmycc07d")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-libc" ,rust-libc-0.2)))) + (home-page "https://github.com/RustCrypto/utils") + (synopsis "Alternative to the @code{is_x86_feature_detected!} macro") + (description + "Cpufeatures is a lightweight and efficient no-std compatible alternative +to the @code{is_x86_feature_detected!} macro.") + (license (list license:expat license:asl2.0)))) + (define-public rust-cpuid-bool-0.1 (package (name "rust-cpuid-bool") -- cgit 1.4.1 From c695df8c5f90b263f7a42e7a38fadea53df3678c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 2 Jun 2021 22:38:04 +0200 Subject: gnu: rust-sha2-0.9: Update to 0.9.5. * gnu/packages/crates-io.scm (rust-sha2-0.9): Update to 0.9.5. --- gnu/packages/crates-io.scm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 0a2768aacc..df0a01336b 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -38369,7 +38369,7 @@ code is translated from C to Rust using c2rust.") (define-public rust-sha2-0.9 (package (name "rust-sha2") - (version "0.9.3") + (version "0.9.5") (source (origin (method url-fetch) @@ -38378,17 +38378,16 @@ code is translated from C to Rust using c2rust.") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1phjvjcvc33xa3xdpxw3a324ksbnrg9qhjnig13z9dwsn8a7m0ps")))) + "04lzf4swq6cijvxnc6facr3g72h5v7a5z8lz3xrkf8gxa9bswqmk")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs (("rust-block-buffer" ,rust-block-buffer-0.9) ("rust-cfg-if" ,rust-cfg-if-1) - ("rust-cpuid-bool" ,rust-cpuid-bool-0.1) + ("rust-cpufeatures" ,rust-cpufeatures-0.1) ("rust-digest" ,rust-digest-0.9) - ("rust-libc" ,rust-libc-0.2) ("rust-opaque-debug" ,rust-opaque-debug-0.3) - ("rust-sha2-asm" ,rust-sha2-asm-0.5)) + ("rust-sha2-asm" ,rust-sha2-asm-0.6)) #:cargo-development-inputs (("rust-digest" ,rust-digest-0.9) ("rust-hex-literal" ,rust-hex-literal-0.2)))) -- cgit 1.4.1 From c0796540dec07f93804338d8ccaf30d1a861173a Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 2 Jun 2021 22:39:14 +0200 Subject: gnu: rust-reqwest-0.11: Update to 0.11.3. * gnu/packages/crates-io.scm (rust-reqwest-0.11): Update to 0.11.3. --- gnu/packages/crates-io.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index df0a01336b..8a45169019 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -33152,14 +33152,14 @@ uses finite automata and guarantees linear time matching on all inputs.") (define-public rust-reqwest-0.11 (package (name "rust-reqwest") - (version "0.11.2") + (version "0.11.3") (source (origin (method url-fetch) (uri (crate-uri "reqwest" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1m12j00if0gj0alhad4r7w0air4j0gqlpiwiqpsxna4l51zha4mz")))) + (base32 "097i9z42jq2sn3va3r6pksz3gzffbnr3c4aapk6fhy9rqpxg55i2")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t -- cgit 1.4.1 From ef0daad2112f8c984d9f9ff82800b128d555bbbc Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 3 Jun 2021 14:23:37 +0200 Subject: gnu: rust-reqwest-0.11: Fix build. * gnu/packages/crates-io.scm (rust-reqwest-0.11)[arguments]: Add missing Cargo development inputs. --- gnu/packages/crates-io.scm | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 8a45169019..5f166306e8 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -33203,7 +33203,16 @@ uses finite automata and guarantees linear time matching on all inputs.") ("rust-wasm-bindgen-futures" ,rust-wasm-bindgen-futures-0.4) ("rust-web-sys" ,rust-web-sys-0.3) ("rust-webpki-roots" ,rust-webpki-roots-0.21) - ("rust-winreg" ,rust-winreg-0.7)))) + ("rust-winreg" ,rust-winreg-0.7)) + #:cargo-development-inputs + (("rust-brotli" ,rust-brotli-3) + ("rust-doc-comment" ,rust-doc-comment-0.3) + ("rust-env-logger" ,rust-env-logger-0.8) + ("rust-hyper" ,rust-hyper-0.14) + ("rust-libflate" ,rust-libflate-1) + ("rust-serde" ,rust-serde-1) + ("rust-tokio" ,rust-tokio-1) + ("rust-wasm-bindgen-test" ,rust-wasm-bindgen-test-0.3)))) (home-page "https://github.com/seanmonstar/reqwest") (synopsis "High level HTTP client library") (description "This package provides a high level HTTP client library.") -- cgit 1.4.1 From 2282d21fd614cd4f8143efd7087915c7fe11976a Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 2 Jun 2021 22:40:16 +0200 Subject: gnu: rust-regex-syntax-0.6: Update to 0.6.25. * gnu/packages/crates-io.scm (rust-regex-syntax-0.6): Update to 0.6.25. --- gnu/packages/crates-io.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 5f166306e8..abad47fdc8 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -32976,14 +32976,14 @@ uses finite automata and guarantees linear time matching on all inputs.") (define-public rust-regex-syntax-0.6 (package (name "rust-regex-syntax") - (version "0.6.22") + (version "0.6.25") (source (origin (method url-fetch) (uri (crate-uri "regex-syntax" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "10b56ylil35jkb4nwqxm8hbyx3zq7fws0wpydjln165s8xql3sxm")))) + (base32 "16y87hz1bxmmz6kk360cxwfm3jnbsxb3x4zw9x1gzz7khic2i5zl")))) (build-system cargo-build-system) (home-page "https://github.com/rust-lang/regex") (synopsis "Regular expression parser") -- cgit 1.4.1 From a04dd9b01b42f4b118827346014fb3fa13510dc3 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 2 Jun 2021 22:40:46 +0200 Subject: gnu: rust-memchr-2: Update to 2.4.0. * gnu/packages/crates-io.scm (rust-memchr-2): Update to 2.4.0. --- gnu/packages/crates-io.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index abad47fdc8..729f6fd46f 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -23420,7 +23420,7 @@ unstable -Z self-profile flag.") (define-public rust-memchr-2 (package (name "rust-memchr") - (version "2.3.4") + (version "2.4.0") (source (origin (method url-fetch) @@ -23429,7 +23429,7 @@ unstable -Z self-profile flag.") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "098m9clfs495illlw00hv2gg67mhm7jflld3msyclvi5m9xc9q8f")))) + "1p478fqf4nia2ma0kv4npb8x1hli0zz6k16517ikb51jkryx8sxi")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t -- cgit 1.4.1 From 71beab1c1ae69eb43118f520d4c8bd45987fa994 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 2 Jun 2021 22:41:16 +0200 Subject: gnu: rust-aho-corasick-0.7: Update to 0.7.18. * gnu/packages/crates-io.scm (rust-aho-corasick-0.7): Update to 0.7.18. --- gnu/packages/crates-io.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 729f6fd46f..2a969a412c 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -1486,14 +1486,14 @@ using AES-NI for high performance.") (define-public rust-aho-corasick-0.7 (package (name "rust-aho-corasick") - (version "0.7.15") + (version "0.7.18") (source (origin (method url-fetch) (uri (crate-uri "aho-corasick" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1rb8gzhljl8r87dpf2n5pnqnkl694casgns4ma0sqzd4zazzw13l")))) + (base32 "0vv50b3nvkhyy7x7ip19qnsq11bqlnffkmj2yx2xlyk5wzawydqy")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs -- cgit 1.4.1 From b7c5f275795b50d65c441a1e2e6ef74ba96ca775 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 2 Jun 2021 22:42:14 +0200 Subject: gnu: rust-regex-1: Update to 1.5.4. * gnu/packages/crates-io.scm (rust-regex-1): Update to 1.5.4. --- gnu/packages/crates-io.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 2a969a412c..398c7084ed 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -32856,21 +32856,20 @@ functionality.") (define-public rust-regex-1 (package (name "rust-regex") - (version "1.4.3") + (version "1.5.4") (source (origin (method url-fetch) (uri (crate-uri "regex" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "12llbg82js69mdl50lav4yn1iqlx71ckb18dww467q99w4wi49fr")))) + (base32 "0qf479kjbmb582h4d1d6gfl75h0j8aq2nrdi5wg6zdcy6llqcynh")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs (("rust-aho-corasick" ,rust-aho-corasick-0.7) ("rust-memchr" ,rust-memchr-2) - ("rust-regex-syntax" ,rust-regex-syntax-0.6) - ("rust-thread-local" ,rust-thread-local-1)) + ("rust-regex-syntax" ,rust-regex-syntax-0.6)) #:cargo-development-inputs (("rust-lazy-static" ,rust-lazy-static-1) ("rust-quickcheck" ,rust-quickcheck-0.8) -- cgit 1.4.1 From 08f1400becf93607cd83ffc4057fc9cf5ded7e0e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 2 Jun 2021 22:43:09 +0200 Subject: gnu: monolith: Update to 2.5.0. * gnu/packages/web.scm (monolith): Update to 2.5.0. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 41d815c0e5..4753eca8da 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -317,7 +317,7 @@ Interface} specification.") (define-public monolith (package (name "monolith") - (version "2.4.1") + (version "2.5.0") (source (origin (method git-fetch) @@ -326,7 +326,7 @@ Interface} specification.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1z0bcvk2cvx2cd0hs8addzcb070xvrkcxvg25691xw0ikiynpkwz")))) + (base32 "0s6jyhz51d39ccz0ghr7hy1fww84b0pzsyb8s63qgxbndp2c42l0")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs -- cgit 1.4.1 From cc0f152ffda5c7c2d7485eae81729a7c28337cb2 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 3 Jun 2021 14:29:08 +0200 Subject: gnu: emacs-ebdb: Update to 0.6.23. * gnu/packages/emacs-xyz.scm (emacs-ebdb): Update to 0.6.23. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 81aec3097d..085160d443 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -24930,14 +24930,14 @@ federated microblogging social network.") (define-public emacs-ebdb (package (name "emacs-ebdb") - (version "0.6.22") + (version "0.6.23") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "ebdb-" version ".tar")) (sha256 - (base32 "0dljl21n6508c7ash7l6zgxhpn2wdfzga0va63d4k9nwnqmkvsgz")))) + (base32 "0j3jvy9s606qjqcmcjzgck3dp8bhpgly2g00wnswzcgk4makdzld")))) (build-system emacs-build-system) (home-page "https://github.com/girzel/ebdb") (synopsis "EIEIO port of BBDB, Emacs's contact-management package") -- cgit 1.4.1 From 7668c2cbe89960d2d782fc4c9c8f3c5bc90208f1 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 3 Jun 2021 14:45:13 +0200 Subject: gnu: emacs-closql: Update to 1.0.5. * gnu/packages/emacs-xyz.scm (emacs-closql): Update to 1.0.5. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 085160d443..6449e937b6 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -16086,7 +16086,7 @@ official @command{sqlite3} executable to access SQL database.") (define-public emacs-closql (package (name "emacs-closql") - (version "1.0.4") + (version "1.0.5") (source (origin (method git-fetch) @@ -16096,7 +16096,7 @@ official @command{sqlite3} executable to access SQL database.") (file-name (git-file-name name version)) (sha256 (base32 - "06j0sc6dx8f34wc8i7dzkp8jwvwnrpnl8i93vpc1qw0ih0jwa2zh")))) + "01l4w3wc7rm7mca8pbkyz0yrks4z8i00ppy5c4bmrnn6akf7h9ih")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-emacsql" ,emacs-emacsql))) -- cgit 1.4.1 From cf6be24529960c50706c6b4164193ed6c1dd5bc2 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 3 Jun 2021 14:49:15 +0200 Subject: gnu: emacs-epkg: Update to 3.3.0. * gnu/packages/emacs-xyz.scm (emacs-epkg): Update to 3.3.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 6449e937b6..f8326a94d9 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -16113,7 +16113,7 @@ add any additional instance slots.") (define-public emacs-epkg (package (name "emacs-epkg") - (version "3.2.2") + (version "3.3.0") (source (origin (method git-fetch) @@ -16123,7 +16123,7 @@ add any additional instance slots.") (file-name (git-file-name name version)) (sha256 (base32 - "1pxz611qb3m33r6343h0xhwqvvhjl131zyc2klplzgb23rkm8lk0")))) + "03zsysj78w43q902wi9dhck64q9va247avr6fhdw8ynf2lvb78d3")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-closql" ,emacs-closql) -- cgit 1.4.1 From 606b200fe7448b85de5f4ed9d4aa7677b227a980 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 3 Jun 2021 01:30:37 +0200 Subject: gnu: mtools: Update to 4.0.29. * gnu/packages/mtools.scm (mtools): Update to 4.0.29. --- gnu/packages/mtools.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/mtools.scm b/gnu/packages/mtools.scm index 6e662a80c6..5f79253d6d 100644 --- a/gnu/packages/mtools.scm +++ b/gnu/packages/mtools.scm @@ -29,14 +29,14 @@ (define-public mtools (package (name "mtools") - (version "4.0.27") + (version "4.0.29") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/mtools/mtools-" version ".tar.bz2")) (sha256 (base32 - "1crqi10adwfahj8xyw60lx70hkpcc5g00b5r8277cm2f4kcwi24w")) + "1izymrj7cjya3da5qgvlmywqs0kkjdk9940hl15ybbz70d30pdf6")) (patches (search-patches "mtools-mformat-uninitialized.patch")))) (build-system gnu-build-system) -- cgit 1.4.1 From e348436589795c72d5e7007eb64ef0efdbe75726 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 3 Jun 2021 01:31:27 +0200 Subject: gnu: amule: Update to 2.3.3. * gnu/packages/networking.scm (amule): Update to 2.3.3. [source]: Remove patch. * gnu/packages/patches/amule-crypto-6.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/networking.scm | 6 ++--- gnu/packages/patches/amule-crypto-6.patch | 45 ------------------------------- 3 files changed, 2 insertions(+), 50 deletions(-) delete mode 100644 gnu/packages/patches/amule-crypto-6.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index a5820b5827..8c235f50c8 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -809,7 +809,6 @@ dist_patch_DATA = \ %D%/packages/patches/akonadi-not-relocatable.patch \ %D%/packages/patches/akonadi-timestamps.patch \ %D%/packages/patches/allegro-mesa-18.2.5-and-later.patch \ - %D%/packages/patches/amule-crypto-6.patch \ %D%/packages/patches/anki-mpv-args.patch \ %D%/packages/patches/antiword-CVE-2014-8123.patch \ %D%/packages/patches/antlr3-3_1-fix-java8-compilation.patch \ diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 945123e600..5be5cfd606 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2947,7 +2947,7 @@ file for more details.") (define-public amule (package (name "amule") - (version "2.3.2") + (version "2.3.3") (source (origin (method git-fetch) (uri (git-reference @@ -2956,9 +2956,7 @@ file for more details.") (file-name (git-file-name name version)) (sha256 (base32 - "010wxm6g9f92x6fympj501zbnjka32rzbx0sk3a2y4zpih5d2nsn")) - ;; Patch for adopting crypto++ >= 6.0. - (patches (search-patches "amule-crypto-6.patch")))) + "1nm4vxgmisn1b6l3drmz0q04x067j2i8lw5rnf0acaapwlp8qwvi")))) (build-system gnu-build-system) (arguments `(#:phases diff --git a/gnu/packages/patches/amule-crypto-6.patch b/gnu/packages/patches/amule-crypto-6.patch deleted file mode 100644 index 21a86ab0fa..0000000000 --- a/gnu/packages/patches/amule-crypto-6.patch +++ /dev/null @@ -1,45 +0,0 @@ -From d1d1368c7909ffd8423730afaa811ce7b6a3a8aa Mon Sep 17 00:00:00 2001 -From: Tommy Jerry Mairo -Date: Sun, 4 Feb 2018 12:42:00 -0800 -Subject: [PATCH 1/2] Bugfix: API mismatch with crypto++ 6.0.0 - ---- - src/ClientCreditsList.cpp | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/src/ClientCreditsList.cpp b/src/ClientCreditsList.cpp -index 3bea9fe2d..a7ae1e34c 100644 ---- a/src/ClientCreditsList.cpp -+++ b/src/ClientCreditsList.cpp -@@ -312,7 +312,7 @@ void CClientCreditsList::InitalizeCrypting() - // calculate and store public key - CryptoPP::RSASSA_PKCS1v15_SHA_Verifier pubkey(*static_cast(m_pSignkey)); - CryptoPP::ArraySink asink(m_abyMyPublicKey, 80); -- pubkey.DEREncode(asink); -+ pubkey.AccessMaterial().Save(asink); - m_nMyPublicKeyLen = asink.TotalPutLength(); - asink.MessageEnd(); - } catch (const CryptoPP::Exception& e) { - -From 88ba0ac952b78382445f2fff73c6792c0474dc62 Mon Sep 17 00:00:00 2001 -From: Tommy Jerry Mairo -Date: Wed, 21 Mar 2018 11:56:28 -0700 -Subject: [PATCH 2/2] Update: Change AccessMaterial to GetMaterial - ---- - src/ClientCreditsList.cpp | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/src/ClientCreditsList.cpp b/src/ClientCreditsList.cpp -index a7ae1e34c..69e881fd8 100644 ---- a/src/ClientCreditsList.cpp -+++ b/src/ClientCreditsList.cpp -@@ -312,7 +312,7 @@ void CClientCreditsList::InitalizeCrypting() - // calculate and store public key - CryptoPP::RSASSA_PKCS1v15_SHA_Verifier pubkey(*static_cast(m_pSignkey)); - CryptoPP::ArraySink asink(m_abyMyPublicKey, 80); -- pubkey.AccessMaterial().Save(asink); -+ pubkey.GetMaterial().Save(asink); - m_nMyPublicKeyLen = asink.TotalPutLength(); - asink.MessageEnd(); - } catch (const CryptoPP::Exception& e) { -- cgit 1.4.1 From 0dd2670ad5f2970c35de9a6d8314adace3787258 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 3 Jun 2021 01:31:56 +0200 Subject: gnu: amule: Use HTTPS home page. * gnu/packages/networking.scm (amule)[home-page]: Use HTTPS. --- gnu/packages/networking.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 5be5cfd606..1be47e6102 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2992,7 +2992,7 @@ file for more details.") ("crypto++" ,crypto++) ("libpng" ,libpng) ("wxwidgets-gtk2" ,wxwidgets-gtk2))) - (home-page "http://amule.org/") + (home-page "https://amule.org/") (synopsis "Peer-to-peer client for the eD2K and Kademlia networks") (description "aMule is an eMule-like client for the eD2k and Kademlia peer-to-peer -- cgit 1.4.1 From 240cd1a099b3619e8fca7958cb6fc76bd5f250e4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 3 Jun 2021 12:40:52 +0200 Subject: gnu: fltk: Update to 1.3.6. * gnu/packages/fltk.scm (fltk): Update to 1.3.6. --- gnu/packages/fltk.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/fltk.scm b/gnu/packages/fltk.scm index d0f20b20fd..fbdc47e506 100644 --- a/gnu/packages/fltk.scm +++ b/gnu/packages/fltk.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2016 Kei Kebreau ;;; Copyright © 2018 Mark H Weaver ;;; Copyright © 2018 Efraim Flashner +;;; Copyright © 2021 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -42,7 +43,7 @@ (define-public fltk (package (name "fltk") - (version "1.3.5") + (version "1.3.6") (source (origin (method url-fetch) @@ -50,8 +51,7 @@ (first (string-split version #\-)) "/fltk-" version "-source.tar.gz")) (sha256 - (base32 - "00jp24z1818k9n6nn6lx7qflqf2k13g4kxr0p8v1d37kanhb4ac7")))) + (base32 "1arp1niiz3qxm8iacpmilwpc5rinsm6hsk4a6fsxfywvkvppbb4s")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit 1.4.1 From 0e8d650c4f578a27b30891751780b75239ffd3f8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 3 Jun 2021 18:23:06 +0200 Subject: gnu: php: Update to 7.4.20. * gnu/packages/php.scm (php): Update to 7.4.20. --- gnu/packages/php.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/php.scm b/gnu/packages/php.scm index 5e5b1c72d2..71e4f5ca5e 100644 --- a/gnu/packages/php.scm +++ b/gnu/packages/php.scm @@ -60,7 +60,7 @@ (define-public php (package (name "php") - (version "7.4.19") + (version "7.4.20") (home-page "https://secure.php.net/") (source (origin (method url-fetch) @@ -68,7 +68,7 @@ "php-" version ".tar.xz")) (sha256 (base32 - "1ck72j56a4xw2s8hirgblfh74g5nkf4xwllp9mlwn72198n1f5vc")) + "0db3nqfbfqfd8fkvrw1k8l6698qcbzv1v5j8rgr0ny0dg6k6r90z")) (modules '((guix build utils))) (snippet '(with-directory-excursion "ext" -- cgit 1.4.1 From 38adfcd6f5f772695c8958022c1c0fcd9e7aa988 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 3 Jun 2021 01:30:06 +0200 Subject: gnu: rasdaemon: Update to 0.6.7. * gnu/packages/linux.scm (rasdaemon): Update to 0.6.7. [arguments]: Add a "--with-sysconfdefdir" configure flag. --- gnu/packages/linux.scm | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 8d93e9e19c..74d5f63df8 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -8065,7 +8065,7 @@ provides user-space tools for creating EROFS file systems.") (define-public rasdaemon (package (name "rasdaemon") - (version "0.6.6") + (version "0.6.7") (source (origin (method git-fetch) @@ -8074,14 +8074,17 @@ provides user-space tools for creating EROFS file systems.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "13g39x19lfjf9izdcb0nlyfjrgpliivhv4nw3ndgyzi59l3yqc0v")))) + (base32 "12ih96jwmr7imp9zyckf9zjqqm5ra1kv5fj6kbw71y6yl31069dz")))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) ("libtool" ,libtool))) (inputs `(("sqlite" ,sqlite))) (arguments - `(#:configure-flags '("--enable-all" - "--localstatedir=/var") + `(#:configure-flags + (list "--enable-all" + ;; Don't install unused /etc/sysconfig/rasdaemon environment file. + "--with-sysconfdefdir=." + "--localstatedir=/var") #:phases (modify-phases %standard-phases (add-before 'configure 'munge-autotools -- cgit 1.4.1 From 9703a51048fbc1d322595d676ff0d63b1eb89304 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Thu, 3 Jun 2021 18:17:07 +0200 Subject: gnu: Add rfcat. * gnu/packages/radio.scm (rfcat): New variable. --- gnu/packages/radio.scm | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 1145c12c87..c0b1ed13e0 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -1952,3 +1952,59 @@ acts a general-purpose software FSK modem, and includes support for various standard FSK protocols such as Bell103, Bell202, RTTY, TTY/TDD, NOAA SAME, and Caller-ID.") (license license:gpl3+))) + +(define-public rfcat + ;; Use a commit for now because some fixes to make rfcat work with + ;; Python 3 instead of Python 2 are not in a release yet. + (let ((commit "725bf79af27d47cdec64107317c1c8fe3f7ad7b8") + (revision "1")) + (package + (name "rfcat") + (version (git-version "1.9.5" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/atlas0fd00m/rfcat") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0dbc6n4pxsa73wzxny773khc73r1dn3ma5hi7xv76vcykjvzkdi3")))) + (build-system python-build-system) + (inputs + `(("python-future" ,python-future) + ("python-ipython" ,python-ipython) + ("python-numpy" ,python-numpy) + ("python-pyserial" ,python-pyserial) + ("python-pyside-2" ,python-pyside-2) + ("python-pyusb" ,python-pyusb))) + (arguments + `(#:tests? #f ; Tests want to use a serial port + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-permissions + (lambda _ + (make-file-writable "rflib/rflib_version.py"))) + (add-after 'install 'install-udev-rules + (lambda* (#:key outputs #:allow-other-keys) + (install-file "etc/udev/rules.d/20-rfcat.rules" + (string-append (assoc-ref outputs "out") + "/lib/udev/rules.d"))))))) + (home-page "https://github.com/atlas0fd00m/rfcat") + (synopsis "Program to control some radio dongles") + (description + "@code{rfcat} is a program to control some radio dongles operating in +ISM bands. + +Supported dongles: +@itemize +@item YARD Stick One +@item cc1111emk +@item chronos watch dongle +@item imme (limited support) +@end itemize + +To install the rfcat udev rules, you must extend @code{udev-service-type} with +this package. E.g.: @code{(udev-rules-service 'rfcat rfcat)}") + (license (list license:bsd-3 + license:gpl2))))) -- cgit 1.4.1 From 97b4a7e37c75fd15a14ef49fa85b83e522aa78aa Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 3 Jun 2021 21:13:23 +0200 Subject: gnu: emacs-calibredb: Update to 2.10.0. * gnu/packages/emacs-xyz.scm (emacs-calibredb): Update to 2.10.0. --- gnu/packages/emacs-xyz.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index f8326a94d9..9a14e71c7c 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -24038,7 +24038,7 @@ all of your projects, then override or add variables on a per-project basis.") (define-public emacs-calibredb (package (name "emacs-calibredb") - (version "2.8.0") + (version "2.10.0") (source (origin (method git-fetch) @@ -24047,7 +24047,7 @@ all of your projects, then override or add variables on a per-project basis.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "19gc05k2p1l8wlkrqij9cw6d61hzknd6a9n64kzlpi87cpbav3lv")))) + (base32 "0s26a2fy1xldd0q57avds7zn0h7lkis2hjh9zmm1qhwn8409hys9")))) (build-system emacs-build-system) (arguments '(#:phases @@ -24060,8 +24060,7 @@ all of your projects, then override or add variables on a per-project basis.") ("calibredb-program" (string-append calibre "/bin/calibredb")) ("calibredb-fetch-metadata-program" - (string-append calibre "/bin/fetch-ebook-metadata")))) - #t))))) + (string-append calibre "/bin/fetch-ebook-metadata"))))))))) (inputs `(("calibre" ,calibre))) (propagated-inputs -- cgit 1.4.1 From bb414c9352de0fad4c28612b4f089049514b6343 Mon Sep 17 00:00:00 2001 From: Leo Prikler Date: Thu, 3 Jun 2021 21:46:28 +0200 Subject: gnu: komikku: Update to 0.29.0. * gnu/packages/gnome.scm (komikku): Update to 0.29.0. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 2b9fb0c6d7..2f579a2f82 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -11995,7 +11995,7 @@ integrated profiler via Sysprof, debugging support, and more.") (define-public komikku (package (name "komikku") - (version "0.28.1") + (version "0.29.0") (source (origin (method git-fetch) @@ -12005,7 +12005,7 @@ integrated profiler via Sysprof, debugging support, and more.") (file-name (git-file-name name version)) (sha256 (base32 - "0ifcwp5fw74yypxkq7i0yc3002bsvj3p5c1icspr8s2kyjyllm6i")))) + "1sirwgny1s6jv9rb0lildqv4p7nfa15rvw957pwxnvrjasxyf6bq")))) (build-system meson-build-system) (arguments `(#:glib-or-gtk? #t -- cgit 1.4.1 From 41d73dfba1b1d13116b9d6c3f68d66b4bd273428 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 3 Jun 2021 16:10:18 -0400 Subject: gnu: linux-libre: Update to 5.12.9. * gnu/packages/linux.scm (linux-libre-5.12-version): Update to 5.12.9. (linux-libre-5.12-pristine-source): Update hash. (deblob-scripts-5.12): Update hash. --- gnu/packages/linux.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 74d5f63df8..c2e2fc2df9 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -356,15 +356,15 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernels. That is, the most recently released major ;; versions that are still supported upstream. -(define-public linux-libre-5.12-version "5.12.8") +(define-public linux-libre-5.12-version "5.12.9") (define deblob-scripts-5.12 (linux-libre-deblob-scripts linux-libre-5.12-version (base32 "1vdsr9y4gckknrbqcjyfakwva3k0vb5zcivzk3k1s9mh7qp9dils") - (base32 "1qp25fd4wgjyk7dzdq9yirm1z5w68sd1p3wv8lch8259i51gwjnf"))) + (base32 "1p1jzrci97sipjdx3h0vmdnw35z2vyvczinxmp65xi1ja7ww0g14"))) (define-public linux-libre-5.12-pristine-source (let ((version linux-libre-5.12-version) - (hash (base32 "134g8d5zvbzdqxy7z6a527dqcmiq4ixf7s05rnnsc4qcajpbcimd"))) + (hash (base32 "0vg71h8r90fl01a8khyf1776y76rgqisxafky89cswa2fpsvxyn7"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.12))) -- cgit 1.4.1 From f23d5340c2f54c1449f853355b93cc19c5396210 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 3 Jun 2021 16:10:48 -0400 Subject: gnu: linux-libre 5.10: Update to 5.10.42. * gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.42. (linux-libre-5.10-pristine-source): Update hash. (deblob-scripts-5.10): Update hash. --- gnu/packages/linux.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index c2e2fc2df9..688924b9a9 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -372,15 +372,15 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; -(define-public linux-libre-5.10-version "5.10.41") +(define-public linux-libre-5.10-version "5.10.42") (define deblob-scripts-5.10 (linux-libre-deblob-scripts linux-libre-5.10-version (base32 "1rmnx1px4sizs2lq831yd2g9dyflg0vmykz3cv9443x2a2vwy81f") - (base32 "0hh27ccqimagr3aij7ygwikxw66y63sqwd0xlf49bhpjd090r9a7"))) + (base32 "1zsr02zmpx3968277sy8pfs2mdlgh86ifymwyj0r56wnhzf5q6hk"))) (define-public linux-libre-5.10-pristine-source (let ((version linux-libre-5.10-version) - (hash (base32 "0wb739q7dha8nxkd72x42k4in5nw633yw065ppwc8rq7x2fpa17n"))) + (hash (base32 "1r86v6q7ml7zv001f25w3h667nqqy39439s94vnqsyyn7g3jg84b"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.10))) -- cgit 1.4.1 From a75aa36e0a82826fbe6ca0be76c147d9dc7fa914 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 3 Jun 2021 16:11:05 -0400 Subject: gnu: linux-libre 5.4: Update to 5.4.124. * gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.124. (linux-libre-5.4-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 688924b9a9..234da30880 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -385,7 +385,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.10))) -(define-public linux-libre-5.4-version "5.4.123") +(define-public linux-libre-5.4-version "5.4.124") (define deblob-scripts-5.4 (linux-libre-deblob-scripts linux-libre-5.4-version @@ -393,7 +393,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1xghbbnaisjd0k1klbyn1p7r6r4x5a1bpmkm56a3gh2zvw4s7mj8"))) (define-public linux-libre-5.4-pristine-source (let ((version linux-libre-5.4-version) - (hash (base32 "1pi223dls52piw65s3v4ml23wdyy73xpbdvp511187b6zgzk7zlf"))) + (hash (base32 "10kxa1ng9w9xd2d5xh48fbhp1kri650p90nihrcpnb845gd9vwpp"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.4))) -- cgit 1.4.1 From 37ec3f3bec91b7b61cf835ef5152c99242183cbe Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 3 Jun 2021 16:17:06 -0400 Subject: gnu: linux-libre 4.19: Update to 4.19.193. * gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.193. (linux-libre-4.19-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 234da30880..07998d7125 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -398,7 +398,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.4))) -(define-public linux-libre-4.19-version "4.19.192") +(define-public linux-libre-4.19-version "4.19.193") (define deblob-scripts-4.19 (linux-libre-deblob-scripts linux-libre-4.19-version @@ -406,7 +406,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1jiaw0as1ippkrjdpd52657w5mz9qczg3y2hlra7m9k0xawwiqlf"))) (define-public linux-libre-4.19-pristine-source (let ((version linux-libre-4.19-version) - (hash (base32 "1680dz4wjg721a8lqwh6ijd90zcr2f3wzcvhwgn3shbwgjkwsk87"))) + (hash (base32 "17ci49ak5iw01kfkn3fcgncg9hm4j188417bxi3bnsq9il5ymhl4"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.19))) -- cgit 1.4.1 From ba85dff34479873ab5b7d0a53b78b6adf57d859d Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 3 Jun 2021 16:17:24 -0400 Subject: gnu: linux-libre 4.14: Update to 4.14.235. * gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.235. (linux-libre-4.14-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 07998d7125..6feca8ac8c 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -411,7 +411,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.19))) -(define-public linux-libre-4.14-version "4.14.234") +(define-public linux-libre-4.14-version "4.14.235") (define deblob-scripts-4.14 (linux-libre-deblob-scripts linux-libre-4.14-version @@ -419,7 +419,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1qij18inijj6c3ma8hv98yjagnzxdxyn134da9fd23ky8q6hbvky"))) (define-public linux-libre-4.14-pristine-source (let ((version linux-libre-4.14-version) - (hash (base32 "1mwqb9sq6qd9angl3xysdsrfpgppf46g3kiwg1svqgpgrx7cqn1b"))) + (hash (base32 "03k793hj294zf7jncs1h8zh5dh6xagkfvnydd9jadxvq2z8vvl8f"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.14))) -- cgit 1.4.1 From 6fa18e48a74ebee52955e414d9cf47f1d7599619 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 3 Jun 2021 16:17:42 -0400 Subject: gnu: linux-libre 4.9: Update to 4.9.271. * gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.271. (linux-libre-4.9-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 6feca8ac8c..31a59a3e15 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -424,7 +424,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.14))) -(define-public linux-libre-4.9-version "4.9.270") +(define-public linux-libre-4.9-version "4.9.271") (define deblob-scripts-4.9 (linux-libre-deblob-scripts linux-libre-4.9-version @@ -432,7 +432,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0fxajshb75siq39lj5h8xvhdj8lcmddkslwlyj65rhlwk6g2r4b2"))) (define-public linux-libre-4.9-pristine-source (let ((version linux-libre-4.9-version) - (hash (base32 "0ck5abzpla291gcxrxjindj5szgcvmb2fwfilvdnzc6pnqk00ay3"))) + (hash (base32 "1480miixphkf0b8w00m753ar7yp1rnl3zyr9wp4inngi2f90553r"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.9))) -- cgit 1.4.1 From 6b6b87f1c3c99dfa649aada8fca667f516df42da Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 3 Jun 2021 16:18:02 -0400 Subject: gnu: linux-libre 4.4: Update to 4.4.271. * gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.271. (linux-libre-4.4-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 31a59a3e15..c8ec310665 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -437,7 +437,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-4.9))) -(define-public linux-libre-4.4-version "4.4.270") +(define-public linux-libre-4.4-version "4.4.271") (define deblob-scripts-4.4 (linux-libre-deblob-scripts linux-libre-4.4-version @@ -445,7 +445,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0hhin1jpfkd6nwrb6xqxjzl3hdxy4pn8a15hy2d3d83yw6pflbsf"))) (define-public linux-libre-4.4-pristine-source (let ((version linux-libre-4.4-version) - (hash (base32 "1lz48gv1v3wvw9xvd3y9q4py7ii1g9fj4dwyvvjdzbipyw7s21pq"))) + (hash (base32 "0n5h2lv1p542a45pas3pi0vkhgrk096vwrps79a7v3a6c1q2dxx6"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.4))) -- cgit 1.4.1 From 6148172c3ea7b567ba94b344cb317305a0f6a7bc Mon Sep 17 00:00:00 2001 From: Raghav Gururajan Date: Thu, 3 Jun 2021 23:35:12 -0400 Subject: gnu: gajim-omemo: Update to 2.7.14. * gnu/packages/messaging.scm (gajim-omemo)[version]: Update to 2.7.14. --- gnu/packages/messaging.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index b326b68952..96cbf95fe9 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -1144,7 +1144,7 @@ and OpenPGP) and available in 29 languages.") (define-public gajim-omemo (package (name "gajim-omemo") - (version "2.7.13") + (version "2.7.14") (source (origin (method url-fetch/zipbomb) @@ -1153,7 +1153,7 @@ and OpenPGP) and available in 29 languages.") "https://ftp.gajim.org/plugins_releases/omemo_" version ".zip")) (sha256 - (base32 "1msr71rvik05wjpa2inpkadddad2rxaqbqcww5qrdrcz75pm8brn")))) + (base32 "0jmyjqfc4vimvq5vdqsvz25dsij6bh92alml8qnn59p5farnf86v")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) -- cgit 1.4.1 From f1bfd9f1948a5ff336d737c0614b9a30c2bb3097 Mon Sep 17 00:00:00 2001 From: Raghav Gururajan Date: Thu, 3 Jun 2021 23:46:04 -0400 Subject: gnu: remmina: Update to 1.4.18. * gnu/packages/vnc.scm (remmina)[version]: Update to 1.4.18. --- gnu/packages/vnc.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/vnc.scm b/gnu/packages/vnc.scm index a28cb512ab..4ad202b164 100644 --- a/gnu/packages/vnc.scm +++ b/gnu/packages/vnc.scm @@ -61,7 +61,7 @@ (define-public remmina (package (name "remmina") - (version "1.4.17") + (version "1.4.18") (source (origin (method git-fetch) @@ -71,7 +71,7 @@ (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0aww3j5g3770j8fcnc14j1g1g0452kj48jn4awxdj2yx7i58rc91")))) + (base32 "0s4ry2vacn4pw4whfkq6vgg7p5jsj4nyvx1h1cp60ihqg0grx99v")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; No target -- cgit 1.4.1 From 4f773bc22df4aebd340f1a4a7d05d357351925a1 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Fri, 4 Jun 2021 10:59:50 +0200 Subject: gnu: sbcl-nibbles: Update to 0.14-2.dad2524. * gnu/packages/lisp-xyz.scm (sbcl-nibbles): Update to 0.14-2.dad2524. --- gnu/packages/lisp-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index a692a373eb..04954647fc 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -2081,8 +2081,8 @@ than the body of the lambda.") (define-public sbcl-nibbles ;; No tagged release since 2018. - (let ((commit "8e6b9b42d9f69000f55e5c45ad974d9e376ffdbd") - (revision "1")) + (let ((commit "dad25240928d5cf8f7df69c4398244e03570bb35") + (revision "2")) (package (name "sbcl-nibbles") (version (git-version "0.14" revision commit)) @@ -2093,7 +2093,7 @@ than the body of the lambda.") (url "https://github.com/sharplispers/nibbles/") (commit commit))) (sha256 - (base32 "15qlsm82h36pjgvfnbzdg60l21qxbaii4d049jc5y0dn56y93amb")) + (base32 "0r6ljlpgjmkf87pmvdwzva8qj15bhznc3ylgcjjqyy4frbx9lygz")) (file-name (git-file-name "nibbles" version)))) (build-system asdf-build-system/sbcl) (native-inputs -- cgit 1.4.1 From d06ae0580848f9fafdbd4337aef58f80b537d662 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 4 Jun 2021 12:55:28 +0200 Subject: gnu: Add pigx-sars-cov2-ww. * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable. --- gnu/packages/bioinformatics.scm | 48 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 408c93bd34..6cfe82fc90 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10633,6 +10633,54 @@ and interactive quality reports. The pipeline is designed to work with UMI based methods.") (license license:gpl3+))) +(define-public pigx-sars-cov2-ww + (package + (name "pigx-sars-cov2-ww") + (version "0.0.1") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/BIMSBbioinfo/pigx_sarscov2_ww/" + "releases/download/v" version + "/pigx_sars-cov2-ww-" version ".tar.gz")) + (sha256 + (base32 + "1h1rfl3dyf7pid74xxgiyr4x1l5yj000wcz5crm1bdbaz8p7b7ic")))) + (build-system gnu-build-system) + (inputs + `(("bash-minimal" ,bash-minimal) + ("bwa" ,bwa) + ("ensembl-vep" ,ensembl-vep) + ("fastqc" ,fastqc) + ("kraken2" ,kraken2) + ("krona-tools" ,krona-tools) + ("lofreq" ,lofreq) + ("multiqc" ,multiqc) + ("prinseq" ,prinseq) + ("python-pyyaml" ,python-pyyaml) + ("python-wrapper" ,python-wrapper) + ("r-base64url" ,r-base64url) + ("r-dplyr" ,r-dplyr) + ("r-dt" ,r-dt) + ("r-ggplot2" ,r-ggplot2) + ("r-magrittr" ,r-magrittr) + ("r-minimal" ,r-minimal) + ("r-plotly" ,r-plotly) + ("r-qpcr" ,r-qpcr) + ("r-reshape2" ,r-reshape2) + ("r-rmarkdown" ,r-rmarkdown) + ("r-stringr" ,r-stringr) + ("r-tidyr" ,r-tidyr) + ("samtools" ,samtools) + ("snakemake" ,snakemake))) + (home-page "https://bioinformatics.mdc-berlin.de/pigx/") + (synopsis "Analysis pipeline for wastewater sequencing") + (description "PiGx SARS-CoV-2 is a pipeline for analysing data from +sequenced wastewater samples and identifying given variants-of-concern of +SARS-CoV-2. The pipeline can be used for continuous sampling. The output +report will provide an intuitive visual overview about the development of +variant abundance over time and location.") + (license license:gpl3+))) + (define-public pigx (package (name "pigx") -- cgit 1.4.1 From 8190f5bb97be4696b7ab6a88ff8397d5a28299e8 Mon Sep 17 00:00:00 2001 From: Maxime Devos Date: Tue, 25 May 2021 15:20:34 +0200 Subject: gnu: ci: Use 'inputs' in build phases instead of '%build-inputs'. In build phases, the former is preferred. * gnu/packages/ci.scm (cuirass)[arguments]<#:phases>{wrap-program}: Use 'inputs' argument instead of '%build-inputs'. Signed-off-by: Mathieu Othacehe --- gnu/packages/ci.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm index 0a5f3afbd2..58fdefb429 100644 --- a/gnu/packages/ci.scm +++ b/gnu/packages/ci.scm @@ -141,7 +141,7 @@ (guix (assoc-ref inputs "guix")) (deps (list avahi gcrypt json zmq squee git bytes fibers zlib matd tls mail guix)) - (guile (assoc-ref %build-inputs "guile")) + (guile (assoc-ref inputs "guile")) (effective (read-line (open-pipe* OPEN_READ -- cgit 1.4.1 From f5f78d0d0227e80d00cafa1861a8a72a180de074 Mon Sep 17 00:00:00 2001 From: Maxime Devos Date: Tue, 25 May 2021 15:22:24 +0200 Subject: gnu: smalltalk: Use 'inputs' in phases instead of '%build-inputs'. In build phases, the former is preferred. * gnu/packages/smalltalk.scm (smalltalk)[arguments]<#:phases>{fix-libc}: Use 'inputs' argument instead of '%build-inputs'. Signed-off-by: Mathieu Othacehe --- gnu/packages/smalltalk.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/smalltalk.scm b/gnu/packages/smalltalk.scm index ea1798ac13..a572570b13 100644 --- a/gnu/packages/smalltalk.scm +++ b/gnu/packages/smalltalk.scm @@ -102,8 +102,8 @@ (find-files "doc" "\\.info")) #t)) (add-before 'configure 'fix-libc - (lambda _ - (let ((libc (assoc-ref %build-inputs "libc"))) + (lambda* (#:key inputs #:allow-other-keys) + (let ((libc (assoc-ref inputs "libc"))) (substitute* "libc.la.in" (("@LIBC_SO_NAME@") "libc.so") (("@LIBC_SO_DIR@") (string-append libc "/lib")))) -- cgit 1.4.1 From 09be86744f296b54680755fd873c22602b739ad8 Mon Sep 17 00:00:00 2001 From: Maxime Devos Date: Tue, 25 May 2021 15:41:15 +0200 Subject: gnu: neovim: Use 'inputs' in phases instead of '%build-inputs'. In build phases, the former is preferred. * gnu/packages/vim.scm (neovim)[arguments]<#:phases>{set-lua-path}: Use 'inputs' argument instead of '%build-inputs'. Signed-off-by: Mathieu Othacehe --- gnu/packages/vim.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index ebab790ee0..238c25d486 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -695,7 +695,7 @@ are detected, the user is notified."))) (lambda (prefix) (let ((path (string-append prefix "/share/lua/" lua-version))) (string-append path "/?.lua;" path "/?/?.lua")))) - (lua-inputs (map (cute assoc-ref %build-inputs <>) + (lua-inputs (map (cute assoc-ref inputs <>) '("lua" "lua-luv" "lua-lpeg" -- cgit 1.4.1 From 156b8f9cd2bbbb9580dd01a30a9891fddf79362c Mon Sep 17 00:00:00 2001 From: Maxime Devos Date: Tue, 25 May 2021 15:49:05 +0200 Subject: gnu: qemacs: Use 'native-inputs' instead of '%build-inputs'. In build phases, the former (or 'inputs', as appropriate) is preferred. * gnu/packages/text-editors.scm (qemacs)[arguments]<#:phases>{install-extra-documentation}: Use 'native-inputs' argument instead of '%build-inputs'. Signed-off-by: Mathieu Othacehe --- gnu/packages/text-editors.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm index eb557cb80a..193b6ba702 100644 --- a/gnu/packages/text-editors.scm +++ b/gnu/packages/text-editors.scm @@ -524,13 +524,14 @@ OpenBSD team.") #t))) (add-after 'install 'install-extra-documentation ;; Install sample configuration file, Info, and HTML manual. - (lambda* (#:key outputs #:allow-other-keys) + (lambda* (#:key native-inputs inputs outputs #:allow-other-keys) (let* ((share (string-append (assoc-ref outputs "out") "/share")) (doc (string-append share "/doc/" ,name "-" ,version)) (html (string-append share "/html")) (info (string-append share "/info")) - (makeinfo (string-append (assoc-ref %build-inputs "texinfo") - "/bin/makeinfo"))) + (makeinfo (string-append + (assoc-ref (or native-inputs inputs) "texinfo") + "/bin/makeinfo"))) ;; First fix Texinfo documentation, create appropriate ;; directories, then generate Info and HTML files there. (substitute* "qe-doc.texi" -- cgit 1.4.1 From 4a600ada5a79fbf3c04011452593d2ee62d50a27 Mon Sep 17 00:00:00 2001 From: Maxime Devos Date: Tue, 25 May 2021 15:58:33 +0200 Subject: gnu: ding: Use 'inputs' in build phases instead of '%build-inputs'. In build phases, the former is preferred. * gnu/packages/dictionaries.scm (ding)[arguments]<#:phases>{install}: Use 'inputs' argument instead of '%build-inputs'. Signed-off-by: Mathieu Othacehe --- gnu/packages/dictionaries.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/dictionaries.scm b/gnu/packages/dictionaries.scm index 30995bf986..2b1f7f0ad1 100644 --- a/gnu/packages/dictionaries.scm +++ b/gnu/packages/dictionaries.scm @@ -175,11 +175,10 @@ work, such as sentence length and other readability measures.") (delete 'build) (delete 'check) (replace 'install - (lambda _ + (lambda* (#:key inputs #:allow-other-keys) (let ((bindir (string-append (assoc-ref %outputs "out") "/bin")) - (wish (string-append - (assoc-ref %build-inputs "tk") + (wish (string-append (assoc-ref inputs "tk") "/bin/wish8.6")) (sharedir (string-append (assoc-ref %outputs "out") -- cgit 1.4.1 From 961a8f130275dc18cc8e602e0b2ab08b780eb46f Mon Sep 17 00:00:00 2001 From: Maxime Devos Date: Mon, 31 May 2021 13:54:17 +0200 Subject: gnu: smalltalk: Move 'zip' from 'inputs' to 'native-inputs'. The 'zip' package is not in the references of 'smalltalk'. As such, it probably should be a native input, not a regular input. This can be confirmed by trying to cross-compile the 'smalltalk' package, without this commit. The configure script will ask to install InfoZIP. * gnu/packages/smalltalk.scm (smalltalk)[inputs]{zip}: Move to ... (smalltalk)[native-inputs]{zip} ... here. Signed-off-by: Mathieu Othacehe --- gnu/packages/smalltalk.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/smalltalk.scm b/gnu/packages/smalltalk.scm index a572570b13..af4b7642ff 100644 --- a/gnu/packages/smalltalk.scm +++ b/gnu/packages/smalltalk.scm @@ -64,7 +64,8 @@ ;; XXX: To be removed with the next release of Smalltalk. ("autoconf" ,autoconf) ("automake" ,automake) - ("libtool" ,libtool))) + ("libtool" ,libtool) + ("zip" ,zip))) ;; TODO: These optional dependencies raise the closure size to ~1 GiB ;; from the current ~100 MiB, although some of them might be very ;; useful for end users: @@ -81,8 +82,7 @@ ("libffi" ,libffi) ("libltdl" ,libltdl) ("libsigsegv" ,libsigsegv) - ("lightning" ,lightning) - ("zip" ,zip))) + ("lightning" ,lightning))) (arguments `(#:phases (modify-phases %standard-phases -- cgit 1.4.1 From f50a88c1fa2e07a668ee87402a5462267d1baf12 Mon Sep 17 00:00:00 2001 From: Maxime Devos Date: Mon, 31 May 2021 14:07:50 +0200 Subject: gnu: smalltalk: Find glibc even when cross-compiling. glibc is named "cross-libc" instead of "libc" when cross-compiling. Smalltalk still fails to cross-compile though. * gnu/packages/smalltalk.scm (smalltalk)[arguments]{phases}<#:fix-libc>: Also search for "cross-libc" instead of only "libc" in 'inputs'. Signed-off-by: Mathieu Othacehe --- gnu/packages/smalltalk.scm | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/smalltalk.scm b/gnu/packages/smalltalk.scm index af4b7642ff..26f7ab2c76 100644 --- a/gnu/packages/smalltalk.scm +++ b/gnu/packages/smalltalk.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2016 Nicolas Goaziou ;;; Copyright © 2016 Ludovic Courtès ;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2021 Maxime Devos ;;; ;;; This file is part of GNU Guix. ;;; @@ -103,7 +104,11 @@ #t)) (add-before 'configure 'fix-libc (lambda* (#:key inputs #:allow-other-keys) - (let ((libc (assoc-ref inputs "libc"))) + (let ((libc (or (assoc-ref inputs "libc") + ;; When cross-compiling, the input + ;; is named "cross-libc" instead of + ;; simply "libc". + (assoc-ref inputs "cross-libc")))) (substitute* "libc.la.in" (("@LIBC_SO_NAME@") "libc.so") (("@LIBC_SO_DIR@") (string-append libc "/lib")))) -- cgit 1.4.1 From 1ea00cceefa4a2e3832423bb80180256531ff589 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Fri, 4 Jun 2021 13:49:01 +0200 Subject: gnu: wfview: Update to 1.0. * gnu/packages/radio.scm (wfview): Update to 1.0. --- gnu/packages/radio.scm | 111 ++++++++++++++++++++++++------------------------- 1 file changed, 54 insertions(+), 57 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index c0b1ed13e0..6a9d2db084 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -1856,61 +1856,58 @@ software-defined radio receivers.") (license license:gpl3+))) (define-public wfview - ;; No tagged release, use commit directly. - (let ((commit "274e905d214a7360e8cf2dd0421dbe3712a0ddcc") - (revision "1")) - (package - (name "wfview") - (version (git-version "20210511" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://gitlab.com/eliggett/wfview") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1dmxn15xs63wx1y4mh1mlv8qc1xz32vgbyl3rk82gf6knw518svp")))) - (build-system qt-build-system) - (inputs - `(("qcustomplot" ,qcustomplot) - ("qtbase" ,qtbase) - ("qtmultimedia" ,qtmultimedia) - ("qtserialport" ,qtserialport))) - (arguments - `(#:tests? #f ; No test suite. - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-paths - (lambda* (#:key outputs #:allow-other-keys) - (substitute* "wfview.pro" - (("\\.\\./wfview/") - "../")) - (substitute* '("wfmain.cpp") - (("/usr/share") - (string-append (assoc-ref outputs "out") "/share"))))) - (replace 'configure - (lambda _ - (mkdir-p "build") - (chdir "build") - (invoke "qmake" "../wfview.pro"))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out"))) - (install-file "wfview" - (string-append out "/bin")) - (install-file "wfview.png" - (string-append out "/share/pixmaps")) - (install-file "wfview.desktop" - (string-append out "/share/applications")) - (let ((dir (string-append - out "/share/wfview/stylesheets/qdarkstyle"))) - (mkdir-p dir) - (copy-recursively "qdarkstyle" dir)))))))) - (home-page "https://wfview.org/") - (synopsis "Software to control Icom radios") - (description - "@code{wfview} is a program to control modern Icom radios and view the + (package + (name "wfview") + (version "1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/eliggett/wfview") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "16a9afm0nkqx4pzwfxisspybimhqdyr3yjpr7ac7wgpp3520ikzi")))) + (build-system qt-build-system) + (inputs + `(("qcustomplot" ,qcustomplot) + ("qtbase" ,qtbase) + ("qtmultimedia" ,qtmultimedia) + ("qtserialport" ,qtserialport))) + (arguments + `(#:tests? #f ; No test suite. + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-paths + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "wfview.pro" + (("\\.\\./wfview/") + "../")) + (substitute* '("wfmain.cpp") + (("/usr/share") + (string-append (assoc-ref outputs "out") "/share"))))) + (replace 'configure + (lambda _ + (mkdir-p "build") + (chdir "build") + (invoke "qmake" "../wfview.pro"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out"))) + (install-file "wfview" + (string-append out "/bin")) + (install-file "wfview.png" + (string-append out "/share/pixmaps")) + (install-file "wfview.desktop" + (string-append out "/share/applications")) + (let ((dir (string-append + out "/share/wfview/stylesheets/qdarkstyle"))) + (mkdir-p dir) + (copy-recursively "qdarkstyle" dir)))))))) + (home-page "https://wfview.org/") + (synopsis "Software to control Icom radios") + (description + "@code{wfview} is a program to control modern Icom radios and view the spectrum waterfall. It supports at least the following models: @itemize @@ -1921,8 +1918,8 @@ spectrum waterfall. It supports at least the following models: @item IC-7851 @item IC-9700 @end itemize\n") - (license (list license:expat - license:gpl3))))) + (license (list license:expat + license:gpl3)))) (define-public minimodem (package -- cgit 1.4.1 From bb934ab79d014198404c3678e8a278c1b334b6fb Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 4 Jun 2021 14:50:59 +0200 Subject: gnu: python-pydantic: Update to 1.8.2. * gnu/packages/python-xyz.scm (python-pydantic): Update to 1.8.2. [arguments]: Disable some new tests. [native-inputs]: Add PYTHON-PYTEST-MOCK. [propagated-inputs]: Add PYTHON-TYPING-EXTENSIONS. --- gnu/packages/python-xyz.scm | 31 +++++++++++++++++++++++-------- 1 file changed, 23 insertions(+), 8 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a5cc04edaf..f21fb53cc5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4527,7 +4527,7 @@ which can produce feeds in RSS 2.0, RSS 0.91, and Atom formats.") (define-public python-pydantic (package (name "python-pydantic") - (version "1.6.1") + (version "1.8.2") (source (origin (method git-fetch) @@ -4536,24 +4536,39 @@ which can produce feeds in RSS 2.0, RSS 0.91, and Atom formats.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1380s9k77g6q15by9fkxndczjk89q6xpz09jdrqip535xws2z3j8")))) + (base32 "06162dss6mvi7wiy2lzxwvzajwxgy8b2fyym7qipaj7zibcqalq2")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases - ;; Reported upstream: - ;; . - ;; Disable the faulty test as the fix is unclear. (add-before 'check 'disable-test (lambda _ + ;; Reported upstream: + ;; . + ;; Disable the faulty test as the fix is unclear. (substitute* "tests/test_validators.py" (("test_assert_raises_validation_error") "_test_assert_raises_validation_error")) - #t)) + + ;; These fail because of . + ;; Remove after Python has been upgraded to >= 3.9. + (substitute* "tests/test_generics.py" + (("assert replace_types\\(Callable, \\{T: int\\}\\) == Callable") + "")) + (substitute* "tests/test_schema.py" + (("test_unenforced_constraints_schema") + "_test_unenforced_constraints_schema")) + + ;; Disable tests for the Hypothesis plugin because it is tricky + ;; to configure in the build container. + (delete-file "tests/test_hypothesis_plugin.py"))) (replace 'check - (lambda _ (invoke "pytest" "-vv" "tests")))))) + (lambda _ (invoke "pytest" "-vv")))))) (native-inputs - `(("python-pytest" ,python-pytest))) + `(("python-pytest" ,python-pytest) + ("python-pytest-mock" ,python-pytest-mock))) + (propagated-inputs + `(("python-typing-extensions" ,python-typing-extensions))) (home-page "https://github.com/samuelcolvin/pydantic") (synopsis "Python data validation and settings management") (description -- cgit 1.4.1 From 29745d23b87529275a677ee7962b0405594e84db Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Wed, 19 May 2021 20:44:12 +1000 Subject: gnu: Use define-public in (gnu packages xiph). * gnu/pakages/xiph.scm: Replace all manual package #:exports with define-public. Signed-off-by: Mathieu Othacehe --- gnu/packages/xiph.scm | 39 ++++++++++++++------------------------- 1 file changed, 14 insertions(+), 25 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xiph.scm b/gnu/packages/xiph.scm index 8ed0e518a7..fbbcbd6e61 100644 --- a/gnu/packages/xiph.scm +++ b/gnu/packages/xiph.scm @@ -10,6 +10,7 @@ ;;; Copyright © 2018–2021 Tobias Geerinckx-Rice ;;; Copyright © 2018 Leo Famulari ;;; Copyright © 2020 Vincent Legoll +;;; Copyright © 2021 Brendan Tildesley ;;; ;;; This file is part of GNU Guix. ;;; @@ -44,21 +45,9 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) - #:use-module (guix build-system gnu) - #:export (libogg - libvorbis - libtheora - speex - speexdsp - ao - flac - libkate - vorbis-tools - opus - opusfile - opus-tools)) + #:use-module (guix build-system gnu)) -(define libogg +(define-public libogg (package (name "libogg") (version "1.3.4") @@ -83,7 +72,7 @@ periodic timestamps for seeking.") "See COPYING in the distribution.")) (home-page "https://xiph.org/ogg/"))) -(define libvorbis +(define-public libvorbis (package (name "libvorbis") (version "1.3.7") @@ -110,7 +99,7 @@ polyphonic) audio and music at fixed and variable bitrates from 16 to "See COPYING in the distribution.")) (home-page "https://xiph.org/vorbis/"))) -(define libtheora +(define-public libtheora (package (name "libtheora") (version "1.1.1") @@ -136,7 +125,7 @@ compressed video format.") (license license:bsd-3) (home-page "https://xiph.org/theora/"))) -(define speex +(define-public speex (package (name "speex") (version "1.2.0") @@ -167,7 +156,7 @@ stereo encoding, and voice activity detection.") (license (license:non-copyleft "file://COPYING" "See COPYING in the distribution.")))) -(define speexdsp +(define-public speexdsp (package (name "speexdsp") (version "1.2.0") @@ -193,7 +182,7 @@ work from the @code{speex} codec.") (license (license:non-copyleft "file://COPYING" "See COPYING in the distribution.")))) -(define ao +(define-public ao (package (name "ao") ;; We need a few commits on top of 1.2.2 to fix CVE-2017-11548. @@ -249,7 +238,7 @@ It currently supports: (properties '((cpe-name . "libao"))) (home-page "https://www.xiph.org/ao/"))) -(define flac +(define-public flac (package (name "flac") (version "1.3.3") @@ -273,7 +262,7 @@ meaning that audio is compressed in FLAC without any loss in quality.") "See COPYING in the distribution.")) ; and LGPL and GPL (home-page "https://xiph.org/flac/"))) -(define libkate +(define-public libkate (package (name "libkate") (version "0.4.1") @@ -309,7 +298,7 @@ Kate stream.") (license license:bsd-3) (home-page "https://wiki.xiph.org/OggKate"))) -(define vorbis-tools +(define-public vorbis-tools (package (name "vorbis-tools") (version "1.4.2") @@ -343,7 +332,7 @@ ogginfo, to obtain information (tags, bitrate, length, etc.) about (license license:gpl2) (home-page "https://xiph.org/vorbis/"))) -(define opus +(define-public opus (package (name "opus") (version "1.3.1") @@ -367,7 +356,7 @@ incorporated technology from Skype's SILK codec and Xiph.Org's CELT codec.") (license license:bsd-3) (home-page "https://www.opus-codec.org"))) -(define opus-tools +(define-public opus-tools (package (name "opus-tools") (version "0.2") @@ -403,7 +392,7 @@ decoding .opus files.") (license license:bsd-3) (home-page "https://www.opus-codec.org"))) -(define opusfile +(define-public opusfile (package (name "opusfile") (version "0.12") -- cgit 1.4.1 From e639da604f987bae41f1c00bf0726331937a925f Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 1 Jun 2021 10:20:10 +0200 Subject: gnu: python-anndata: Update to 0.7.6. * gnu/packages/python-xyz.scm (python-anndata): Update to 0.7.6. --- gnu/packages/python-xyz.scm | 35 +++++++++++++++++++++++++---------- 1 file changed, 25 insertions(+), 10 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f21fb53cc5..f3404178ba 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21061,28 +21061,41 @@ N-dimensional arrays for Python.") (define-public python-anndata (package (name "python-anndata") - (version "0.7.1") + (version "0.7.6") (source (origin (method url-fetch) (uri (pypi-uri "anndata" version)) (sha256 (base32 - "0rnfbpr55j1a1bi2kd4mz444741hrn74kz90h5rnjr59jmpfnh09")))) + "1ch8yp0xmag6z0kl01pljm35lbbwax7lrimfhiclpkd4m6xngk53")))) (build-system python-build-system) (arguments - `(#:phases + `(#:tests? #f ; The tarball from PyPi doesn't include tests. + #:phases (modify-phases %standard-phases - (add-after 'unpack 'delete-inconvenient-tests - (lambda _ - ;; This test depends on python-scikit-learn. - (delete-file "anndata/tests/test_inplace_subset.py") - #t)) (delete 'check) - (add-after 'install 'check + (add-before 'build 'relax-dependency-requirements + (lambda _ + ;; We need to upgrade python-pandas to avoid + ;; https://github.com/pandas-dev/pandas/issues/35446 + (substitute* "pyproject.toml" + (("pandas>=1.1.1") "pandas>=1.0.5")))) + (replace 'build + (lambda _ + ;; ZIP does not support timestamps before 1980. + (setenv "SOURCE_DATE_EPOCH" "315532800") + (invoke "flit" "build"))) + (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys) (add-installed-pythonpath inputs outputs) - (invoke "pytest" "-vv")))))) + (let ((out (assoc-ref outputs "out"))) + (for-each (lambda (wheel) + (format #true wheel) + (invoke "python" "-m" "pip" "install" + wheel (string-append "--prefix=" out))) + (find-files "dist" "\\.whl$"))) + #t))))) (propagated-inputs `(("python-h5py" ,python-h5py) ("python-importlib-metadata" ,python-importlib-metadata) @@ -21095,6 +21108,8 @@ N-dimensional arrays for Python.") (native-inputs `(("python-joblib" ,python-joblib) ("python-pytest" ,python-pytest) + ("python-toml" ,python-toml) + ("python-flit" ,python-flit) ("python-setuptools-scm" ,python-setuptools-scm))) (home-page "https://github.com/theislab/anndata") (synopsis "Annotated data for data analysis pipelines") -- cgit 1.4.1 From 7382aa00b82860762bc326dec6b45f8cd2161327 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 1 Jun 2021 10:25:12 +0200 Subject: gnu: python-scanpy: Update to 1.7.2. * gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2. --- gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++---- 1 file changed, 21 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6cfe82fc90..c1cfabc27f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -122,6 +122,7 @@ #:use-module (gnu packages popt) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) + #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) #:use-module (gnu packages python-compression) #:use-module (gnu packages python-science) @@ -11328,14 +11329,14 @@ implementation differs in these ways: (define-public python-scanpy (package (name "python-scanpy") - (version "1.4.6") + (version "1.7.2") (source (origin (method url-fetch) (uri (pypi-uri "scanpy" version)) (sha256 (base32 - "0s2b6cvaigx4wzw3850qb93sjwwxbzh22kpbp498zklc5rjpbz4l")))) + "0c66adnfizsyk0h8bv2yhmay876z0klpxwpn4z6m71wly7yplpmd")))) (build-system python-build-system) (arguments `(#:phases @@ -11346,12 +11347,25 @@ implementation differs in these ways: (delete-file-recursively "scanpy/tests/notebooks") (delete-file "scanpy/tests/test_clustering.py") (delete-file "scanpy/tests/test_datasets.py") + (delete-file "scanpy/tests/test_highly_variable_genes.py") ;; TODO: I can't get the plotting tests to work, even with Xvfb. (delete-file "scanpy/tests/test_plotting.py") (delete-file "scanpy/tests/test_preprocessing.py") (delete-file "scanpy/tests/test_read_10x.py") + ;; The following tests need anndata.tests, which aren't included + ;; in the final python-anndata package. + (delete-file "scanpy/tests/test_combat.py") + (delete-file "scanpy/tests/test_embedding_plots.py") + (delete-file "scanpy/tests/test_normalization.py") + (delete-file "scanpy/tests/test_pca.py") + (delete-file "scanpy/tests/external/test_scrublet.py") + + ;; The following tests requires 'scanorama', which isn't + ;; packaged yet. + (delete-file "scanpy/tests/external/test_scanorama_integrate.py") + (setenv "PYTHONPATH" (string-append (getcwd) ":" (getenv "PYTHONPATH"))) @@ -11376,11 +11390,14 @@ implementation differs in these ways: ("python-seaborn" ,python-seaborn) ("python-statsmodels" ,python-statsmodels) ("python-tables" ,python-tables) + ("python-pytoml" ,python-pytoml) ("python-tqdm" ,python-tqdm) ("python-umap-learn" ,python-umap-learn))) (native-inputs - `(("python-pytest" ,python-pytest) - ("python-setuptools-scm" ,python-setuptools-scm))) + `(("python-leidenalg" ,python-leidenalg) + ("python-pytest" ,python-pytest) + ("python-setuptools-scm" ,python-setuptools-scm) + ("python-sinfo" ,python-sinfo))) (home-page "https://github.com/theislab/scanpy") (synopsis "Single-Cell Analysis in Python.") (description "Scanpy is a scalable toolkit for analyzing single-cell gene -- cgit 1.4.1 From f98837a6baca957098d073d5bb8d440ddf9ffefb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 00:33:00 +0200 Subject: gnu: pigx-rnaseq: Update to 0.0.13. * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.13. [arguments]: Remove obsolete substitutions. [inputs]: Remove fastqc and trim-galore; add hisat2 and fastp. --- gnu/packages/bioinformatics.scm | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c1cfabc27f..dab097381a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10355,7 +10355,7 @@ once. This package provides tools to perform Drop-seq analyses.") (define-public pigx-rnaseq (package (name "pigx-rnaseq") - (version "0.0.10") + (version "0.0.13") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/" @@ -10363,7 +10363,7 @@ once. This package provides tools to perform Drop-seq analyses.") "/pigx_rnaseq-" version ".tar.gz")) (sha256 (base32 - "0z3hr120wk2vrlmlpz1vp3n9wy3rq4y2mnzh2vf08qgqn2xfdwcw")))) + "0z9zid2c8q16lfzlnjd63nparknhv31qgv4h79algmvhkakm2pgk")))) (build-system gnu-build-system) (arguments `(#:parallel-tests? #f ; not supported @@ -10373,19 +10373,17 @@ once. This package provides tools to perform Drop-seq analyses.") (add-after 'unpack 'disable-resource-intensive-test (lambda _ (substitute* "Makefile.in" - (("(^ tests/test_trim_galore/test.sh).*" _ m) m) (("^ tests/test_multiqc/test.sh") "") - (("^ test.sh") "")) - #t))))) + (("^ test.sh") ""))))))) (inputs `(("coreutils" ,coreutils) ("sed" ,sed) ("gzip" ,gzip) ("snakemake" ,snakemake) - ("fastqc" ,fastqc) ("multiqc" ,multiqc) ("star" ,star-for-pigx) - ("trim-galore" ,trim-galore) + ("hisat2" ,hisat2) + ("fastp" ,fastp) ("htseq" ,htseq) ("samtools" ,samtools) ("r-minimal" ,r-minimal) -- cgit 1.4.1 From d5c08f11e1c17a10625d413b1aa7350218f61dfc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 4 Jun 2021 16:07:03 +0200 Subject: gnu: Add r-aplot. * gnu/packages/cran.scm (r-aplot): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ab21707d92..eee883a0c7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17673,6 +17673,33 @@ making it possible to download files over HTTPS across platforms. The external dependencies. This package has is implemented purely in R.") (license license:gpl2))) +(define-public r-aplot + (package + (name "r-aplot") + (version "0.0.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "aplot" version)) + (sha256 + (base32 + "08kqrm9r57l8zgij897wpp428l4i50qfhp7y78r3pk5pjz37bsan")))) + (properties `((upstream-name . "aplot"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-magrittr" ,r-magrittr) + ("r-patchwork" ,r-patchwork))) + (home-page "https://github.com/YuLab-SMU/aplot") + (synopsis "Decorate a ggplot with associated information") + (description + "Users may want to align plots with associated information that requires +axes to be exactly matched in subplots, e.g. hierarchical clustering with a +heatmap. This package provides utilities to align associated subplots to a +main plot at different sides (left, right, top and bottom) with axes exactly +matched.") + (license license:artistic2.0))) + (define-public r-rex (package (name "r-rex") -- cgit 1.4.1 From 41ea9bed977d9974a0a48af9b19cd0254a9cc29d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 4 Jun 2021 16:07:10 +0200 Subject: gnu: Add r-ggnewscale. * gnu/packages/cran.scm (r-ggnewscale): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index eee883a0c7..b3adc65195 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17700,6 +17700,27 @@ main plot at different sides (left, right, top and bottom) with axes exactly matched.") (license license:artistic2.0))) +(define-public r-ggnewscale + (package + (name "r-ggnewscale") + (version "0.4.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggnewscale" version)) + (sha256 + (base32 + "1hjysfagd2lqy8yivqq9q7l6hbvyq8kasw3zqh5fk9xn18ikc702")))) + (properties `((upstream-name . "ggnewscale"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2))) + (home-page "https://cran.r-project.org/package=ggnewscale") + (synopsis "Multiple fill and color scales in ggplot2") + (description + "This package lets you use multiple fill and color scales in ggplot2.") + (license license:gpl3))) + (define-public r-rex (package (name "r-rex") -- cgit 1.4.1 From b71f21339ff0c9ded5f6dc3e15d0ea7ab55f6578 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 4 Jun 2021 16:07:17 +0200 Subject: gnu: Add r-ggpointdensity. * gnu/packages/cran.scm (r-ggpointdensity): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b3adc65195..cf24d0fb37 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17721,6 +17721,31 @@ matched.") "This package lets you use multiple fill and color scales in ggplot2.") (license license:gpl3))) +(define-public r-ggpointdensity + (package + (name "r-ggpointdensity") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggpointdensity" version)) + (sha256 + (base32 + "0c9a14j3b0hvamqylhzldw2hjdxmfbllwahjkf3gg2rw337ld9iy")))) + (properties + `((upstream-name . "ggpointdensity"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2))) + (home-page "https://github.com/LKremer/ggpointdensity") + (synopsis "Cross between a 2D density plot and a scatter plot") + (description + "This package provides a cross between a 2D density plot and a scatter +plot, implemented as a ggplot2 @code{geom}. Points in the scatter plot are +colored by the number of neighboring points. This is useful to visualize the +2D-distribution of points in case of overplotting.") + (license license:gpl3))) + (define-public r-rex (package (name "r-rex") -- cgit 1.4.1 From ab66c9a2cda10edfbf5f2f11481d4d2d1d604bf5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 4 Jun 2021 16:07:23 +0200 Subject: gnu: Add r-arrow. * gnu/packages/cran.scm (r-arrow): New variable. --- gnu/packages/cran.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index cf24d0fb37..2e7e9041c6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17746,6 +17746,43 @@ colored by the number of neighboring points. This is useful to visualize the 2D-distribution of points in case of overplotting.") (license license:gpl3))) +(define-public r-arrow + (package + (name "r-arrow") + (version "4.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "arrow" version)) + (sha256 + (base32 + "19kzfjxp90ybi1px3r93mfx59nqmnagxr4g73y7iby5blwl1bblc")))) + (properties `((upstream-name . "arrow"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-bit64" ,r-bit64) + ("r-cpp11" ,r-cpp11) + ("r-purrr" ,r-purrr) + ("r-r6" ,r-r6) + ("r-rlang" ,r-rlang) + ("r-tidyselect" ,r-tidyselect) + ("r-vctrs" ,r-vctrs))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) + (home-page "https://github.com/apache/arrow/") + (synopsis "R integration to Apache Arrow") + (description + "Apache Arrow is a cross-language development platform for in-memory +data. It specifies a standardized language-independent columnar memory format +for flat and hierarchical data, organized for efficient analytic operations on +modern hardware. This package provides an R interface to the Arrow C++ +library.") + (license license:asl2.0))) + (define-public r-rex (package (name "r-rex") -- cgit 1.4.1 From ce99b4da633c79352dfaf5ae2c1c2bab3d773908 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 01:46:54 +0200 Subject: gnu: Add r-restfulr. * gnu/packages/bioconductor.scm (r-restfulr): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7a584e4211..56906bddbd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3959,6 +3959,33 @@ Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.") (license license:expat))) +;; This is a CRAN package, but it depends on a Bioconductor package: +;; s4vectors. +(define-public r-restfulr + (package + (name "r-restfulr") + (version "0.0.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "restfulr" version)) + (sha256 + (base32 + "1dk45mzrr6ka92yjz7hfhkj12kpx1wg4szv1h1mg80mgga4ganbv")))) + (properties `((upstream-name . "restfulr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcurl" ,r-rcurl) + ("r-rjson" ,r-rjson) + ("r-s4vectors" ,r-s4vectors) + ("r-xml" ,r-xml) + ("r-yaml" ,r-yaml))) + (home-page "https://cran.r-project.org/package=restfulr") + (synopsis "R interface to RESTful web services") + (description + "This package models a RESTful service as if it were a nested R list.") + (license license:artistic2.0))) + (define-public r-rtracklayer (package (name "r-rtracklayer") -- cgit 1.4.1 From efefb2be3a3992dacbe8a1c9ed210fb4a80331ab Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 01:47:08 +0200 Subject: gnu: Add r-trajectoryutils. * gnu/packages/bioconductor.scm (r-trajectoryutils): New variable. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 56906bddbd..dab37d59de 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4157,6 +4157,36 @@ purposes. The package also contains legacy support for early single-end, ungapped alignment formats.") (license license:artistic2.0))) +(define-public r-trajectoryutils + (package + (name "r-trajectoryutils") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "TrajectoryUtils" version)) + (sha256 + (base32 + "1b7mg3ypp1ay98cav47h9vn692lx0n9b5b0hpansgnkr5prb823b")))) + (properties + `((upstream-name . "TrajectoryUtils"))) + (build-system r-build-system) + (propagated-inputs + `(("r-igraph" ,r-igraph) + ("r-matrix" ,r-matrix) + ("r-s4vectors" ,r-s4vectors) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/TrajectoryUtils") + (synopsis "Single-cell trajectory analysis utilities") + (description + "This package implements low-level utilities for single-cell trajectory +analysis, primarily intended for re-use inside higher-level packages. It +includes a function to create a cluster-level minimum spanning tree and data +structures to hold pseudotime inference results.") + (license license:gpl3))) + (define-public r-slingshot (package (name "r-slingshot") -- cgit 1.4.1 From fd4fa40ac4cf342e737a95766e7ca28de64f2294 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 01:47:24 +0200 Subject: gnu: Add r-scaledmatrix. * gnu/packages/bioconductor.scm (r-scaledmatrix): New variable. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dab37d59de..0302c74ca1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5647,6 +5647,34 @@ to search for all neighbors within a given distance. Parallelization is achieved for all methods using the BiocParallel framework.") (license license:gpl3))) +(define-public r-scaledmatrix + (package + (name "r-scaledmatrix") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ScaledMatrix" version)) + (sha256 + (base32 + "1j96fvw1waqxbv5c8myfmhsidq370z03yz13yqmrs4nn1rpn1a06")))) + (properties `((upstream-name . "ScaledMatrix"))) + (build-system r-build-system) + (propagated-inputs + `(("r-delayedarray" ,r-delayedarray) + ("r-matrix" ,r-matrix) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/LTLA/ScaledMatrix") + (synopsis "Create a DelayedMatrix of scaled and centered values") + (description + "This package provides delayed computation of a matrix of scaled and +centered values. The result is equivalent to using the @code{scale} function +but avoids explicit realization of a dense matrix during block processing. +This permits greater efficiency in common operations, most notably matrix +multiplication.") + (license license:gpl3))) + (define-public r-biocsingular (package (name "r-biocsingular") -- cgit 1.4.1 From ab4a91b25280f4e57f007e5b3cea72a30091f647 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 01:47:39 +0200 Subject: gnu: Add r-treeio. * gnu/packages/bioconductor.scm (r-treeio): New variable. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0302c74ca1..10463b29c2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5675,6 +5675,38 @@ This permits greater efficiency in common operations, most notably matrix multiplication.") (license license:gpl3))) +(define-public r-treeio + (package + (name "r-treeio") + (version "1.16.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "treeio" version)) + (sha256 + (base32 + "0ypl4h80m08sf7r4zfvqgvpsz46x15wvcl1idq5pd813bp1w2sws")))) + (properties `((upstream-name . "treeio"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-dplyr" ,r-dplyr) + ("r-jsonlite" ,r-jsonlite) + ("r-magrittr" ,r-magrittr) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble) + ("r-tidytree" ,r-tidytree))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/YuLab-SMU/treeio") + (synopsis "Base classes and functions for Phylogenetic tree input and output") + (description + "This is an R package to make it easier to import and store phylogenetic +trees with associated data; and to link external data from different sources +to phylogeny. It also supports exporting phylogenetic trees with +heterogeneous associated data to a single tree file and can be served as a +platform for merging tree with associated data and converting file formats.") + (license license:artistic2.0))) + (define-public r-biocsingular (package (name "r-biocsingular") -- cgit 1.4.1 From 8caab758834cc6e6c3c664e7c7cb138662413fb0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 01:47:52 +0200 Subject: gnu: Add r-ggtree. * gnu/packages/bioconductor.scm (r-ggtree): New variable. --- gnu/packages/bioconductor.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 10463b29c2..d779a11643 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5707,6 +5707,42 @@ heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.") (license license:artistic2.0))) +(define-public r-ggtree + (package + (name "r-ggtree") + (version "3.0.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ggtree" version)) + (sha256 + (base32 + "0i665b5jxgsv3ncxmczy7n0h911br44dw9f7m4jwv3pjmr5mm6vk")))) + (properties `((upstream-name . "ggtree"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-aplot" ,r-aplot) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-magrittr" ,r-magrittr) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-rvcheck" ,r-rvcheck) + ("r-scales" ,r-scales) + ("r-tidyr" ,r-tidyr) + ("r-tidytree" ,r-tidytree) + ("r-treeio" ,r-treeio))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://yulab-smu.top/treedata-book/") + (synopsis "R package for visualization of trees and annotation data") + (description + "This package extends the ggplot2 plotting system which implements a +grammar of graphics. ggtree is designed for visualization and annotation of +phylogenetic trees and other tree-like structures with their annotation +data.") + (license license:artistic2.0))) + (define-public r-biocsingular (package (name "r-biocsingular") -- cgit 1.4.1 From 53ec97713a74da0acb9def81d25ff3e6dd6112f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 01:48:07 +0200 Subject: gnu: Add r-metapod. * gnu/packages/bioconductor.scm (r-metapod): New variable. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d779a11643..fe365b4d86 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5743,6 +5743,35 @@ phylogenetic trees and other tree-like structures with their annotation data.") (license license:artistic2.0))) +(define-public r-metapod + (package + (name "r-metapod") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "metapod" version)) + (sha256 + (base32 + "1hbcwr6d8gyrf4azh0gi588xkrg6gz7gsb5hbvzqkhplbsp6shlv")))) + (properties `((upstream-name . "metapod"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/metapod") + (synopsis "Meta-analyses on p-values of differential analyses") + (description + "This package implements a variety of methods for combining p-values in +differential analyses of genome-scale datasets. Functions can combine +p-values across different tests in the same analysis (e.g., genomic windows in +ChIP-seq, exons in RNA-seq) or for corresponding tests across separate +analyses (e.g., replicated comparisons, effect of different treatment +conditions). Support is provided for handling log-transformed input p-values, +missing values and weighting where appropriate.") + (license license:gpl3))) + (define-public r-biocsingular (package (name "r-biocsingular") -- cgit 1.4.1 From 1b0338d76b86a522045ca9a6060e7531578dc8f5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 01:44:46 +0200 Subject: gnu: r-rhdf5lib: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.14.0. [source]: Update deletions. [arguments]: Update substitutions. [inputs]: Move zlib from here... [propagated-inputs]: ...to here. --- gnu/packages/bioconductor.scm | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fe365b4d86..81fbbab82a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12253,22 +12253,21 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "14fnq4gijxp2l7985pksfk52i6klvy81r3892lnna73c6hh1dj28")) + "1ypqmd4nz4hxlb2qsay7f5784dqdjhc3b19pckzkhb65bfycdn87")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled binaries (delete-file-recursively "src/wininclude/") - (delete-file-recursively "src/winlib-4.9.3/") (delete-file-recursively "src/winlib-8.3.0/") - (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz") + (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz") #t)))) (properties `((upstream-name . "Rhdf5lib"))) (build-system r-build-system) @@ -12280,7 +12279,9 @@ block processing.") (for-each delete-file '("configure" "configure.ac")) ;; Do not make other packages link with the proprietary libsz. (substitute* "R/zzz.R" - ((" \"%s/libsz.a\"") "")) + ((" \"%s/libsz.a\"") "") + (("patharch, .getDynamicLinks") + ".getDynamicLinks")) (with-directory-excursion "src" (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) @@ -12319,12 +12320,10 @@ block processing.") (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n")) ;; szip is non-free software (("cp \"\\$\\{SZIP_LIB\\}.*") "") - (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) - #t))))) - (inputs - `(("zlib" ,zlib))) + (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))))))) (propagated-inputs - `(("hdf5" ,hdf5-1.10))) + `(("hdf5" ,hdf5-1.10) + ("zlib" ,zlib))) (native-inputs `(("hdf5-source" ,(package-source hdf5-1.10)) ("r-knitr" ,r-knitr))) -- cgit 1.4.1 From d0a7dc0cb6304ee017604aba60e4471bc11e3d81 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 4 Jun 2021 16:06:22 +0200 Subject: gnu: r-bioccheck: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.28.0. [arguments]: Remove. --- gnu/packages/bioconductor.scm | 23 ++--------------------- 1 file changed, 2 insertions(+), 21 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 81fbbab82a..646196cd8c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11350,35 +11350,16 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib")))) + "1h0l5w33c9jpc20pynq634qmx8jbfa802d7jslmf4haljmrxm4a1")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - ;; This package can be used by calling BiocCheck() from - ;; within R, or by running R CMD BiocCheck . This phase - ;; makes sure the latter works. For this to work, the BiocCheck - ;; script must be somewhere on the PATH (not the R bin directory). - (add-after 'install 'install-bioccheck-subcommand - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (dest-dir (string-append out "/bin")) - (script-dir - (string-append out "/site-library/BiocCheck/script/"))) - (mkdir-p dest-dir) - (symlink (string-append script-dir "/checkBadDeps.R") - (string-append dest-dir "/checkBadDeps.R")) - (symlink (string-append script-dir "/BiocCheck") - (string-append dest-dir "/BiocCheck"))) - #t))))) (propagated-inputs `(("r-codetools" ,r-codetools) ("r-graph" ,r-graph) -- cgit 1.4.1 From 5d13aab6cad11255eed430e5fef0ffaaa51978f1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 01:39:07 +0200 Subject: gnu: r-msnid: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-msnid): Update to 1.26.0. [arguments]: Set HOME variable. --- gnu/packages/bioconductor.scm | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 646196cd8c..f87a8d3bd0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3475,16 +3475,21 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d")))) + "0r3vgigf4fk0xzfg8gcvad01jdh0fysh6x22m9qy77x6glyrxcj2")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-annotationhub" ,r-annotationhub) -- cgit 1.4.1 From 87d06a725f9bebd117dd9f88efe1a4a53275ac1f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 01:39:56 +0200 Subject: gnu: r-mzr: Update to 2.26.0. * gnu/packages/bioconductor.scm (r-mzr): Update to 2.26.0. [arguments]: Remove obsolute substitution. --- gnu/packages/bioconductor.scm | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f87a8d3bd0..6f466ca4aa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3563,14 +3563,14 @@ specific parser.") (define-public r-mzr (package (name "r-mzr") - (version "2.24.1") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg")) + "1m5xvnv0rxyrfri4jwyyryr13d55nyhqvfc5xxg5mpskw2v029kp")) (modules '((guix build utils))) (snippet '(begin @@ -3585,10 +3585,6 @@ specific parser.") (lambda _ (substitute* "src/Makevars" (("\\./boost/libs.*") "") - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\(RHDF5_LIBS\\)" match) - (string-append match "/libhdf5.a")) (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ") (("\\ARCH_OBJS=" line) (string-append line @@ -3597,7 +3593,7 @@ specific parser.") #t))))) (inputs `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.24.1. + ;; mzR version 2.26.0. ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources ("zlib" ,zlib))) (propagated-inputs -- cgit 1.4.1 From 782d27f77d6b3acfdcec993b22f853db340d8769 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 01:48:30 +0200 Subject: gnu: r-rhdf5: Update to 2.36.0. * gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.36.0. [arguments]: Remove. --- gnu/packages/bioconductor.scm | 15 ++------------- 1 file changed, 2 insertions(+), 13 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6f466ca4aa..4d881195c5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3855,25 +3855,14 @@ browser.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi")))) + "1a5kw9ry9cr258al0x3q0ss5xn1ymscdypx51vzzgzamhy7dqakz")))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-linking - (lambda _ - (substitute* "src/Makevars" - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\(RHDF5_LIBS\\)" match) - (string-append match "/libhdf5.a"))) - #t))))) (propagated-inputs `(("r-rhdf5filters" ,r-rhdf5filters) ("r-rhdf5lib" ,r-rhdf5lib))) -- cgit 1.4.1 From 5c37a048bb06e4350a49de71bdfe2a18c4ad7e6a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 01:48:51 +0200 Subject: gnu: r-cytolib: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-cytolib): Update to 2.4.0. [arguments]: Remove. [native-inputs]: Remove pkg-config. --- gnu/packages/bioconductor.scm | 18 +++--------------- 1 file changed, 3 insertions(+), 15 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4d881195c5..37d39ef3f8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9313,30 +9313,18 @@ cluster count and membership by stability evidence in unsupervised analysis.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.2.1") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "0y8mxrg3jh9bahsf9rblgyja37m1x1ncxfnrli91xjyg0582kh7r")))) + "0wl7zqwv0i38dfzqfsz40n3mcbxi38ffn1rbd5pm9s7hq16zr4nv")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-linking - (lambda _ - (substitute* "src/Makevars.in" - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\(RHDF5_LIBS\\)" match) - (string-append match "/libhdf5.a"))) - #t))))) (native-inputs - `(("r-knitr" ,r-knitr) - ("pkg-config" ,pkg-config))) + `(("r-knitr" ,r-knitr))) (propagated-inputs `(("r-bh" ,r-bh) ("r-rcpp" ,r-rcpp) -- cgit 1.4.1 From b9751b629c37c6cd48093e3cbc8bdee63164776c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 01:49:20 +0200 Subject: gnu: r-ncdfflow: Update to 2.38.0. * gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.38.0. [arguments]: Remove. --- gnu/packages/bioconductor.scm | 15 ++------------- 1 file changed, 2 insertions(+), 13 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 37d39ef3f8..49d39fabd0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9400,27 +9400,16 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac")))) + "1lm88qnfv6rnnr7wmgbvwyj272imjjjn7h3agxqqzsbmn8vyrnf0")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-linking - (lambda _ - (substitute* "src/Makevars" - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\(RHDF5_LIBS\\)" match) - (string-append match "/libhdf5.a"))) - #t))))) (propagated-inputs `(("r-bh" ,r-bh) ("r-biobase" ,r-biobase) -- cgit 1.4.1 From 764e2dba209b3283ebe35a22b49dc4771d42f181 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 01:50:03 +0200 Subject: gnu: r-flowworkspace: Update to 4.4.0. * gnu/packages/bioconductor.scm (r-flowworkspace): Update to 4.4.0. [arguments]: Remove. [propagated-inputs]: Add r-delayedarray and r-s4vectors. --- gnu/packages/bioconductor.scm | 17 ++++------------- 1 file changed, 4 insertions(+), 13 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 49d39fabd0..b1ccf01485 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9569,27 +9569,16 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.2.0") + (version "4.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag")))) + "1a9qb2dcvwgb3z0vdbbzn1rzy77d3da72kirs272344hdx9b2cx9")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-linking - (lambda _ - (substitute* "src/Makevars" - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\{h5lib\\}" match) - (string-append match "/libhdf5.a"))) - #t))))) (propagated-inputs `(("r-aws-s3" ,r-aws-s3) ("r-aws-signature" ,r-aws-signature) @@ -9598,6 +9587,7 @@ for other R packages to compile and link against.") ("r-biocgenerics" ,r-biocgenerics) ("r-cytolib" ,r-cytolib) ("r-data-table" ,r-data-table) + ("r-delayedarray" ,r-delayedarray) ("r-digest" ,r-digest) ("r-dplyr" ,r-dplyr) ("r-flowcore" ,r-flowcore) @@ -9614,6 +9604,7 @@ for other R packages to compile and link against.") ("r-rgraphviz" ,r-rgraphviz) ("r-rhdf5lib" ,r-rhdf5lib) ("r-rprotobuflib" ,r-rprotobuflib) + ("r-s4vectors" ,r-s4vectors) ("r-scales" ,r-scales) ("r-xml" ,r-xml))) (native-inputs -- cgit 1.4.1 From bfa23ec526ac69b490848937c52a1560612d5905 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 01:50:34 +0200 Subject: gnu: r-cytoml: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-cytoml): Update to 2.4.0. [arguments]: Remove. --- gnu/packages/bioconductor.scm | 15 ++------------- 1 file changed, 2 insertions(+), 13 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b1ccf01485..13a1515516 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9703,27 +9703,16 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.2.2") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "0ckjb7bkz0cy46scrv4vl9w37g54c0yihvzmbkzilip1ikpvhxd1")))) + "0ixy7mmnipk8wy61wz6qy7jfbc5zhs6p5iqaii8hdprjnb841ri7")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-linking - (lambda _ - (substitute* "src/Makevars.in" - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\{h5lib\\}" match) - (string-append match "/libhdf5.a"))) - #t))))) (inputs `(("libxml2" ,libxml2) ("zlib" ,zlib))) -- cgit 1.4.1 From 75817956c165a7233cf079d341f8a67c1c8c3826 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:33:38 +0200 Subject: gnu: r-hdf5array: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.20.0. [arguments]: Remove. [propagated-inputs]: Add r-rhdf5filters. --- gnu/packages/bioconductor.scm | 16 +++------------- 1 file changed, 3 insertions(+), 13 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 13a1515516..ae0df635bf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12140,27 +12140,16 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "14v2adhwi0yac834g23kvfid740raclhmribzd28k10gsjk9cj7g")))) + "1718hplz5qlbwxwb87509bl7lir9kilvn1s7p2haz551pg48zvrc")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-linking - (lambda _ - (substitute* "src/Makevars" - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\(RHDF5LIB_LIBS\\)" match) - (string-append match "/libhdf5.a"))) - #t))))) (inputs `(("zlib" ,zlib))) (propagated-inputs @@ -12169,6 +12158,7 @@ provided.") ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) ("r-rhdf5" ,r-rhdf5) + ("r-rhdf5filters" ,r-rhdf5filters) ("r-rhdf5lib" ,r-rhdf5lib) ("r-s4vectors" ,r-s4vectors))) (home-page "https://bioconductor.org/packages/HDF5Array") -- cgit 1.4.1 From 405b38665630b0a397e588fe24d90fdb8fa5da09 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:35 +0200 Subject: gnu: r-aneufinder: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-aneufinder): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ae0df635bf..62da2311de 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1001,13 +1001,13 @@ All datasets are restricted to protein coding genes.") (define-public r-aneufinder (package (name "r-aneufinder") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinder" version)) (sha256 (base32 - "1j2n6i3ja63i98y1mbb8ndn6cn2a0pw97zz6al4myycnv55w49j3")))) + "0m6wphlriq7y21ih1p2kzml5jzcic79jc52kkk59dkjj8j88yllk")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From b05761a5a94e9522e5c17f7a33059653b399fe5e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:38 +0200 Subject: gnu: r-biocversion: Update to 3.13.1. * gnu/packages/bioconductor.scm (r-biocversion): Update to 3.13.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 62da2311de..e31b974fce 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1321,14 +1321,14 @@ across the entire multi-'omics experiment.") (define-public r-biocversion (package (name "r-biocversion") - (version "3.12.0") + (version "3.13.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk")))) + "0rsw8g4g1pcjw1zbx8x17yd3drhxqk4sx3cy3ddzy5731hl6mbfi")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") -- cgit 1.4.1 From 7bac473d0634b910e74fa414cc77ad11ce8fdefd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:38 +0200 Subject: gnu: r-biocgenerics: Update to 0.38.0. * gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e31b974fce..4a64f3d37c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1341,13 +1341,13 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.36.1") + (version "0.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "0x8cllriayrs99wd5l003iq6i28rb1mci23qcn13ga85578f5lz5")))) + "1kv7lzmyki3hi771v01nml1v1hzz8pyhqqv0xcdzqy354mlgx4m6")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) -- cgit 1.4.1 From e6c5d8ce2c53e7c9e0698a5aac6fb9992e3b40c2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:39 +0200 Subject: gnu: r-coverageview: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-coverageview): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4a64f3d37c..60c36417c2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1361,13 +1361,13 @@ packages.") (define-public r-coverageview (package (name "r-coverageview") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj")))) + "1xhirbjdw09cqm4xvysxqicvqjbahavwvs7shg4cb05gwyd2ha8g")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) -- cgit 1.4.1 From 116df58449e0cc5aa322a1c084a11ffe92a8310c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:39 +0200 Subject: gnu: r-cummerbund: Update to 2.34.0. * gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 60c36417c2..f63ace7507 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1388,13 +1388,13 @@ how the coverage distributed across the genome.") (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj")))) + "1avvmvrmldbscc7xd6a6k22xjykbzafvqf87wh5z9rx3qlzswsjx")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From dec096f827eefa2659e6c6ded2f7a1351b5278e2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:39 +0200 Subject: gnu: r-decipher: Update to 2.20.0. * gnu/packages/bioconductor.scm (r-decipher): Update to 2.20.0. [propagated-inputs]: Add r-dbi, r-iranges, r-s4vectors, and r-xvector. --- gnu/packages/bioconductor.scm | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f63ace7507..34df07c977 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1418,17 +1418,21 @@ used visualizations.") (define-public r-decipher (package (name "r-decipher") - (version "2.18.1") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DECIPHER" version)) (sha256 (base32 - "0jz2lffks9rrk5wzbvnr8yal91kf8rg2xn0fmg9ywk45ql657sm9")))) + "0mr7glkx2d37l9nszs52m0kycpm14vxl5gdp3z7i5j7yig1sw2nk")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) - ("r-rsqlite" ,r-rsqlite))) + ("r-dbi" ,r-dbi) + ("r-iranges" ,r-iranges) + ("r-rsqlite" ,r-rsqlite) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) (home-page "https://www.bioconductor.org/packages/DECIPHER/") (synopsis "Tools for deciphering and managing biological sequences") (description "This package provides a toolset for deciphering and managing -- cgit 1.4.1 From f0f839c1240d8d42bab6351ab463d0ca38985e2f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:39 +0200 Subject: gnu: r-deepsnv: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-deepsnv): Update to 1.38.0. [inputs]: Remove zlib. [native-inputs]: Add r-knitr. --- gnu/packages/bioconductor.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 34df07c977..a7b4aded61 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1442,17 +1442,15 @@ biological sequences.") (define-public r-deepsnv (package (name "r-deepsnv") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deepSNV" version)) (sha256 (base32 - "1lbvx9liql8fkb4y020kwpgp61vzg67cy640dc4kybglcw9dx6j0")))) + "0zz56hf417m7bgg2g2wpbaik30pi6h2nam1n5bviqgdn4mv8n0bs")))) (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) (propagated-inputs `(("r-biostrings" ,r-biostrings) ("r-genomicranges" ,r-genomicranges) @@ -1461,6 +1459,8 @@ biological sequences.") ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-variantannotation" ,r-variantannotation) ("r-vgam" ,r-vgam))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/gerstung-lab/deepSNV/") (synopsis "Detection of subclonal SNVs in deep sequencing data") (description -- cgit 1.4.1 From 8eb0c715e38f2ba9588b4e08e5aa82b811858684 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:39 +0200 Subject: gnu: r-delayedarray: Update to 0.18.0. * gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a7b4aded61..80bf7f7b56 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1478,13 +1478,13 @@ bases such as COSMIC.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.16.3") + (version "0.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0w1wppy6m2iv41852dscg3y19sq84ahdx3m7c2p2pxjcznmv6hys")))) + "0w632262dqzcnvq9s6jvc7naz93dayx51fsv05s0zb6cjwygbqjr")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) -- cgit 1.4.1 From 4075ac72870674c4947d35b89745d38098d6f482 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:39 +0200 Subject: gnu: r-bluster: Update to 1.2.1. * gnu/packages/bioconductor.scm (r-bluster): Update to 1.2.1. [propagated-inputs]: Add r-cluster. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 80bf7f7b56..e57cfddde5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1511,18 +1511,19 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-bluster (package (name "r-bluster") - (version "1.0.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "bluster" version)) (sha256 (base32 - "0izrf82m5znyrgai5y5jss4k2brabh4ajxdvnlwwc92l5bw7jp61")))) + "128zd5vwlhmrkq0bpp1dxnkrcqfz1mjmdjlla4wqbjv7v6yyn6lg")))) (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs `(("r-biocneighbors" ,r-biocneighbors) ("r-biocparallel" ,r-biocparallel) + ("r-cluster" ,r-cluster) ("r-igraph" ,r-igraph) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) -- cgit 1.4.1 From cfd4c05bd4e7945cc5a0f9191ac9c6d53f73ba02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:39 +0200 Subject: gnu: r-ideoviz: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-ideoviz): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e57cfddde5..ee298d53b2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1541,13 +1541,13 @@ and evaluate clustering results.") (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq")))) + "17sx0v5lq2zmg098ps4ksj1h0yla3vlh6s2w1ahqsq0nvm193scm")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From 60b95464722cf0ebe46acbd90a45f92ee9dae946 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:39 +0200 Subject: gnu: r-iranges: Update to 2.26.0. * gnu/packages/bioconductor.scm (r-iranges): Update to 2.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ee298d53b2..e9c5a9e15b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1565,13 +1565,13 @@ arbitrary genomic intervals along chromosomal ideogram.") (define-public r-iranges (package (name "r-iranges") - (version "2.24.1") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52")))) + "0dzj8wqbjzilh2dsaj3ylx958xqrv0c688ayfq2r1z7rs75qy7kx")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) -- cgit 1.4.1 From af04e2cc12db9f6eb3401eb7cef4972aef9f69c8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:40 +0200 Subject: gnu: r-affy: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-affy): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e9c5a9e15b..bd9aeed0ba 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1723,14 +1723,14 @@ performing parallel computations on multicore machines.") (define-public r-affy (package (name "r-affy") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06")))) + "0vz5y92gqcm0qk57qlba85bk683lzdr7vkmxv109rq6i17vdkkrm")))) (build-system r-build-system) (propagated-inputs `(("r-affyio" ,r-affyio) -- cgit 1.4.1 From b045bf2d6f9e03bcc03170007d5ad75fee435231 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:40 +0200 Subject: gnu: r-affycomp: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-affycomp): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bd9aeed0ba..6dd4b2a815 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1751,14 +1751,14 @@ analysis.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk")))) + "07my5scdh6h0y1bx1h9y5m4fa8bnmw389f83gkb7cf19w4vp36b2")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) -- cgit 1.4.1 From bd17befeb1b11e963eea2854ad79a1c55464ee54 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:40 +0200 Subject: gnu: r-affycompatible: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-affycompatible): Update to 1.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6dd4b2a815..e54b2108b8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1772,14 +1772,14 @@ measures for Affymetrix Oligonucleotide Arrays.") (define-public r-affycompatible (package (name "r-affycompatible") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 - "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x")))) + "1xwz22wf2smsvmd0d5lfadbsgscnl3fl9msypy2mml38k048p6vj")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) -- cgit 1.4.1 From 3abb0b6523680ec638e3afa8026a6fc9c3882dc8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:40 +0200 Subject: gnu: r-affycontam: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-affycontam): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e54b2108b8..e5e21c3475 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1800,14 +1800,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b")))) + "0242ga68wrdk1kcmxfdbq73a0d3zhrzdlzkzphfg3q0zjbvg49jj")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a9083169c64c1e41aae0fd19bc4f7d0b93ad4ece Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:40 +0200 Subject: gnu: r-affycoretools: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e5e21c3475..2e60efb8ae 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1825,14 +1825,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0")))) + "1dx861spr3kn1dxwhf43s5l1r7bmrq0h6538l3q64iiwzzc6krdh")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From dfeb135ef00aaf74ce35a9323f1cf2b4a0fc2ec4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:40 +0200 Subject: gnu: r-affyio: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-affyio): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2e60efb8ae..bea37b3ab6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1867,14 +1867,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affyio (package (name "r-affyio") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h")))) + "07kibqsm888g06qqqa4648ph877kriy74kprbri8nyx83y8aspjr")))) (build-system r-build-system) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) -- cgit 1.4.1 From 308067c09cc244c3163eefcf4b60474c8fd94b89 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:40 +0200 Subject: gnu: r-affxparser: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-affxparser): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bea37b3ab6..eee79485a2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1891,14 +1891,14 @@ CDF file formats.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p")))) + "0n3yyrglzqzw0wqxl9igqvkj8qslw6yjkym3vcq0c93kkg7vk01l")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") -- cgit 1.4.1 From 1bb87755b8b34e267b9cd6b26b238bc15142d225 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:40 +0200 Subject: gnu: r-annotate: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-annotate): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eee79485a2..aed40e4c41 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1919,14 +1919,14 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l")))) + "13ny596wh65sw7dbw0zd4h84d6k1w99g91c4sqy83mdzgpv73sz7")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From c7811ed4bf8c30dc9d1b2d8713cc113cb4f43655 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:41 +0200 Subject: gnu: r-annotationdbi: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.54.0. [propagated-inputs]: Add r-keggrest. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aed40e4c41..a81333bb5b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1946,13 +1946,13 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr")))) + "117zh7iqa6phsrxrkv45kxraamm3vbfz5i1a8vkhyalhdbs5ssph")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -1960,6 +1960,7 @@ microarrays.") `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-dbi" ,r-dbi) + ("r-keggrest" ,r-keggrest) ("r-iranges" ,r-iranges) ("r-rsqlite" ,r-rsqlite) ("r-s4vectors" ,r-s4vectors))) -- cgit 1.4.1 From 361f2f647a0443bb769caee6288a03e990e4000c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:41 +0200 Subject: gnu: r-annotationfilter: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-annotationfilter): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a81333bb5b..9239d95340 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1976,13 +1976,13 @@ annotation data packages using SQLite data storage.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9")))) + "0799jja6v7l3jsi26wbjalkr5lriaxid05xb5g36iq93myhaj0sa")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) -- cgit 1.4.1 From 4d13cf066dd4dfbce7d6defe13cbbb12bfbfa053 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:41 +0200 Subject: gnu: r-annotationforge: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9239d95340..be56c86330 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2002,14 +2002,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7")))) + "1by3diy0y4809k97cw97mp4j177gn1dzhqil8myij1r7b8sk7hax")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) -- cgit 1.4.1 From 2071ed58d5c6a92a286ba465559dc67f45c1f8cf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:41 +0200 Subject: gnu: r-annotationhub: Update to 3.0.0. * gnu/packages/bioconductor.scm (r-annotationhub): Update to 3.0.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index be56c86330..0a75b8389d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2034,14 +2034,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.22.1") + (version "3.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "08d7m0n4jkpajsj0bvi5xd4vi1zqczl6lnrh8kqi2fbjkrvwdqp5")))) + "1p9773fv7j7q4x1sjqqaw32qy9lqn2gf6gkynh1d8n1kd7v7sclp")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 3e290768c6b37644bae70fcc6c6554b5471f459b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:41 +0200 Subject: gnu: r-aroma-light: Update to 3.22.0. * gnu/packages/bioconductor.scm (r-aroma-light): Update to 3.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0a75b8389d..c73f55ebf7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2075,14 +2075,14 @@ by the user, helping with quick and reproducible access.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.20.0") + (version "3.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "0pi37rlfqh24p9wd7l1xb3f7c7938xdscgcc5agp8c9qhajq25a0")))) + "1yvq6l1p8cpijvlib4fn9y88ihn0gaalrmgx82jgrfmnszkqn3y5")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From baaed6fd683257928a09a67849c7df18f9f63caf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:41 +0200 Subject: gnu: r-bamsignals: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-bamsignals): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c73f55ebf7..d2d6117f31 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2102,14 +2102,14 @@ classes.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv")))) + "1ljrip0jlxjcljqac7vzvwqbcqil5v4f4s4bhpq4akvdkshas6mn")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit 1.4.1 From 8be5d4f6fc33c27820fff251df9f8a064224df0c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:41 +0200 Subject: gnu: r-biobase: Update to 2.52.0. * gnu/packages/bioconductor.scm (r-biobase): Update to 2.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d2d6117f31..89a6930f67 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2132,13 +2132,13 @@ paired-end data.") (define-public r-biobase (package (name "r-biobase") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4")))) + "1sg8w8860zhlz9s1pf75xa8asd2hyqsj13fh5xc37hf5yqdfkavr")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) -- cgit 1.4.1 From f9ae0a4102fd225a0a78287c0ab4446dcff85bbd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:41 +0200 Subject: gnu: r-biomart: Update to 2.48.0. * gnu/packages/bioconductor.scm (r-biomart): Update to 2.48.0. [propagated-inputs]: Remove r-openssl and r-xml2; add r-digest. --- gnu/packages/bioconductor.scm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 89a6930f67..59d4f09c1a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2154,26 +2154,25 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.46.3") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7")))) + "1h8lzd63qvy1y75nlnhazpkyhl6g1hz80baqg20gpxbv38wkyf55")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biocfilecache" ,r-biocfilecache) + ("r-digest" ,r-digest) ("r-httr" ,r-httr) - ("r-openssl" ,r-openssl) ("r-progress" ,r-progress) ("r-rappdirs" ,r-rappdirs) ("r-stringr" ,r-stringr) - ("r-xml" ,r-xml) - ("r-xml2" ,r-xml2))) + ("r-xml" ,r-xml))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/biomaRt") -- cgit 1.4.1 From 3eedef80e4483b3d4d0af66693e0de2504fe4043 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:42 +0200 Subject: gnu: r-biocparallel: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 59d4f09c1a..73dd9c6c8d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2191,13 +2191,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism")))) + "17w4gdajxxmsfgiwycp1d7rbxdqhc5jnngcb58ky0fv5xbv9f4j0")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) -- cgit 1.4.1 From 16fe6abd27619b3e659f8da03e6d28be6fd7261d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:42 +0200 Subject: gnu: r-biostrings: Update to 2.60.0. * gnu/packages/bioconductor.scm (r-biostrings): Update to 2.60.0. [propagated-inputs]: Add r-genomeinfodb. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 73dd9c6c8d..d3dc22c91e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2246,19 +2246,20 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5")))) + "0xidh6wp0l47g1j9x8d4fs91ky6pi5nzf85ry801gqd2gqajh2zy")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-crayon" ,r-crayon) + ("r-genomeinfodb" ,r-genomeinfodb) ("r-iranges" ,r-iranges) ("r-s4vectors" ,r-s4vectors) ("r-xvector" ,r-xvector))) -- cgit 1.4.1 From 98f3c559993134742f4c47d53dc61971cfb67bbc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:42 +0200 Subject: gnu: r-biovizbase: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-biovizbase): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d3dc22c91e..f19548eb05 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2274,14 +2274,14 @@ biological sequences or sets of sequences.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq")))) + "14jyyg3ggdhaqhp0j4qf6dapykh76fygbaa4lr7czqbc5mr0iw23")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From e039d07bf85ffafe5f7efd86c370260096446b41 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:42 +0200 Subject: gnu: r-bsgenome: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-bsgenome): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f19548eb05..36dc450875 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2316,13 +2316,13 @@ effort and encourages consistency.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq")))) + "1jhissp9ad1rn2p0bzr3yslbn84yqbaqgnn5p9hyacwr7mr091cn")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) -- cgit 1.4.1 From 336107c13d5fed79f50bb6df8d0658263ce7d266 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:42 +0200 Subject: gnu: r-category: Update to 2.58.0. * gnu/packages/bioconductor.scm (r-category): Update to 2.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 36dc450875..a2153ee84d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2347,14 +2347,14 @@ genome data packages and support for efficient SNP representation.") (define-public r-category (package (name "r-category") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr")))) + "0f76pb7h8qc51mca5pq00m9p02sbkcj6ywfzli20qai2ykpfr71x")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From ca10bafc6581d4f122e69b4228e9afdd57ce30a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:42 +0200 Subject: gnu: r-chipseeker: Update to 1.28.3. * gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.28.3. [inputs]: Remove r-knitr. [native-inputs]: Add r-knitr. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a2153ee84d..d56bcc7714 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2378,15 +2378,15 @@ analysis.") (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.26.2") + (version "1.28.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "1r197qwsriap6s6nb2p9j3521pjs2f0lgyzvppvlxj1531sa6g6z")))) + "18hdgml80770c0xgd06zrl8px1ql9fa65rirfkq07z7rzpnd23rw")))) (build-system r-build-system) - (inputs + (native-inputs `(("r-knitr" ,r-knitr))) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From d296ac9cde42332898aa08941ceb40895c9f9d5b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:42 +0200 Subject: gnu: r-chipseq: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-chipseq): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d56bcc7714..b16abef583 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2425,14 +2425,14 @@ annotation, distance to TSS, and overlap of peaks or genes.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v")))) + "078p9h0zghlhpd6cr54nww1mk7q97imx8yqfayw5m2yq4097ivbi")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit 1.4.1 From a8cfce4852f17962e0736c2a0d57718ff800ea07 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:43 +0200 Subject: gnu: r-complexheatmap: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-complexheatmap): Update to 2.8.0. [propagated-inputs]: Remove r-s4vectors; add r-doparallel and r-foreach. --- gnu/packages/bioconductor.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b16abef583..713a728c48 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2451,14 +2451,14 @@ experiments.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.6.2") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x")))) + "0jl96msj1njdrvngg68s50vmphvhi2lfwlv34x07pcdzgkjjs41f")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) @@ -2468,13 +2468,14 @@ experiments.") ("r-clue" ,r-clue) ("r-colorspace" ,r-colorspace) ("r-digest" ,r-digest) + ("r-doparallel" ,r-doparallel) + ("r-foreach" ,r-foreach) ("r-getoptlong" ,r-getoptlong) ("r-globaloptions" ,r-globaloptions) ("r-iranges" ,r-iranges) ("r-matrixstats" ,r-matrixstats) ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-s4vectors" ,r-s4vectors))) + ("r-rcolorbrewer" ,r-rcolorbrewer))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page -- cgit 1.4.1 From 2835e7c0be8d49ea71dbdf2846713aee30add95c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:43 +0200 Subject: gnu: r-copywriter: Update to 2.24.0. * gnu/packages/bioconductor.scm (r-copywriter): Update to 2.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 713a728c48..3250110133 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2491,14 +2491,14 @@ self-defined annotation graphics.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f")))) + "0pacs714d9b1fdz68pp9ca0x77d376s19lxb82np4l9fgx0rgkxp")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 45225c60cc997ed130ef143387dfe6b9894a0381 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:43 +0200 Subject: gnu: r-deseq2: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-deseq2): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3250110133..fbf96b8ae7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2562,14 +2562,14 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "1i0jpzsm1vl7q6qdmplj45w13lsaycxrx5pazlanjba2khn79k19")))) + "0r1brwmj7av0bj72jajn27vx3zs1bgg8qfbhf02fln6kf7im4kaz")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From e9445cdd785c620cd487f574789a33a25c58377e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:43 +0200 Subject: gnu: r-dexseq: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-dexseq): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fbf96b8ae7..4ddd206bba 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2600,14 +2600,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi")))) + "1zywh30f4j4rj0f9w6yk5xr9mvdbg8gicy3wsb8yxdnamadyr7x4")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 30ce1f9b6688285d42ff4be9d805e770e013607a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:43 +0200 Subject: gnu: r-dirichletmultinomial: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-dirichletmultinomial): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4ddd206bba..6fb78ea7b4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2645,14 +2645,14 @@ exploration of the results.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk")))) + "0ikmj0300lfzj6q1vyahfyx5kwi5h59mds7ym4f2j1bbxqzy6ssl")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) -- cgit 1.4.1 From f998c95d6052439adbffafce7500116e08c1b876 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:43 +0200 Subject: gnu: r-edaseq: Update to 2.26.0. * gnu/packages/bioconductor.scm (r-edaseq): Update to 2.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6fb78ea7b4..59abeeee5d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2674,14 +2674,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-edaseq (package (name "r-edaseq") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip")))) + "1mqpi2iz4azr31b3ajsqb4n9izjh85dx642844n059c8s2pfmivh")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From bdc1b908d38b7cb2db2ad203b8a1cfab1b1a9ef7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:43 +0200 Subject: gnu: r-edger: Update to 3.34.0. * gnu/packages/bioconductor.scm (r-edger): Update to 3.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 59abeeee5d..12fb72832c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2714,13 +2714,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.32.1") + (version "3.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp")))) + "1ikl9y6hj2p92nrb1ydxy2410b3wrax83rfy2imaj0vgfmhsgx6g")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 6abbb53c3e263e356b288ee596b74399a5cd6651 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:43 +0200 Subject: gnu: r-ensembldb: Update to 2.16.0. * gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 12fb72832c..dfeaad1b6d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2742,14 +2742,14 @@ CAGE.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.14.1") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40")))) + "100m2mzxl4pmldqixzfdznnd4nqbykk2l7n4xazqjpnlpcldy2dj")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From ff59b34dc343cfec1db8f6116510eed55639837c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:44 +0200 Subject: gnu: r-fastseg: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-fastseg): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dfeaad1b6d..dd7df8e157 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2787,14 +2787,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f")))) + "006v7qs707xmnr35b7rw135pyvacrmhv55a3c53birkpsrjgkps0")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From f22f4caa6915fd8f13f0c780f692fe17c09ab750 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:44 +0200 Subject: gnu: r-gage: Update to 2.42.0. * gnu/packages/bioconductor.scm (r-gage): Update to 2.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dd7df8e157..36a31d5c3a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2817,14 +2817,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.40.2") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178")))) + "0z7hrwdm6my6p7z04bcpfhqk72pd0s1bdzvsiiym59qj79fbvb83")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From 389ce4e42b1ee031126bb6c339c0ba7b683ea596 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:44 +0200 Subject: gnu: r-genefilter: Update to 1.74.0. * gnu/packages/bioconductor.scm (r-genefilter): Update to 1.74.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 36a31d5c3a..ad67677023 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2848,14 +2848,14 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.72.1") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn")))) + "0dy9pmlb0pc9b4ks5fb9zgnmhc9f2mkqmsdlb7f5z88xmj68y4qk")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran) -- cgit 1.4.1 From 3c024e9e96c356a9c6f441efe7acdd8111adfb00 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:44 +0200 Subject: gnu: r-geneoverlap: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-geneoverlap): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ad67677023..11d49b74d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2876,13 +2876,13 @@ high-throughput sequencing experiments.") (define-public r-geneoverlap (package (name "r-geneoverlap") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GeneOverlap" version)) (sha256 (base32 - "0bvh00n4fx0h1m83bypib3jvln1ihcv77ywrrn9xm20y73gymhkh")))) + "1kfw3h68rvbafhklds6sfmviwv91nms8wk0ywzkjg5h3mmgxbsv9")))) (build-system r-build-system) (propagated-inputs `(("r-rcolorbrewer" ,r-rcolorbrewer) -- cgit 1.4.1 From ef7bbc40def8d394817c12cbe83ef5208f647d1a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:44 +0200 Subject: gnu: r-genomation: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-genomation): Update to 1.24.0. [propagated-inputs]: Remove r-runit. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 11d49b74d1..368afb3053 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2896,13 +2896,13 @@ and visualize the results.") (define-public r-genomation (package (name "r-genomation") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g")))) + "0qa3b4mfd7l1sy4pw64zr2d90y5apah900krxjl4x39acygg0i2r")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) @@ -2923,7 +2923,6 @@ and visualize the results.") ("r-reshape2" ,r-reshape2) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) - ("r-runit" ,r-runit) ("r-s4vectors" ,r-s4vectors) ("r-seqpattern" ,r-seqpattern))) (native-inputs -- cgit 1.4.1 From f88ab81fc7a7bf8ff5122c96c19da8f0f07e43cc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:44 +0200 Subject: gnu: r-genomeinfodb: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 368afb3053..797630f5b9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2943,13 +2943,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.26.7") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0fp7sp3jmc2a1hk4r624lfavx8gc2ik3lv43ksc2jmspg6cvh516")))) + "0wjd7sh7kr9lfcdbzm5jdynl84nfsl7nqvly92qqrdcxd2sjfr63")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) -- cgit 1.4.1 From 570e80d62f93f237be93c3c651ad46760b7d4d56 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:44 +0200 Subject: gnu: r-genomicalignments: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-genomicalignments): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 797630f5b9..2c31d46be9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2973,13 +2973,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr")))) + "00rq110jkh89nxgk05zh8kssxk8mb4dq0wjg3n7ivfmmm9wdwhp2")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) -- cgit 1.4.1 From 62889b9915c6b76b40c8253eb3bc563650f8859f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:45 +0200 Subject: gnu: r-genomicfeatures: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.44.0. [propagated-inputs]: Add r-biocio. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2c31d46be9..32abf5f947 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3006,13 +3006,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.42.3") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz")))) + "0y7lnvfcfrs72xbkn67xcqyz9csl5696mr2zl425fkhmnmimm4fg")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -3020,6 +3020,7 @@ alignments.") `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) + ("r-biocio" ,r-biocio) ("r-biomart" ,r-biomart) ("r-biostrings" ,r-biostrings) ("r-dbi" ,r-dbi) -- cgit 1.4.1 From d491b7eb1a7c64bbeef39ffce398bdb600d102a5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:45 +0200 Subject: gnu: r-genomicfiles: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-genomicfiles): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 32abf5f947..d8b0a6451b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3050,14 +3050,14 @@ extracting the desired features in a convenient format.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz")))) + "1plh14m7w6calw5yxcxp7g4bg8q00ax85m517wap78bni975k13y")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 1b44202e207f10e4288fefc31705a5ef1d2e685a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:45 +0200 Subject: gnu: r-genomicranges: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-genomicranges): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d8b0a6451b..2a6aebe1eb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3084,13 +3084,13 @@ provide added flexibility for data combination and manipulation.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i")))) + "1qxc6dcwdlkan3hg0j9yfhz7gyi9qg671yj6zizsk6mzl7qqva0x")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) -- cgit 1.4.1 From 214e784b577ae91995e50a3ac949f79c1ecf6253 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:45 +0200 Subject: gnu: r-gostats: Update to 2.58.0. * gnu/packages/bioconductor.scm (r-gostats): Update to 2.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2a6aebe1eb..778bb52b04 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3115,14 +3115,14 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-gostats (package (name "r-gostats") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j")))) + "0jjswy6qmfgr2f6vk3y9pdvs9x91gn31h55qllgh0qb2cb26g9wa")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 330a7fe3b1a3ad25eadb21eaa59bc1a09a80abf3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:45 +0200 Subject: gnu: r-gseabase: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-gseabase): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 778bb52b04..dfaf33318f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3146,14 +3146,14 @@ testing and other simple calculations.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.52.1") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i")))) + "0946kkykms79mqnx262q20xzrrhv7cv723xh378335ff41qyf63n")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 78eb1fdf3eb8fca8bf641d802a826ade05731a5f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:45 +0200 Subject: gnu: r-hpar: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-hpar): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dfaf33318f..e78d24c514 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3175,14 +3175,14 @@ Enrichment Analysis} (GSEA).") (define-public r-hpar (package (name "r-hpar") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr")))) + "0q5pp04rq2gsh1kibvp8bvjkqc1kb46qpnj6agqp2vyqhrrfrm99")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From 76fc8a53b21bc50017784d76ad06a449b832ab56 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:45 +0200 Subject: gnu: r-rhtslib: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-rhtslib): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e78d24c514..466008c269 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3195,14 +3195,14 @@ the Human Protein Atlas project.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4")))) + "0acpgv98529ic2i2k03knz05akb6h51wbz7sr5zgi8gk4nmawrlf")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, -- cgit 1.4.1 From 94b4e64fd0bc509498b01dfedb221822bebeac07 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:45 +0200 Subject: gnu: r-impute: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-impute): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 466008c269..80bb10bf0a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3226,13 +3226,13 @@ of other R packages who wish to make use of HTSlib.") (define-public r-impute (package (name "r-impute") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa")))) + "0pprkv25avxhllddcssvqvy3nibmqkfwaq4xnlhka7858gyiyd1k")))) (native-inputs `(("gfortran" ,gfortran))) (build-system r-build-system) -- cgit 1.4.1 From 2cbb8e19af10d3af9de8b6a0d05caf7a173dd36a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:46 +0200 Subject: gnu: r-interactivedisplaybase: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-interactivedisplaybase): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 80bb10bf0a..d395cb739b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3246,14 +3246,14 @@ microarray data, using nearest neighbor averaging.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "08id2hkx4ssxj34dildx00a4j3z0nv171b7b0wl6xjks7wk6lv01")))) + "00rgrrmglslgb6j7whp0m5dlyl4436r647br05rrpv8cxrmbs2iv")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) -- cgit 1.4.1 From 60b598ee16f63b382fc119c923af31cd8b87eabd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:46 +0200 Subject: gnu: r-keggrest: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-keggrest): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d395cb739b..0a898d22b6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3273,14 +3273,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s")))) + "15313d20v3ziyn52fhc6fbzcy1kxjkdx18124bxhdfd14f4aypcd")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 595b75e05c149f4c99a40fbf6b573cb9c54369f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:46 +0200 Subject: gnu: r-limma: Update to 3.48.0. * gnu/packages/bioconductor.scm (r-limma): Update to 3.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0a898d22b6..61cf933b74 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3299,13 +3299,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-limma (package (name "r-limma") - (version "3.46.0") + (version "3.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz")))) + "1mkpl2b1ksylc6dih4a6kgjjia8advikzmqmv762j4r7gya950pf")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") -- cgit 1.4.1 From 0b3fd7e89ae63a51c96e4b76d44eb6f064576e42 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:46 +0200 Subject: gnu: r-methylkit: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-methylkit): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 61cf933b74..e45cef6bb5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3318,13 +3318,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3")))) + "147nag4rz2xpjkkf8rmhja9k4ixjj1hsb0lq3lw7mw6q67zxsvf3")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From c966cef2b45363375a6d77e4fa1b0730721237e6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:46 +0200 Subject: gnu: r-mutationalpatterns: Update to 3.2.0. * gnu/packages/bioconductor.scm (r-mutationalpatterns): Update to 3.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e45cef6bb5..2c6baf5278 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3392,14 +3392,14 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "3.0.1") + (version "3.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35")))) + "0433i4xbz8hrfaj8fxgzps3x8dqrl5vgwzg7qmp4cy5sb1lw5wvs")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From d647eb090bcec1748c6bd3b3fee6d77bd507cf50 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:46 +0200 Subject: gnu: r-msnbase: Update to 2.18.0. * gnu/packages/bioconductor.scm (r-msnbase): Update to 2.18.0. [propagated-inputs]: Remove r-preprocesscore; add r-mscoreutils. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2c6baf5278..e63598706d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3437,14 +3437,14 @@ in SNV base substitution data.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.16.1") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h")))) + "1z7s17j6zgb70m0khyf9icqlnbnzlivca7vw7j0vxyw417ld9lkr")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -3459,11 +3459,11 @@ in SNV base substitution data.") ("r-lattice" ,r-lattice) ("r-maldiquant" ,r-maldiquant) ("r-mass" ,r-mass) + ("r-mscoreutils" ,r-mscoreutils) ("r-mzid" ,r-mzid) ("r-mzr" ,r-mzr) ("r-pcamethods" ,r-pcamethods) ("r-plyr" ,r-plyr) - ("r-preprocesscore" ,r-preprocesscore) ("r-protgenerics" ,r-protgenerics) ("r-rcpp" ,r-rcpp) ("r-s4vectors" ,r-s4vectors) -- cgit 1.4.1 From 00b217493036a6bf7836fe880c2734f10f3c43a6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:46 +0200 Subject: gnu: r-mzid: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-mzid): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e63598706d..e2701d17df 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3539,14 +3539,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-mzid (package (name "r-mzid") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2")))) + "1wsy6frxa5602jqb1nlqv39mzgpid8wfyvb9m2jb6srv7p59rgys")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 5d37cee6c133d07320624de19bab83e180e5f19d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:46 +0200 Subject: gnu: r-organismdbi: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-organismdbi): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e2701d17df..cd57576e37 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3627,14 +3627,14 @@ previously been used in XCMS.") (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw")))) + "0p8ccpdchdwci4kv9y07wdadzgms8nipvg6rm1rll35jcflnnkxi")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 0ec6177cc12b0d127d1c224b4a1b23799477a637 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:47 +0200 Subject: gnu: r-pcamethods: Update to 1.84.0. * gnu/packages/bioconductor.scm (r-pcamethods): Update to 1.84.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cd57576e37..297c9641ef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3659,14 +3659,14 @@ the fact that each of these packages implements a select methods.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.82.0") + (version "1.84.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0")))) + "1ccqsxn487dy92c2d1iffh9917z4zq5ia92zv2h6pi00jjc6ymb5")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From dc67525ae6fd57dfdc19843d12912c7e9c6c7559 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:47 +0200 Subject: gnu: r-protgenerics: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-protgenerics): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 297c9641ef..8211632676 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3689,14 +3689,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz")))) + "1c79k8nc28782w5gxi7pkm8jmddq1hdw6khs9kgsp8dyk60ak6fq")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") -- cgit 1.4.1 From 7c45bc9391991e6e2750568e14e0bb9a5143f329 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:47 +0200 Subject: gnu: r-rbgl: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-rbgl): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8211632676..6d08744ec5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3709,14 +3709,14 @@ proteomics packages.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz")))) + "0l40ibf8g5s4ay83s92l198jjqc5l09hcmxqcjrpifvp5pjf9yy5")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 38fa99c1d09323dff6962489b33f00f765d9b66f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:47 +0200 Subject: gnu: r-rcas: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-rcas): Update to 1.18.0. [propagated-inputs]: Add r-knitr. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6d08744ec5..c20a2499c4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3732,13 +3732,13 @@ the graph algorithms contained in the Boost library.") (define-public r-rcas (package (name "r-rcas") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m")))) + "0l92v870ndna8zjqwzf22fb9vyhkh6942v4gaiqr1yc4qr521p5p")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs @@ -3757,6 +3757,7 @@ the graph algorithms contained in the Boost library.") ("r-ggseqlogo" ,r-ggseqlogo) ("r-gprofiler2" ,r-gprofiler2) ("r-iranges" ,r-iranges) + ("r-knitr" ,r-knitr) ("r-pbapply" ,r-pbapply) ("r-pheatmap" ,r-pheatmap) ("r-plotly" ,r-plotly) -- cgit 1.4.1 From 2da4ee4c777e44ca032468b100c9d026413c0ed3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:47 +0200 Subject: gnu: r-regioner: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-regioner): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c20a2499c4..a76d0194a8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3782,14 +3782,14 @@ library implementing most of the pipeline's features.") (define-public r-regioner (package (name "r-regioner") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi")))) + "0xzzaz3cl6pyxfsg0d931v8k15wbd05s5mnsb7igxldc5qqg3nsl")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 51bee5c40f9b5233671c5d45f3a0b0da792695b5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:47 +0200 Subject: gnu: r-reportingtools: Update to 2.32.0. * gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a76d0194a8..af7d5fe4a0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3813,14 +3813,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.30.2") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "1vvra7l29s7lnq996nwlpzbkrbdkr3ivkgmfp4kndfykxsl9q4vb")))) + "0v6wzfswwcd1xdxgwa9gzlkmavr4p55jy11k84anh0rs0xx3dmmj")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) -- cgit 1.4.1 From f2f4ca7456320b60891386e009462c4e6306af1b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:47 +0200 Subject: gnu: r-rhdf5filters: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-rhdf5filters): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index af7d5fe4a0..3d86360f31 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3891,14 +3891,14 @@ the available RAM.") (define-public r-rhdf5filters (package (name "r-rhdf5filters") - (version "1.2.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5filters" version)) (sha256 (base32 - "1bjlgc76vx0z81s8vci9ln1d2s3b157qnm32xs36mnyjk31ivasz")))) + "133v0s452acspi4dbf6gsa2xrr0qza86jdjjbpwhdv6zfd1djbgc")))) (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From e22d743aa67da6ff4ea75da7f242385a4b0798e5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:47 +0200 Subject: gnu: r-rsamtools: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-rsamtools): Update to 2.8.0. --- gnu/packages/bioconductor.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3d86360f31..12c5dfece8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3917,13 +3917,13 @@ HDF5 datasets.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554")))) + "0arhh5bbx3pmxmkh5sjgczcswqy83d35r7cjhd2knpczdvrixaq5")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -3935,8 +3935,7 @@ HDF5 datasets.") (substitute* "DESCRIPTION" (("zlibbioc, ") "")) (substitute* "NAMESPACE" - (("import\\(zlibbioc\\)") "")) - #t))))) + (("import\\(zlibbioc\\)") ""))))))) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) -- cgit 1.4.1 From 5ce21e7153badd490eb98587bf5db2e77c36b8eb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:48 +0200 Subject: gnu: r-rtracklayer: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-rtracklayer): Update to 1.52.0. [propagated-inputs]: Add r-biocio and r-restfulr. --- gnu/packages/bioconductor.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 12c5dfece8..16c2a79473 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3986,13 +3986,13 @@ tab-delimited (tabix) files.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8")))) + "0iic0g0clsjd9ypdmfs6k52hrnmfszhxzg0xx89nszpasf69wghv")))) (build-system r-build-system) (arguments `(#:phases @@ -4002,20 +4002,21 @@ tab-delimited (tabix) files.") (substitute* "DESCRIPTION" ((" zlibbioc,") "")) (substitute* "NAMESPACE" - (("import\\(zlibbioc\\)") "")) - #t))))) + (("import\\(zlibbioc\\)") ""))))))) (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("zlib" ,zlib))) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocio" ,r-biocio) ("r-biostrings" ,r-biostrings) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-rcurl" ,r-rcurl) + ("r-restfulr" ,r-restfulr) ("r-rsamtools" ,r-rsamtools) ("r-s4vectors" ,r-s4vectors) ("r-xml" ,r-xml) -- cgit 1.4.1 From 58ae27d46cc1ddb0df7f11be3cd62fc0acf2c213 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:48 +0200 Subject: gnu: r-seqlogo: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-seqlogo): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 16c2a79473..4df086b59f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4065,14 +4065,14 @@ differential expression analysis, RNAseq data and related problems.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1")))) + "1253sj1hc6bbrff0iv5xa3v9znqvisll0fy6fdjka9c778fn4mcp")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs -- cgit 1.4.1 From 76edc5ae98ccdc17d3f0a8da07b2b9b6e7593e0d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:48 +0200 Subject: gnu: r-seqpattern: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-seqpattern): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4df086b59f..6290911fed 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4088,13 +4088,13 @@ Stephens (1990).") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq")))) + "0h74z84zyvfzclsm0g13b95hirn99185wc6lp53jkzah9yyi59ay")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) -- cgit 1.4.1 From 15f371cc89dde46f9d71281be64b4f892edb27fc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:48 +0200 Subject: gnu: r-shortread: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-shortread): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6290911fed..8a1f3a222b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4115,14 +4115,14 @@ reference point and sorted by a user defined feature.") (define-public r-shortread (package (name "r-shortread") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9")))) + "0zqinw3c6h5v1c5nhzkiziirws16nbviccgw8nj2d22r33dbqwp3")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs -- cgit 1.4.1 From 8e0dac09c4f7afea565e5b4b8f907d0fac148c9e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:48 +0200 Subject: gnu: r-slingshot: Update to 2.0.0. * gnu/packages/bioconductor.scm (r-slingshot): Update to 2.0.0. [propagated-inputs]: Remove r-ape; add r-s4vectors and r-trajectoryutils. --- gnu/packages/bioconductor.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8a1f3a222b..de7be4c8a7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4188,21 +4188,22 @@ structures to hold pseudotime inference results.") (define-public r-slingshot (package (name "r-slingshot") - (version "1.8.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "slingshot" version)) (sha256 (base32 - "0sz4frlk7c1g8adyfcgi1mf1xsf9n5zib4bw7j9kl711dbhvkqwl")))) + "1aqsz2kxwax8d8d5iv3zk5hlyk5aya1wbxs1wky2rgccw4d35whx")))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-igraph" ,r-igraph) + `(("r-igraph" ,r-igraph) ("r-matrixstats" ,r-matrixstats) ("r-princurve" ,r-princurve) + ("r-s4vectors" ,r-s4vectors) ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-trajectoryutils" ,r-trajectoryutils))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/slingshot") -- cgit 1.4.1 From 8c0f2d9e0a68fc323da9ce05a81710344bb36cc8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:48 +0200 Subject: gnu: r-structuralvariantannotation: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-structuralvariantannotation): Update to 1.8.0. [propagated-inputs]: Add r-rlang. [native-inputs]: Add r-knitr. --- gnu/packages/bioconductor.scm | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index de7be4c8a7..07f123859f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4220,24 +4220,27 @@ graph construction.") (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "StructuralVariantAnnotation" version)) (sha256 (base32 - "0ff40703iyf5wk77hbqhphfxnzc2wcshnjhvh66c5l0jvj9z8xvc")))) + "10h63h1v87nvm3bfyr6dsjlbmzxf1vks30d0xz6q4hssqq9xlzgv")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) + `(("r-assertthat" ,r-assertthat) + ("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) ("r-dplyr" ,r-dplyr) ("r-genomicranges" ,r-genomicranges) + ("r-rlang" ,r-rlang) ("r-rtracklayer" ,r-rtracklayer) ("r-stringr" ,r-stringr) - ("r-assertthat" ,r-assertthat) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/") (synopsis "R package designed to simplify structural variant analysis") (description -- cgit 1.4.1 From 6eaa9221d93a4b6ffb75dd5cb0043b3f897c218a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:48 +0200 Subject: gnu: r-summarizedexperiment: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-summarizedexperiment): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 07f123859f..ffa77c191d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4253,13 +4253,13 @@ involving two separate genomic loci encoded as GRanges objects.") (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "04x6d4mcsnvz6glkmf6k2cv3fs8zk03i9rvv0ahpl793n8l411ps")))) + "16np5ik6jgbi68mhlib6yskywwbaa50mlr7m3sh1hqk889whfn1g")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) -- cgit 1.4.1 From 81c55df9a87bc1d5502ce87c7b07fd67ab9cdc3a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:48 +0200 Subject: gnu: r-sva: Update to 3.40.0. * gnu/packages/bioconductor.scm (r-sva): Update to 3.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ffa77c191d..50e7504b57 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4287,14 +4287,14 @@ samples.") (define-public r-sva (package (name "r-sva") - (version "3.38.0") + (version "3.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy")))) + "12jkcybdfspabh7x124d44l9fj1hwwg3gvcqxvz5wpkiflc2vkji")))) (build-system r-build-system) (propagated-inputs `(("r-edger" ,r-edger) -- cgit 1.4.1 From 7728c5909f7a980ada444ac4127e8a55506fdbcc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:49 +0200 Subject: gnu: r-systempiper: Update to 1.26.2. * gnu/packages/bioconductor.scm (r-systempiper): Update to 1.26.2. [propagated-inputs]: Add r-testthat. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 50e7504b57..853d01c29a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4318,14 +4318,14 @@ unmodeled, or latent sources of noise.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.24.6") + (version "1.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "05qnn105gm423fka4kb84vpgzjmz1py6mxpfa2agwwmc5v012qbp")))) + "1apqi5ih06s37v7wpp13ybksiinrwj0ii6mx6vvvfkb6ix0wljws")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -4351,6 +4351,7 @@ unmodeled, or latent sources of noise.") ("r-shortread" ,r-shortread) ("r-stringr" ,r-stringr) ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-testthat" ,r-testthat) ("r-yaml" ,r-yaml) ("r-variantannotation" ,r-variantannotation))) (native-inputs -- cgit 1.4.1 From ad6ba3de6506ad054ceabf03d410a3ddd6731a50 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:49 +0200 Subject: gnu: r-topgo: Update to 2.44.0. * gnu/packages/bioconductor.scm (r-topgo): Update to 2.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 853d01c29a..aa50ea895a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4373,13 +4373,13 @@ annotation infrastructure.") (define-public r-topgo (package (name "r-topgo") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl")))) + "1ggi7yrhkyi85p3sfj3yd95n9mzq1xpff28ixa4dl9yzasks1v5a")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) -- cgit 1.4.1 From 2817a8f2921ea0df05d93d3eb64a4c3233fdbdd5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:49 +0200 Subject: gnu: r-tximport: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-tximport): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aa50ea895a..6081a13c1d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4406,13 +4406,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-tximport (package (name "r-tximport") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34")))) + "0ip2yr0zspf2aagskxl4dwncr48dw5qb90an3sswnnh2dqdb82if")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From c73b9d6c66f29169c91924b2ebf975d49a083342 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:49 +0200 Subject: gnu: r-variantannotation: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-variantannotation): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6081a13c1d..72e4e359db 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4430,13 +4430,13 @@ of gene-level counts.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw")))) + "0c9r00j8a3bs6n0dv4wi17jc1ljzvr3r2bi4h9axhcsf2ip906rh")))) (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs -- cgit 1.4.1 From e4a34df239341bb98df80d57d0d3af639f214750 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:49 +0200 Subject: gnu: r-vsn: Update to 3.60.0. * gnu/packages/bioconductor.scm (r-vsn): Update to 3.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 72e4e359db..77977d55dc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4468,14 +4468,14 @@ coding changes and predict coding outcomes.") (define-public r-vsn (package (name "r-vsn") - (version "3.58.0") + (version "3.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb")))) + "0nppph3kv8z83368snb8s3n4vcqj829yyi1kh4q09qvq18rhvssv")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) -- cgit 1.4.1 From 092d2a8d85710e3a3a190626b6d224b5e9df640f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:49 +0200 Subject: gnu: r-xvector: Update to 0.32.0. * gnu/packages/bioconductor.scm (r-xvector): Update to 0.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 77977d55dc..eb23bcd507 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4504,13 +4504,13 @@ and specific in detecting differential transcription.") (define-public r-xvector (package (name "r-xvector") - (version "0.30.0") + (version "0.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq")))) + "1cw34gd9iaspl0v737xl7rngq63zrj03a5ngai15ggrnv1sq2aqr")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) -- cgit 1.4.1 From 473371dfc182465f224beb06624f928ca8cd3112 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:49 +0200 Subject: gnu: r-zlibbioc: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-zlibbioc): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eb23bcd507..f0e2a68f05 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4540,13 +4540,13 @@ and specific in detecting differential transcription.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg")))) + "1dv5bf12kzk1yzyfs3g5syim16sbi44kalvzj2i2xcnxnl6x60ip")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) -- cgit 1.4.1 From c68607725bcf6cb46f22a14662c3f6449fc45fb1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:50 +0200 Subject: gnu: r-geneplotter: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-geneplotter): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f0e2a68f05..479f5105f7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4559,14 +4559,14 @@ libraries for systems that do not have these available via other means.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx")))) + "1d085lfa3yif5wkys1fb0zzgg0cqwd1y18vasgqqdr6rva075d4z")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) -- cgit 1.4.1 From 2c9c656f4747cb9e089e9d8e0f8407bfd97505fc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:50 +0200 Subject: gnu: r-oligoclasses: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-oligoclasses): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 479f5105f7..82ed999f2d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4584,14 +4584,14 @@ libraries for systems that do not have these available via other means.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy")))) + "1nsfyfpj264h6y322pzz0i001b0m862j3skbq5rjwlrj1p8j2gi7")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 359c350c7dfc74dc4b67ef7750660c6ea61f1528 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:50 +0200 Subject: gnu: r-oligo: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-oligo): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 82ed999f2d..a84270523e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4619,14 +4619,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.54.1") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3")))) + "0fyq77im6s79havjwbchhqhnllxs134jsi98g6msxz66h16lj3al")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit 1.4.1 From 371149da6f63ab46946a80c98006449a4925f9d8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:50 +0200 Subject: gnu: r-qvalue: Update to 2.24.0. * gnu/packages/bioconductor.scm (r-qvalue): Update to 2.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a84270523e..5bf5635528 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4655,14 +4655,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qvalue (package (name "r-qvalue") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5")))) + "0xssanffh1hr7f48mnazcpwi25rdp7mxlyb9nbf4q2mp7m40jnpm")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) -- cgit 1.4.1 From 941a86851544dd94269f9f073f2cef4b5d70a08d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:50 +0200 Subject: gnu: r-apeglm: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-apeglm): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5bf5635528..adfe4c9c86 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4710,13 +4710,13 @@ integration with @code{Rcpp}.") (define-public r-apeglm (package (name "r-apeglm") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 - "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2")))) + "1xld6ar440achik4dbd7vhiw6jfj0sb96jm52n7hav5bv4gag3mh")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 737a2287029c7b0bb3aa730501c2ce71b85fcbcd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:51 +0200 Subject: gnu: r-greylistchip: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-greylistchip): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index adfe4c9c86..518ea8569f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4737,13 +4737,13 @@ posterior for individual coefficients.") (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6")))) + "1g9ja8p90czx83ar0l9ran7m6aggvszdbqm714fq7z4rxq9b4hs3")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 27abca93b13fae9f6040891ceda3fae710da6ed6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:51 +0200 Subject: gnu: r-diffbind: Update to 3.2.1. * gnu/packages/bioconductor.scm (r-diffbind): Update to 3.2.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 518ea8569f..f84dd1579f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4764,14 +4764,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.0.15") + (version "3.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "06f613s8d9z51njyf839g22gwybx9zs5n6xghwr5j1ad2n4m6qwi")))) + "12x80z1a8gihqrlaxmzk80nc5700la72lival58s4wjv4k2lhyf3")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From ff7a86f0ca342e9f48c961881c19944d026ef868 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:51 +0200 Subject: gnu: r-mbkmeans: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-mbkmeans): Update to 1.8.0. [propagated-inputs]: Remove r-bluster; add r-rcpparmadillo. --- gnu/packages/bioconductor.scm | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f84dd1579f..aaee7f6e0d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4842,29 +4842,29 @@ processing to visualization and annotation.") (define-public r-mbkmeans (package (name "r-mbkmeans") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mbkmeans" version)) (sha256 (base32 - "0rc83mh9xzwczfn88j0xah86ldzi1kdfqgd938nj57ifx3zci4xh")))) + "1k7ngpx4s50jplrsv19zzjr7izpdl9wwppb218ih5cp0ki1gcc2n")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-clusterr" ,r-clusterr) + `(("r-beachmat" ,r-beachmat) ("r-benchmarkme" ,r-benchmarkme) + ("r-biocparallel" ,r-biocparallel) + ("r-clusterr" ,r-clusterr) + ("r-delayedarray" ,r-delayedarray) ("r-matrix" ,r-matrix) - ("r-bluster" ,r-bluster) - ("r-beachmat" ,r-beachmat) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rhdf5lib" ,r-rhdf5lib) - ("r-biocparallel" ,r-biocparallel))) + ("r-s4vectors" ,r-s4vectors) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://bioconductor.org/packages/mbkmeans") (synopsis "Mini-batch k-means clustering for single-cell RNA-seq") (description "This package implements the mini-batch k-means algorithm for -- cgit 1.4.1 From bed64f7be6534cfe8268d658340f53b39c4f3973 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:51 +0200 Subject: gnu: r-multtest: Update to 2.48.0. * gnu/packages/bioconductor.scm (r-multtest): Update to 2.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aaee7f6e0d..8b3613bec1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4874,14 +4874,14 @@ large datasets, including support for on-disk data representation.") (define-public r-multtest (package (name "r-multtest") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q")))) + "1wi15v4llgv11hpb2j9h4a35nrnawnmvbz5d5dvgy8lhqrlq8w9a")))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival) -- cgit 1.4.1 From fceca5cd824f214f3e1cfa1ab60ebc70630fab4b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:51 +0200 Subject: gnu: r-graph: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-graph): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8b3613bec1..ac1abe7fe3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4912,13 +4912,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4")))) + "1i7s198d5kw4gk6nqqsd3vqaknj4493p822f2za8q95gv6x02rxa")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) -- cgit 1.4.1 From 538605493c534b2259ebb51bda699ff338aa43ab Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:51 +0200 Subject: gnu: r-chippeakanno: Update to 3.26.0. * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.26.0. [propagated-inputs]: Add r-interactionset. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ac1abe7fe3..cf7210a459 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5010,14 +5010,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.24.2") + (version "3.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0l417aygs89wf1j9fjpfjhahzskbpbgcrm8xpx3qm4s0307vfzkw")))) + "1wnmsdrb4wz2qprj5mnd3h0wx32y2mpy3xg7mjbgwlqn9bzpw3gk")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -5034,6 +5034,7 @@ determining dependencies between variables, code improvement suggestions.") ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-graph" ,r-graph) + ("r-interactionset" ,r-interactionset) ("r-iranges" ,r-iranges) ("r-keggrest" ,r-keggrest) ("r-matrixstats" ,r-matrixstats) -- cgit 1.4.1 From 202202c8ada016d40afd640ef5a3834bc0ad6e35 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:51 +0200 Subject: gnu: r-matrixgenerics: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cf7210a459..33d673c0fd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5064,13 +5064,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.2.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "163f0z33cv6038gcjdxn1hadcg9b09qgvm6zc5zn97y4rc8grkrb")))) + "1xq3a9ls125wfnhn13rdbsxzq3f6klsspx7h0znd6l67f5j5k25s")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) -- cgit 1.4.1 From 0045d21f6787a803690554c1c318a2743efd1a34 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:52 +0200 Subject: gnu: r-marray: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-marray): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 33d673c0fd..c52cf81e54 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5091,12 +5091,12 @@ incompatibilities.") (define-public r-marray (package (name "r-marray") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray")))) + (base32 "0wpmrhqpyv27h1hn31hzz21r74r7yqx79ljv8i8gn6ix8lf5ca56")))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma))) -- cgit 1.4.1 From 09c90d8fb43b434bd0c3ec087680c3cadb476ea9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:52 +0200 Subject: gnu: r-cghbase: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-cghbase): Update to 1.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c52cf81e54..ab5dc84bd4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5110,12 +5110,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4")))) + (base32 "1p87k4vw981k97d9bckmprrfg55jwd91658rgxzjj8hnschf28a4")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 1c3e2392709392e939f54d7e42e0e1e7c4486662 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:52 +0200 Subject: gnu: r-cghcall: Update to 2.54.0. * gnu/packages/bioconductor.scm (r-cghcall): Update to 2.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ab5dc84bd4..ef55d861ef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5130,12 +5130,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba")))) + (base32 "1zik04y2q0anzy85l0b4ryzkxpfx2fnmpwp5s7akyk1jfl2r8gw7")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 11c7a044bd8eb25e1922def0127040f8125c1359 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:52 +0200 Subject: gnu: r-qdnaseq: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ef55d861ef..ac76e1ed65 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5153,12 +5153,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph")))) + (base32 "1p4544xlarkbgs9kybrrawq3v7qr6ix62nrc6l7dcksh2ka69yzf")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 38f2e3979f5d21fb7116772d36cb68501815aa38 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:52 +0200 Subject: gnu: r-bayseq: Update to 2.26.0. * gnu/packages/bioconductor.scm (r-bayseq): Update to 2.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ac76e1ed65..5628002476 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5186,14 +5186,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215")))) + "0hyc0sl2nf18bz0jxbzim0v41zwh2rnnr7l3p6zkk9wnw5gn7bbc")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From afc59d2e2c6840e46c0b1d7c8b4b72140c9fb3a5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:52 +0200 Subject: gnu: r-chipcomp: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5628002476..3274426d6f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5212,14 +5212,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7")))) + "1kfxjh1mynrgqsy2q6byf03cbymqc8w7l7672iyd0wj5qzlif4h5")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 0443b3c18058e24f860ae7bcbfe0cbf2f1306848 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:52 +0200 Subject: gnu: r-riboprofiling: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-riboprofiling): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3274426d6f..01244bf2e0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5246,14 +5246,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg")))) + "1jmd8yrv7p7hn4gdibg3svmhqxjyrnfp7cgsqg8zv862lgd75zsl")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 43a0a48a69ebf64a250c5b187954fe451706ed68 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:52 +0200 Subject: gnu: r-riboseqr: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-riboseqr): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 01244bf2e0..f9b7d87efb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5287,14 +5287,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr")))) + "1m5w2j35wr0lzwir4s58z757vrcsj5mglsqrkvs241k0hlmn06qa")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From ba7757cf1f53b96ba19a099d77362b1ed441a596 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:53 +0200 Subject: gnu: r-interactionset: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-interactionset): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f9b7d87efb..9866902d77 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5315,14 +5315,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "0dx6yw6rxgkcidnnyjzv57vzd112nf9n2bj6dkv7r3a2d2wj6xh4")))) + "034xidjmn67n1471fnpdmz7gjm6p05cj8sp9nssc3gxdzn54a6xb")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) -- cgit 1.4.1 From 675f1a91441805932f0ae98d68ea8d5d2ecc3688 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:53 +0200 Subject: gnu: r-genomicinteractions: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9866902d77..7b557f5e2e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5349,14 +5349,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd")))) + "0zjl7rp5fk14kqsx0bkbpq6hqahbkiyvwa9aggp4kfb8hnmz9qal")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) -- cgit 1.4.1 From 87d6e6801521c8fec172ebebe8ae031e36734dcd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:53 +0200 Subject: gnu: r-ctc: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-ctc): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7b557f5e2e..994416cac5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5390,14 +5390,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp")))) + "1v8aysvy6a3r1iafc3xvk885c128kb3pb9zpcdhdjcn0by96k8hh")))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap))) (home-page "https://bioconductor.org/packages/ctc/") -- cgit 1.4.1 From 4485bc7183c98e02d509fa3f6bf7285cbdfce522 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:53 +0200 Subject: gnu: r-goseq: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-goseq): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 994416cac5..d5a506ce92 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5410,14 +5410,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509")))) + "07qrxssx4rb8r958r1smx8xfpzdxpp55hci3201hcmz3mxz77i0s")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From 089f64657bd584e3a13641ca339d1b8a02460dff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:53 +0200 Subject: gnu: r-glimma: Update to 2.2.0. * gnu/packages/bioconductor.scm (r-glimma): Update to 2.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d5a506ce92..0c8d5a9bd0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5436,14 +5436,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv")))) + "0dsk8qmwimzmd1x4k4jwg9q11jm1ahn8cw0gzd6s2gmigfls4hsa")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 481c3222e68026249bf413702745812948ed30e0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:53 +0200 Subject: gnu: r-rots: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-rots): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0c8d5a9bd0..fb2c708092 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5469,14 +5469,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n")))) + "18wyi73l95df182vg3m014sxwdbpggr61vsbazhyw4vyx2fnzmpl")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 79c1e0335f7f7e3584cc447612890379e6acaf82 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:53 +0200 Subject: gnu: r-plgem: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-plgem): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fb2c708092..18debfddfb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5493,14 +5493,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a")))) + "1rz5jk5bgpk7gjknx79jyslahjg46q2f4bx6dgd0vwmarc29a45z")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From c6078d915d2366769dd1b2a0f0a42bba96d109c5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:53 +0200 Subject: gnu: r-inspect: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-inspect): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 18debfddfb..cd2ef1572c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5518,14 +5518,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483")))) + "0jh5db9dv5pb6b50sg22x8q55m3h0h0nkmb9mivvvp22dhyrd82z")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From cac283944796db6d2cedc0b28f4a70b325444800 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:53 +0200 Subject: gnu: r-dnabarcodes: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-dnabarcodes): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cd2ef1572c..1cbd9d177c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5565,14 +5565,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg")))) + "1wiqmzjcb7flp7ldcgbx91asxxrmm1rg9pcfljniab9xcsldhksp")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 618f98c022b6f464b4323cda3172341da3e64c70 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:54 +0200 Subject: gnu: r-ruvseq: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1cbd9d177c..416fd43e94 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5594,14 +5594,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh")))) + "1fy0k1p0m209lzjpd5jhfnifa22lrn63qq3a3kn5g0xhbbmijzac")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From f5ae14832c856bb1ca4a12297b33e7e233bd7834 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:54 +0200 Subject: gnu: r-biocneighbors: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-biocneighbors): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 416fd43e94..f56a854c84 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5622,14 +5622,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.8.2") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7")))) + "0cjidi18wjip9xzx83890wjk40vvjq06prf1ag4m2kac47w01r7v")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 8aef574b84e7d95c3ee9f67c8023520d225a792f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:54 +0200 Subject: gnu: r-biocsingular: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.8.0. [propagated-inputs]: Add r-scaledmatrix. --- gnu/packages/bioconductor.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f56a854c84..e62822b8c1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5779,14 +5779,14 @@ missing values and weighting where appropriate.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni")))) + "1l0xgc3z5ci5sid198nsgg0k5i40rh877jybzmy0ify7rzv8carp")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs @@ -5798,7 +5798,8 @@ missing values and weighting where appropriate.") ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-rsvd" ,r-rsvd) - ("r-s4vectors" ,r-s4vectors))) + ("r-s4vectors" ,r-s4vectors) + ("r-scaledmatrix" ,r-scaledmatrix))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/LTLA/BiocSingular") -- cgit 1.4.1 From a10f236ca3b0e0e0b6511a1ce9856372616a7e94 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:54 +0200 Subject: gnu: r-savr: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-savr): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e62822b8c1..278b8cea97 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5858,14 +5858,14 @@ maps.") (define-public r-savr (package (name "r-savr") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic")))) + "1ynp334hm76zf05j4f6vha6r16s5f2ncxx9yviq4rxidk9r723jq")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 749cf40eccca7e59ec1643298aaee9672e270814 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:54 +0200 Subject: gnu: r-chipexoqual: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-chipexoqual): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 278b8cea97..2459e98e38 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5884,14 +5884,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag")))) + "0fbrf5s6pz115djm7xw95k1d0p7svi40aacbb3d52wmx5azwj424")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From ac27feed69efe43fe1651d4b40e9c41818df5a16 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:54 +0200 Subject: gnu: r-copynumber: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-copynumber): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2459e98e38..d02984249d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5924,13 +5924,13 @@ sequencing data.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm")))) + "03pvjzjrcsbjfw3855s3whfzin45vaipy7cahnj6fywdysvh8hps")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) -- cgit 1.4.1 From 729f6adcf4cc3f3df737374ae00657508740b8ef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:54 +0200 Subject: gnu: r-dnacopy: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d02984249d..0270a479bf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5947,14 +5947,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc")))) + "0mgq814f6c2271d2lxg763bsnv3ma4ari5xa4x1rbksv8yvcjc4d")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit 1.4.1 From 9a67123210c844ad3e8f3a86e83fb2ec3db07c74 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:54 +0200 Subject: gnu: r-ebseq: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-ebseq): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0270a479bf..e7c0f004ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6047,14 +6047,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny")))) + "0h5v3vrb90zim80bdnr3aw58g3h7zjqa4l9i0jwx5j19ywf54fdz")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From c63c44190d669b08bd1e633a7e2e8a58c623d586 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:55 +0200 Subject: gnu: r-karyoploter: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-karyoploter): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e7c0f004ac..5a313a7eb5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6071,13 +6071,13 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2")))) + "11sgxz2xz685pgm8mf0hzm6aryx4fj5g3dlffjzpqxh3awfqa19p")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From 0c15284ad0eeeeb6a253c3b6f568209c9ef55ae5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:55 +0200 Subject: gnu: r-lpsymphony: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5a313a7eb5..df5bec227e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6109,14 +6109,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9")))) + "0aw4b3p5z8ys7zlwy8s3bsqk03xwx42311yxr7q14w3f7sn3shzn")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit 1.4.1 From 2ed5a0844e8de0aaf1ce724f31bf81968b32aeca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:55 +0200 Subject: gnu: r-ihw: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-ihw): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index df5bec227e..05a8171e7d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6139,14 +6139,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0")))) + "0b393a8ayzbnrgkk562w1dj7avacpb3wc7yq7awiki24wi5g2lfw")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 79928c5e585aae10d6a15c18642bc9878f3cfa9c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:55 +0200 Subject: gnu: r-icobra: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-icobra): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 05a8171e7d..edad5fa590 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6171,14 +6171,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "183asczy9v2v1vrzxb7n7pa2yfzym3l24r3737k0jg6hnp2bpw50")))) + "190rkx3sivj68in36hhin5v535yd6fvlvm7l90w1bl38zpb7p6jn")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 12ec22ca50fe580c3210a5cfa27e7d483e722cff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:55 +0200 Subject: gnu: r-mast: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-mast): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index edad5fa590..4a7be7c757 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6207,14 +6207,14 @@ interactive exploration of results.") (define-public r-mast (package (name "r-mast") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn")))) + "1gkpagam5rap36viyr3n4psa658x9vckrxap1h67jasiiyrcfz2d")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 716ac28a58d058d5bd681301b0d4deb778afab9b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:55 +0200 Subject: gnu: r-monocle: Update to 2.20.0. * gnu/packages/bioconductor.scm (r-monocle): Update to 2.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4a7be7c757..457f8ccf11 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6242,14 +6242,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx")))) + "05j1vc51f39xalggdq27y7218gkr3zq7fh7jhzsb4jj7fpn837ry")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From d7390d7c632ab89ff39ebae0362e1c4fbed630e6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:55 +0200 Subject: gnu: r-noiseq: Update to 2.36.0. * gnu/packages/bioconductor.scm (r-noiseq): Update to 2.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 457f8ccf11..e7304e5927 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6361,14 +6361,14 @@ qPCR data, but could be used with other types as well.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f")))) + "18d51dv2ygsm7kkwal341f1wrwrazyns0045j00vld367kic8jiz")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 611024367b94157913667d8ce35f1caed894bd10 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:55 +0200 Subject: gnu: r-scdd: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-scdd): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e7304e5927..ebb2d4d27d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6388,14 +6388,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g")))) + "1dw9m3m99apmbs32461c6lnmy81n5hxbhz3p8jk419gajkh4v1ji")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 6db7802b5bb08f2841bd0ef4eec65614f812d0f5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:56 +0200 Subject: gnu: r-scone: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-scone): Update to 1.16.0. [propagated-inputs]: Add r-matrixgenerics and r-singlecellexperiment. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ebb2d4d27d..7b8981cf31 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6426,14 +6426,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73")))) + "1wlky6nkdpz8fya81l6zaxlxc30wyp2gkyh94y5995jwddll38z5")))) (build-system r-build-system) (propagated-inputs `(("r-aroma-light" ,r-aroma-light) @@ -6448,12 +6448,14 @@ distributions.") ("r-gplots" ,r-gplots) ("r-hexbin" ,r-hexbin) ("r-limma" ,r-limma) + ("r-matrixgenerics" ,r-matrixgenerics) ("r-matrixstats" ,r-matrixstats) ("r-mixtools" ,r-mixtools) ("r-rarpack" ,r-rarpack) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rhdf5" ,r-rhdf5) ("r-ruvseq" ,r-ruvseq) + ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) -- cgit 1.4.1 From 23d3d7af06bea839f7ba251306ddd9ec33070c0d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:56 +0200 Subject: gnu: r-geoquery: Update to 2.60.0. * gnu/packages/bioconductor.scm (r-geoquery): Update to 2.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7b8981cf31..be47cc2c8a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6470,14 +6470,14 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4")))) + "0jhkdbcd03d5n8vn3xkad6f21xjkawyxc9rdwcj8vwc8alx730am")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 7e29fb98e10cc99e21ec705ef99ce8502206f230 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:56 +0200 Subject: gnu: r-illuminaio: Update to 0.34.0. * gnu/packages/bioconductor.scm (r-illuminaio): Update to 0.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index be47cc2c8a..cd833d5b0e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6503,14 +6503,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.32.0") + (version "0.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay")))) + "1sy0i3nbzsw4ymdxaiwpyx1vcg9yp3i8xfjcymqwhv95j3kyglv9")))) (build-system r-build-system) (propagated-inputs `(("r-base64" ,r-base64))) -- cgit 1.4.1 From 18c81e5615be9f9d126525c9b914576b13c71d1e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:56 +0200 Subject: gnu: r-siggenes: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-siggenes): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cd833d5b0e..10c7002c99 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6524,14 +6524,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w")))) + "0lva0f255fcpy625frvij4n14q7nw4jcx8n2hlkxid4mgkfqwlhf")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From 136adea01b8b46ab48e8b96b67aad6b4ab3a5a00 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:56 +0200 Subject: gnu: r-bumphunter: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-bumphunter): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 10c7002c99..60396a7567 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6550,14 +6550,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk")))) + "0wi38vwfi8qr10x4xifhylxx7vfc6fqvqs649iq7lf0y7islwq2v")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From a387e1d89cecd3423d3c93d4a7e762c5c65a3ea7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:56 +0200 Subject: gnu: r-minfi: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-minfi): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 60396a7567..6d37badaa7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6584,14 +6584,14 @@ studies.") (define-public r-minfi (package (name "r-minfi") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi")))) + "189lzppvrz6bw2kpppawgsfjyh2ahyy8bi9z8srpas67qf2r8jmj")))) (build-system r-build-system) (propagated-inputs `(("r-beanplot" ,r-beanplot) -- cgit 1.4.1 From 973d33484b0b326d92875c00d59064931d9c61ab Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:56 +0200 Subject: gnu: r-methylumi: Update to 2.38.0. * gnu/packages/bioconductor.scm (r-methylumi): Update to 2.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6d37badaa7..457487f2a0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6635,14 +6635,14 @@ methylation arrays.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh")))) + "1941rc524ssx8gwhmwk40mgfrhddfs6hgldvs7bi22r29gm4y7qj")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) -- cgit 1.4.1 From f1635d65e720fbc3405a9e436d6cb6a6bbfc50c3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:56 +0200 Subject: gnu: r-lumi: Update to 2.44.0. * gnu/packages/bioconductor.scm (r-lumi): Update to 2.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 457487f2a0..1280c0e755 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6681,14 +6681,14 @@ and Infinium HD arrays are also included.") (define-public r-lumi (package (name "r-lumi") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3")))) + "0qjdxjdzfnnxcm07bf51v38388s5qf1i03l1sdb9jf3gxdh8yh02")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) -- cgit 1.4.1 From ac150da152244abb2e73a1349f136e993918afe8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:57 +0200 Subject: gnu: r-linnorm: Update to 2.16.0. * gnu/packages/bioconductor.scm (r-linnorm): Update to 2.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1280c0e755..6d1f655b1a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6720,14 +6720,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3")))) + "035hrniycqadmkwg8rmzw8szv0amhy31390izy91rfrld31v2yy7")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 0c35cde14f4672b3255f30d12edf13e971b14a9b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:57 +0200 Subject: gnu: r-ioniser: Update to 2.16.0. * gnu/packages/bioconductor.scm (r-ioniser): Update to 2.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6d1f655b1a..580cfafc28 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6781,14 +6781,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx")))) + "0fknlwdfd49v09zspg0337b0zzc8hqza3563yrw51viw3g35d6q3")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 2c5bba139237bb19ab4061452eeb3e7fdcdb1142 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:57 +0200 Subject: gnu: r-tradeseq: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-tradeseq): Update to 1.6.0. [propagated-inputs]: Remove r-clusterexperiment and r-dplyr; add r-matrix, r-matrixstats, and r-viridis. --- gnu/packages/bioconductor.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 580cfafc28..8ffbdd6003 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6878,23 +6878,23 @@ published results; and a routine for graphical display.") (define-public r-tradeseq (package (name "r-tradeseq") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tradeSeq" version)) (sha256 (base32 - "1ncmvn9kaksismvsjs042xsp8bfq1xnm0ds87dwpk95bnpj96a89")))) + "0fgmb309pvqf3chdhqgbd4lzhahcj5g71sica33nzn98qhipldx7")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocparallel" ,r-biocparallel) - ("r-clusterexperiment" ,r-clusterexperiment) - ("r-dplyr" ,r-dplyr) ("r-edger" ,r-edger) ("r-ggplot2" ,r-ggplot2) ("r-igraph" ,r-igraph) ("r-magrittr" ,r-magrittr) + ("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) ("r-mgcv" ,r-mgcv) ("r-monocle" ,r-monocle) ("r-pbapply" ,r-pbapply) @@ -6904,7 +6904,8 @@ published results; and a routine for graphical display.") ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-slingshot" ,r-slingshot) ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tibble" ,r-tibble))) + ("r-tibble" ,r-tibble) + ("r-viridis" ,r-viridis))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://statomics.github.io/tradeSeq/index.html") -- cgit 1.4.1 From 1ade726fdf7b85ca09569a88154f53f3ee6e3754 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:57 +0200 Subject: gnu: r-varianttools: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-varianttools): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8ffbdd6003..1f44603d26 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6948,14 +6948,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89")))) + "1gpzrln2clfrja8rzxhsis6bi1xqglh3h2lhvqlnrx4lqxhbkv9c")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From faf60162a374c4281fc3519dacbb6ffe447c76d3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:57 +0200 Subject: gnu: r-heatplus: Update to 3.0.0. * gnu/packages/bioconductor.scm (r-heatplus): Update to 3.0.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1f44603d26..e899b4f961 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6988,14 +6988,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "2.36.0") + (version "3.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n")))) + "0xwg3sxmihg3p6v3nxgrqy0nrqxi6razg3b3rjh2gcb2vv8gcqng")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 376d9dd825cb4f1bb8158df3ce40a80e139f43af Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:57 +0200 Subject: gnu: r-gosemsim: Update to 2.18.0. * gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e899b4f961..40a163864c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7013,14 +7013,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.16.1") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs")))) + "1fzmaxjzyvq6xj5ny1sjijdwi4krzjgyaz52fczpwrxijq5pnyn1")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From dda291540b0c9ae1a86a1d1a969d2e011342d237 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:57 +0200 Subject: gnu: r-anota: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-anota): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 40a163864c..067a3c12bb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7042,14 +7042,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x")))) + "039bmcv5l44gszb6xapbihp3mfqdaaa8mfc05y702p78i7x93g5y")))) (build-system r-build-system) (propagated-inputs `(("r-multtest" ,r-multtest) -- cgit 1.4.1 From 1bfe5c274f8f1fedaad1b3690c7e0a14bb380e89 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:57 +0200 Subject: gnu: r-sigpathway: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-sigpathway): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 067a3c12bb..59176f56cb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7073,14 +7073,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l")))) + "1xz5nbw5dzyah8az7mpwj8m27fsvpi2jjhfg3n27dsv8rvdncqi8")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") -- cgit 1.4.1 From c8bec0d962c68ad739df040ee0cbedee34ea5a6d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:58 +0200 Subject: gnu: r-fgsea: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-fgsea): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 59176f56cb..e0ae893e98 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7095,14 +7095,14 @@ phenotype of interest.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n")))) + "1mhdgy46nxgv7v54bk9bqfy0vgjzl1law7zy718swdd762xn6g9d")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) -- cgit 1.4.1 From ca136dd70a16f39166491e511e3e69bab489feff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:58 +0200 Subject: gnu: r-dose: Update to 3.18.0. * gnu/packages/bioconductor.scm (r-dose): Update to 3.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e0ae893e98..0a45ab266b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7127,14 +7127,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.16.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4")))) + "1x9cg6qlvbcdb965jh01w07ibc4lj30ikq1v312rdih3sn6zsdck")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 8b0dc8e39ca11cfc4f23d65fb051cf18a96a088c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:58 +0200 Subject: gnu: r-enrichplot: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.12.0. [propagated-inputs]: Add r-ggtree. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0a45ab266b..d95012cb50 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7162,20 +7162,21 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.10.2") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "0lm5yapd567jxcnz9m4a623aymf3q00svjrxp3rf0r9j77dgyisv")))) + "0nvjwwzpmhsfkxqrn8v1a1wcrvr3xl1wn5dy89vsrdydyv31gdc6")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) ("r-dose" ,r-dose) ("r-ggplot2" ,r-ggplot2) ("r-ggraph" ,r-ggraph) + ("r-ggtree" ,r-ggtree) ("r-gosemsim" ,r-gosemsim) ("r-igraph" ,r-igraph) ("r-magrittr" ,r-magrittr) -- cgit 1.4.1 From 2b4c784b2bfa37cf308996b883c4ad2ff561a7c0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:58 +0200 Subject: gnu: r-clusterprofiler: Update to 4.0.0. * gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.0.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d95012cb50..2da0551040 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7199,14 +7199,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "3.18.1") + (version "4.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "04v1xsxfxxy8rdjfswv4crpzkx9592r2sh3cjh1kb54sd4lyb6si")))) + "1lmrb6ddpx1p3kdrwszhxq6nndmbiqipzrclk64mnp63y7g50q56")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) -- cgit 1.4.1 From 2a7532cca8d6a7f8ca519e5429f1f794caac0637 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:58 +0200 Subject: gnu: r-clusterexperiment: Update to 2.12.0. * gnu/packages/bioconductor.scm (r-clusterexperiment): Update to 2.12.0. [propagated-inputs]: Remove r-rspectra; add r-biocsingular. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2da0551040..5ef15bfcb9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7236,19 +7236,20 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.10.1") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "04n3lcm7dh07sjkzyv83m55mx3lz0lkcy8yq9hi0zywqyrhyzz7z")))) + "1fhmayciwn1m124b4dcs3gzbghgk9f7a7qmjnvvxc958cywcwkx5")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) (propagated-inputs `(("r-ape" ,r-ape) ("r-biocgenerics" ,r-biocgenerics) + ("r-biocsingular" ,r-biocsingular) ("r-cluster" ,r-cluster) ("r-delayedarray" ,r-delayedarray) ("r-edger" ,r-edger) @@ -7265,7 +7266,6 @@ profiles (GO and KEGG) of gene and gene clusters.") ("r-pracma" ,r-pracma) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) - ("r-rspectra" ,r-rspectra) ("r-s4vectors" ,r-s4vectors) ("r-scales" ,r-scales) ("r-singlecellexperiment" ,r-singlecellexperiment) -- cgit 1.4.1 From ad3b03d6ad9ce936f13426fc56411c3aed668ba9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:58 +0200 Subject: gnu: r-mlinterfaces: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.72.0. [propagated-inputs]: Add r-magrittr. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5ef15bfcb9..156941121e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7282,14 +7282,14 @@ expression data sets.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r")))) + "0ipzv7wdvfqhdyjiak956qq201igsdxm6dr6rh3dj6cssgsrnrpb")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -7303,6 +7303,7 @@ expression data sets.") ("r-genefilter" ,r-genefilter) ("r-ggvis" ,r-ggvis) ("r-hwriter" ,r-hwriter) + ("r-magrittr" ,r-magrittr) ("r-mass" ,r-mass) ("r-mlbench" ,r-mlbench) ("r-pls" ,r-pls) -- cgit 1.4.1 From 387c0231056211a8571fa7f0e3e3e9daf230f301 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:58 +0200 Subject: gnu: r-annaffy: Update to 1.63.1. * gnu/packages/bioconductor.scm (r-annaffy): Update to 1.63.1. [propagated-inputs]: Add r-biocmanager. --- gnu/packages/bioconductor.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 156941121e..ee2f5bfb3b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7324,14 +7324,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.62.0") + (version "1.63.1") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i")))) + "071qr68dn8k3mvwgpllbk2a4g6f6yyv2087q5rmpb22lkfvi4hwv")))) (build-system r-build-system) (arguments `(#:phases @@ -7339,11 +7339,11 @@ data in R and Bioconductor containers.") (add-after 'unpack 'remove-reference-to-non-free-data (lambda _ (substitute* "DESCRIPTION" - ((", KEGG.db") "")) - #t))))) + ((", KEGG.db") ""))))))) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) + ("r-biocmanager" ,r-biocmanager) ("r-dbi" ,r-dbi) ("r-go-db" ,r-go-db))) (home-page "https://bioconductor.org/packages/annaffy/") -- cgit 1.4.1 From 2aad8aa075aaab0fc1cb1bd41581a774c410a1ca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:59 +0200 Subject: gnu: r-a4core: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-a4core): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ee2f5bfb3b..33e26a4eab 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7360,14 +7360,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2")))) + "00fi753nsayv0xspavw8r9ni1sim8ng33hp3d3kj2b8ihygd1s10")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 319d9dcfb29f452b0a05ae06b69e5ae964806c5b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:59 +0200 Subject: gnu: r-a4classif: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-a4classif): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 33e26a4eab..1e4af894fb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7385,14 +7385,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz")))) + "1lz85bys5dp5d1ir9c9c4wy85wkk62s14niyzzxaqrxpsji2p2iw")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 751b4904b068649c31767f38a6f7e68e360b6e56 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:59 +0200 Subject: gnu: r-a4preproc: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-a4preproc): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e4af894fb..3d64f8e19c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7415,14 +7415,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i")))) + "1jibm2f5glzsrvl64hxc5sf59d4w6ry0f663p619hfr44mi1mpri")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 1217dab2e24ace3507f21528c2c88f72c7c1b279 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:59 +0200 Subject: gnu: r-a4reporting: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-a4reporting): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3d64f8e19c..b2e3e61241 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7440,14 +7440,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy")))) + "09jjfby5znmg2fdkhpbinx2v21zrfa44qq7cylcn9ipffqx3pk86")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 76fb2de29b1840adc99bde474c25951b637a69dd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:59 +0200 Subject: gnu: r-a4base: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-a4base): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b2e3e61241..868828aaec 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7464,14 +7464,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp")))) + "101w4i0w8n7qhki22qr8l8wk8w6zalzmcywqm2g4238qv7xbnr8p")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 822024e6f9eb30e2e02c1814c9d0ed6547fe7939 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:59 +0200 Subject: gnu: r-a4: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-a4): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 868828aaec..fef854ead2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7495,14 +7495,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79")))) + "0bwn185admy5k99fkd2dhhvy7x1f75r0mqn5k24dbbg0paw6nnr8")))) (build-system r-build-system) (propagated-inputs `(("r-a4base" ,r-a4base) -- cgit 1.4.1 From 33bf7b57b1b699f96f5923c26216c96ca741590e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:59 +0200 Subject: gnu: r-abseqr: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-abseqr): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fef854ead2..6bc88c76aa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7520,14 +7520,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f")))) + "1xvk84gd1lfq1icrfwwd6y79zywrisfnc3knprigzzax31aks32c")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs -- cgit 1.4.1 From 2ace8e39c9405708fd81405d62b131061e4baf4e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:59 +0200 Subject: gnu: r-bacon: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-bacon): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6bc88c76aa..8f65897a0f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7568,14 +7568,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47")))) + "1yp0675n1g8rxdjdd7w8al5c9jq96h0kfm8218mc50z0p2fasgbj")))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) -- cgit 1.4.1 From f16dcdc1bfb2e45559d8398fd4d802c62e07a6f8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:49:59 +0200 Subject: gnu: r-rgadem: Update to 2.40.0. * gnu/packages/bioconductor.scm (r-rgadem): Update to 2.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8f65897a0f..8ce296f481 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7595,14 +7595,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw")))) + "05drbhjqn5kik6k4h03vr3d2b6pv5rm65lsnkyx4caxxcdii4jzm")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From b532b80afb83b8c3ca1477ad6b51e5f9d891b09a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:00 +0200 Subject: gnu: r-motifdb: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-motifdb): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8ce296f481..ff54e2288f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7653,12 +7653,12 @@ distributions, modules and filter motifs.") (define-public r-motifdb (package (name "r-motifdb") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5")))) + (base32 "04cmgg5mw1cqbg95zyfc2imykmdxyff16w26rq97xghcxwiq2b3z")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 1390f426db9f1f484cc9cfa51d6690204911e423 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:00 +0200 Subject: gnu: r-motifbreakr: Update to 2.6.0. * gnu/packages/bioconductor.scm (r-motifbreakr): Update to 2.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ff54e2288f..62650c64d8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7680,12 +7680,12 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7")))) + (base32 "0i18qriznad4lr6ynzmz01k5yavs5m3h7hd0adbyg8lppbzm6hh4")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 6e762d2f5a99b0596c3ba98001c741182a24d942 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:00 +0200 Subject: gnu: r-motifstack: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-motifstack): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 62650c64d8..b481fc2c42 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7731,14 +7731,14 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb")))) + "0yn348kmw7v46iym913ncx4yh5nxzmba8bdys52s12ldgjja53gp")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 4627fefcdce514d4efb8057accf892053f5c71a4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:00 +0200 Subject: gnu: r-genomicscores: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-genomicscores): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b481fc2c42..b95dc83045 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7762,14 +7762,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr")))) + "1b8982fj0r7igj749wljsdfn3c985w8n3d5gbhr5rw73llfb8x6w")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 2357a732e55bc93a0a9967dae2ba7c5cb21e4580 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:00 +0200 Subject: gnu: r-atacseqqc: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b95dc83045..8309223d46 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7799,14 +7799,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.14.4") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9")))) + "168g3xkhjzrfjpa1ynifdyfhsxx3rpyrbybsarlzr9kslw1cdkxl")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From b7f6999ee423adfaf33965ea0a4313e64b50ef6e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:00 +0200 Subject: gnu: r-gofuncr: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-gofuncr): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8309223d46..2bb7d7b8f1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7846,14 +7846,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq")))) + "0lp2gmjlsk1yqxim5pi26i27iijw11lrcxmji7ynlag359yfnynd")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 77a1c4a6aaeab63557d0a5938683aa1db788f310 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:00 +0200 Subject: gnu: r-abaenrichment: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-abaenrichment): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2bb7d7b8f1..76927a4dd9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7895,14 +7895,14 @@ annotations and ontologies.") (define-public r-abaenrichment (package (name "r-abaenrichment") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABAEnrichment" version)) (sha256 (base32 - "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c")))) + "15v5n6d3mnj9d86swkh9agfvrsd065dldaywm1adwmkhhk525wmd")))) (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 0cef014f7c30560d70f2b76511a7a4ae742017d3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:00 +0200 Subject: gnu: r-annotationtools: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-annotationtools): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 76927a4dd9..45b93ef20f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7952,14 +7952,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224")))) + "18dd8saqx17fplvv5sbfz4p9fy7ksy3n9348rd3qlczihcrh9i3w")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) -- cgit 1.4.1 From 51e7e0145b76879143f15f756e2b56e9edc941d0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:01 +0200 Subject: gnu: r-allelicimbalance: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-allelicimbalance): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 45b93ef20f..feaddb144e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7977,14 +7977,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl")))) + "1mn6975npncmfjlpjs3s2pgsrm32xgvnyl2vh1922l6vra97dkrc")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) -- cgit 1.4.1 From 7238b3318532295d8901cc672f231cba976b8628 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:01 +0200 Subject: gnu: r-aucell: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-aucell): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index feaddb144e..691e9064d3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8020,14 +8020,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx")))) + "0qdac3qalcki20r90k40cc8d0lfywzn9pffg9d719yvs7nrsfdjr")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 3e1c5855237787292ec7796e8b65f2ad832d9564 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:01 +0200 Subject: gnu: r-ebimage: Update to 4.34.0. * gnu/packages/bioconductor.scm (r-ebimage): Update to 4.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 691e9064d3..dfbf4546cb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8059,14 +8059,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.32.0") + (version "4.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww")))) + "1z3cxxg593d66nczz5hh2hdj1d87wc0lxrzc5sn6bp43n351q8h3")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 9866a9b984fc88e42d171fc9264a82fb7c8761df Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:01 +0200 Subject: gnu: r-yamss: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-yamss): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dfbf4546cb..fb810d8587 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8098,14 +8098,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w")))) + "1al615x778h17jqiyhiyf6djaq9iygs1hlbrna6y4xc0f2kvgxld")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit 1.4.1 From 79469116bd9a224667765791bda0b31b334a95fd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:01 +0200 Subject: gnu: r-gtrellis: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-gtrellis): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fb810d8587..d82108bc9c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8132,14 +8132,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw")))) + "0l5271cpzjlm4m0v6xcdg2vxlbhn53x1fd59ynb9jwll93av5h1f")))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) -- cgit 1.4.1 From 774e916736464eced769f53afdab65c2b7041553 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:01 +0200 Subject: gnu: r-somaticsignatures: Update to 2.28.0. * gnu/packages/bioconductor.scm (r-somaticsignatures): Update to 2.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d82108bc9c..32719a06d3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8161,14 +8161,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801")))) + "0jr11c9hz7m49xc8pi6xrr5fhbv68vafvqpzhr0pmm51vvr1vfs9")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) -- cgit 1.4.1 From 995c43885e61dc210dff3f709f4e666a0e4dc3d8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:01 +0200 Subject: gnu: r-yapsa: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-yapsa): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 32719a06d3..208caea841 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8200,14 +8200,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb")))) + "1xfkgjlm0rxz82qcaqzx95cwirxifd9dsswjg3zcqmz03v7a0gz2")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a72006c9b09b6f0fa0862684626042f3e1ca1b18 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:01 +0200 Subject: gnu: r-gcrma: Update to 2.64.0. * gnu/packages/bioconductor.scm (r-gcrma): Update to 2.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 208caea841..9830651293 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8249,14 +8249,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00")))) + "1z4abw9s2hs3csnx25nli7fpvb3rh3l0swzl0wfqp087fcs78pxi")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) -- cgit 1.4.1 From 8d6a721a94b63e5abeac852c9ee89b6802eb09db Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:02 +0200 Subject: gnu: r-quantro: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-quantro): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9830651293..e5b9ae20b7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8335,14 +8335,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2")))) + "1fkma2ic448h2lrlza8ipg65gpfsz4fhlxcnjpmzhhmzp2xi2p4a")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From 4a9e3d2fbe895a36f805c2c7d1744896f69c20dd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:02 +0200 Subject: gnu: r-yarn: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-yarn): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e5b9ae20b7..a4ae3a0dd3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8368,14 +8368,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp")))) + "1x07l255x52z6cgdc2j8285shqszhr034xm5686rp6d35vah55ji")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From 48737e92e42c88e58ff5d95bdf4bd2fd3c653fa8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:02 +0200 Subject: gnu: r-roar: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-roar): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a4ae3a0dd3..400ddf0cf0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8405,14 +8405,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw")))) + "0vp0n90rvjm8rzwkbrxa3fasb9val56bz2srz72xwsl3jzb5yk6w")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit 1.4.1 From ef30a43ec7fc4f2a30fa8e3c99ae9094592fbb9b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:02 +0200 Subject: gnu: r-massspecwavelet: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 400ddf0cf0..0b33a00225 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8473,14 +8473,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3")))) + "1cs32sig1yvqn9xs0cvhfpmkh2lbllx7aab80sz58x03wnx8v60z")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) -- cgit 1.4.1 From d463b4006deaadd7685de579197a6f89868b6ec4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:02 +0200 Subject: gnu: r-xcms: Update to 3.14.0. * gnu/packages/bioconductor.scm (r-xcms): Update to 3.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0b33a00225..619358a076 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8497,14 +8497,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.12.0") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv")))) + "1fs72lkgz1jik1smi6bb4f8jh6rrlpxdh3a5hydrnnndfxkz5kwx")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From 2da5ef4c5500656826822eda447165975d84b0f2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:02 +0200 Subject: gnu: r-wrench: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-wrench): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 619358a076..1170cbd6e6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8537,14 +8537,14 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wrench (package (name "r-wrench") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx")))) + "0yssmqayaryrc0asjjqxdipqdfg309llrzldx38jrfgdsza6bvs0")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From e91b4088f2c5c3ad611805c68df8c23fea4dc813 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:02 +0200 Subject: gnu: r-wiggleplotr: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-wiggleplotr): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1170cbd6e6..38b2138074 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8563,14 +8563,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad")))) + "13f3g6fcc29k0g21mhnypm3nc6qqjw867vamvfkdzynspsfb32ga")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) -- cgit 1.4.1 From 3a7ad7fb8a9e1905a75724a762c0d362ba7963f4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:02 +0200 Subject: gnu: r-widgettools: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-widgettools): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 38b2138074..a1dfc46d9f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8597,14 +8597,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w")))) + "186xgpgyfyi4angxhz6558lfpzvvszzlpyfr8xnbccs3gshk3db2")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") -- cgit 1.4.1 From 34137c21458c72c3b96c6c27d013d94479741427 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:03 +0200 Subject: gnu: r-webbioc: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-webbioc): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a1dfc46d9f..bf51b4570a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8618,14 +8618,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj")))) + "1mpdw477j78s2nvlf2lzm6mdjcpamyyazjn060h9q3apawn6zajx")))) (build-system r-build-system) (inputs `(("netpbm" ,netpbm) -- cgit 1.4.1 From fc400d10c082315308bd53a76a21b87a80de2946 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:03 +0200 Subject: gnu: r-zinbwave: Update to 1.14.1. * gnu/packages/bioconductor.scm (r-zinbwave): Update to 1.14.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bf51b4570a..e9aec09011 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8651,14 +8651,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zinbwave (package (name "r-zinbwave") - (version "1.12.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "zinbwave" version)) (sha256 (base32 - "0m5f0wrk6kg88m41cchjwi4ssi7kr3196m8h9hrhygak964nsd4q")))) + "0xgjbk35wl1vjqyq4y5c7hna8hkgmf56xjaxcph9bs2q7mbdnqwf")))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) -- cgit 1.4.1 From 6145252f1afdc1026113ccedc6f910b7b57cc417 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:03 +0200 Subject: gnu: r-zfpkm: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-zfpkm): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e9aec09011..e0054e7700 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8684,14 +8684,14 @@ the data.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm")))) + "1k7xaxr2gn26y8bps5l32g2axfhdn07nbk4q3qcx32d5jm75qkx2")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 25ba2d38a14fb1fd59a51c6fcd3937e47a5e3547 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:03 +0200 Subject: gnu: r-rbowtie2: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-rbowtie2): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e0054e7700..18dcfbe7e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8713,14 +8713,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5")))) + "0r5yqjal48xlcv5cidi7p3zwygvsllmv2zzkwkc9kfq083l2i4ih")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (inputs -- cgit 1.4.1 From 7cf4911aa2e21a2d7ca3a56d94b98a27ef4f6aaf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:03 +0200 Subject: gnu: r-progeny: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-progeny): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 18dcfbe7e5..61f159e1ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8738,14 +8738,14 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7")))) + "10vpjvl4wps857xiy8rpzr82jzdfbc5rgwh3ir3my26lfws4hfz8")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From 1dce60550567091840cbd6c0439d79169d29111f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:03 +0200 Subject: gnu: r-arrmnormalization: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-arrmnormalization): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 61f159e1ac..5cfbfcba49 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8768,14 +8768,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95")))) + "0ni3vblcadhwxaq1pf1n9jn66cp3bqch68ww4c8zh19zagil2y7r")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) -- cgit 1.4.1 From 46fc0334ff4e615675a5d439e0976f05fc2fa01b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:03 +0200 Subject: gnu: r-biocfilecache: Update to 2.0.0. * gnu/packages/bioconductor.scm (r-biocfilecache): Update to 2.0.0. [propagated-inputs]: Add r-filelock. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5cfbfcba49..bb828ef748 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8791,14 +8791,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "1.14.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1")))) + "0ymg4hmabk233qgassld62achjylm12rnidxbakfkx4dvvlbhxxv")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -8806,6 +8806,7 @@ Infinium HumanMethylation 450k assay.") ("r-dbi" ,r-dbi) ("r-dbplyr" ,r-dbplyr) ("r-dplyr" ,r-dplyr) + ("r-filelock" ,r-filelock) ("r-httr" ,r-httr) ("r-rappdirs" ,r-rappdirs) ("r-rsqlite" ,r-rsqlite))) -- cgit 1.4.1 From 69295659be169040e77916e631faead4eecc157c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:03 +0200 Subject: gnu: r-iclusterplus: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-iclusterplus): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bb828ef748..85799eed9e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8824,14 +8824,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q")))) + "1haj25c4cmmjjvh181b41a9pvkh92f7k2w4ljn17iqg31vm45za1")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit 1.4.1 From 0e74fff5eb8981396a27c6a73e32e2bbbfe237c2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:03 +0200 Subject: gnu: r-rbowtie: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-rbowtie): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 85799eed9e..dd74111359 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8854,14 +8854,14 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507")))) + "0mfikbrs28q7r3lnsq0jma5x6nkrnm3q46242jh35w9c969jk5yy")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (inputs -- cgit 1.4.1 From eca0820c773be67f854bbb2b822c851a340265fc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:04 +0200 Subject: gnu: r-sgseq: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-sgseq): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dd74111359..ee8a6874c3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8879,14 +8879,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx")))) + "0i1yaw8h8gibakvaf1xd6nnjx2bsb2s9c0q74rbq9lm7haihivp6")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 274b1e2e166f38723899d1a5a28fd9544fc639a5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:04 +0200 Subject: gnu: r-rhisat2: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-rhisat2): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ee8a6874c3..359f670667 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8922,14 +8922,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb")))) + "1hqahh5h22mj2crqp6r9xnm111xmfgk39c100rcaziqrpdy5npk8")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments -- cgit 1.4.1 From f039c22c975d698702bca3b863b37bd131497284 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:04 +0200 Subject: gnu: r-quasr: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-quasr): Update to 1.32.0. [propagated-inputs]: Remove r-genomicalignments and r-rhisat2. --- gnu/packages/bioconductor.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 359f670667..ae9742a282 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8962,14 +8962,14 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8")))) + "1635ff11ahzjrh3cdcxrq5bgd100n444k7mc0maz0jx21vj8qqb1")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs @@ -8981,13 +8981,11 @@ index.") ("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicfiles" ,r-genomicfiles) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-rbowtie" ,r-rbowtie) - ("r-rhisat2" ,r-rhisat2) ("r-rhtslib" ,r-rhtslib) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) -- cgit 1.4.1 From ec78a01db3b5bfa49cef529fc68db7112629bc65 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:04 +0200 Subject: gnu: r-rqc: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-rqc): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ae9742a282..64d3c3cbe6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9005,14 +9005,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9")))) + "02hwj2vd003x0zf273ndnwh7kxy6wc3sz14d3kryp2w2aqjj826f")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From f9c306eb0128dec644c478567983f9150926b210 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:04 +0200 Subject: gnu: r-birewire: Update to 3.24.0. * gnu/packages/bioconductor.scm (r-birewire): Update to 3.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 64d3c3cbe6..fa5e0c7897 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9048,14 +9048,14 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.22.0") + (version "3.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw")))) + "0p6mr67mkw54490sv4dvkyh8l0xkpjfbqy532vi8l41i40qg3gry")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 3d9b6386fa1f6a27a2969b36dff0586b265ba920 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:04 +0200 Subject: gnu: r-multidataset: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-multidataset): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fa5e0c7897..d011ee3644 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9106,14 +9106,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.18.2") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "1wzhxgprriicw6lx1h91z4r9d5yaxar859scp83bm8pr9aznqk2z")))) + "1hyk40xgmy50rqxwdvc64d3pgz5vsg8vmlj5cp5m0n5m0adxcdfj")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 3501292721e2f191417be1c882884294b0fc9ba5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:04 +0200 Subject: gnu: r-ropls: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-ropls): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d011ee3644..fbc4fff944 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9143,14 +9143,14 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5")))) + "1j99kdywyljqzdcns5ysh590w4w8iiwzpddpfk5c8d4whax7vk5b")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From 28472b62d3cde979a04872c3e3c606742eaa2f73 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:04 +0200 Subject: gnu: r-biosigner: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-biosigner): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fbc4fff944..77d4d82103 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9181,14 +9181,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.18.2") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn")))) + "159fbkymn92li7dinsm56nsacjp8wnhsljv7airgs9m82p8wd5sl")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit 1.4.1 From 758c1cd3c221a7efa6daa70602d10a7eb88f8200 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:05 +0200 Subject: gnu: r-annotatr: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-annotatr): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 77d4d82103..d0ae896d69 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9214,14 +9214,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9")))) + "0pcf4jrq05bmfxph41hmdx1x147k1ay5fl2h488y1s4h8qm3c67p")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From db56495f39898a04d27b899f1c38174dc92498c0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:05 +0200 Subject: gnu: r-rsubread: Update to 2.6.1. * gnu/packages/bioconductor.scm (r-rsubread): Update to 2.6.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d0ae896d69..a70560d786 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9255,14 +9255,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.4.3") + (version "2.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0c4akc89p5467n5rzq9bi7h0h15rbpqpvh7fw42qcj7g2vc41wba")))) + "007pbvxkhh930zdkgjaihannjbpbfnbizp3ffc2vyxygw0r4vz68")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit 1.4.1 From 6a7589de24da3cdb28cc2c0b94516d3757219780 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:05 +0200 Subject: gnu: r-flowutils: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-flowutils): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a70560d786..437a88c153 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9281,14 +9281,14 @@ and to both short and long sequence reads.") (define-public r-flowutils (package (name "r-flowutils") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 - "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09")))) + "1sdwgyvrsz0pp60zdfrcgb7bs8s87j7257p8ck813ydizc324x9w")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 4299d9775668ed8813deb249c476b0391539e4d2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:05 +0200 Subject: gnu: r-consensusclusterplus: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-consensusclusterplus): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 437a88c153..e7f0707f9d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9307,14 +9307,14 @@ and to both short and long sequence reads.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp")))) + "163nr50nyvwrsajmm0cgxp70pqk61mgw0k7ams694hcb42162j8b")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) -- cgit 1.4.1 From 19855b595c179a0ec4c6c9da22ce980137d106ee Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:05 +0200 Subject: gnu: r-flowcore: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-flowcore): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e7f0707f9d..0bf1950eb1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9361,14 +9361,14 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8")))) + "13xpbkxi53rxmhvpdiy6bydmhicmxd2gi96d9c1qx4lkss2f14nc")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 5e49dfd00e997223f7d6e18a51a4cc207c3a0dc0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:05 +0200 Subject: gnu: r-flowmeans: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-flowmeans): Update to 1.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0bf1950eb1..b489eed7cb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9393,14 +9393,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734")))) + "1awskkq48qhv4v9glxgfqi0kgwqd62fbj641k4vvxfcwsf2c7bfg")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 417b4108bcc04062cd6e941b5ea8b88eb42cce78 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:05 +0200 Subject: gnu: r-ggcyto: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b489eed7cb..9832d27458 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9450,14 +9450,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m")))) + "0jd6m84m4znnpix4bcgdby7mnflsn206f5x2vw9n8rxnwzx77wpg")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 57a41cd789a35c56a2d50ec5d411c231132234c9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:05 +0200 Subject: gnu: r-flowviz: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-flowviz): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9832d27458..1de2442fe6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9487,14 +9487,14 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k")))) + "17x04xwyw2pp5zkhgvrmxkb8cbrv9wql6xhjsfpq0n6yd9dxqc1v")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From c474b4784ed4eb405df30225b93629f7a3247ea7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:06 +0200 Subject: gnu: r-flowclust: Update to 3.30.0. * gnu/packages/bioconductor.scm (r-flowclust): Update to 3.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1de2442fe6..112e54fb08 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9518,14 +9518,14 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.28.0") + (version "3.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq")))) + "03xsmprrkxwkaksjlaxwp54mqfb3zlg6dbqhp87w78fwscisv76b")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments -- cgit 1.4.1 From a1557adfcf619708e299dc419ef4ed33fa3a757b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:06 +0200 Subject: gnu: r-rprotobuflib: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-rprotobuflib): Update to 2.4.0. [arguments]: Adjust build phase "unpack-bundled-sources". --- gnu/packages/bioconductor.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 112e54fb08..4b0f3a47ae 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9558,14 +9558,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz")))) + "1hyds97ay4mn7nl830yh9v8mlasgsljsx5wsrhz2zsmbbyx6wbnb")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments @@ -9574,8 +9574,7 @@ model with Box-Cox transformation.") (add-after 'unpack 'unpack-bundled-sources (lambda _ (with-directory-excursion "src" - (invoke "tar" "xf" "protobuf-3.10.0.tar.gz")) - #t))))) + (invoke "tar" "xf" "protobuf-3.13.0.tar.gz"))))))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/RProtoBufLib/") -- cgit 1.4.1 From 6489371b80ec1f373a805adb74f6de24f17b82ca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:06 +0200 Subject: gnu: r-flowstats: Update to 4.4.0. * gnu/packages/bioconductor.scm (r-flowstats): Update to 4.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4b0f3a47ae..2563aa772b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9641,14 +9641,14 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "4.2.0") + (version "4.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x")))) + "1yr5m7qmhmm52c70z3d0zy4zgf0hja7r2ig9yljv5w86bzm962x6")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 53c041713a1139b301aab89ba42bed0c11c5958e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:06 +0200 Subject: gnu: r-opencyto: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-opencyto): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2563aa772b..71fa213a87 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9677,14 +9677,14 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v")))) + "1par1d5pk1rjg15q7i5z5wqma7xg6fycb826a823wk8wr52a885x")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 9ed2ec5bffe4fae0c30272344096b2cb56765d18 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:06 +0200 Subject: gnu: r-flowsom: Update to 2.0.0. * gnu/packages/bioconductor.scm (r-flowsom): Update to 2.0.0. [propagated-inputs]: Remove r-tsne; add r-colorramps, r-dplyr, r-ggforce, r-ggnewscale, r-ggplot2, r-ggpointdensity, r-ggpubr, r-ggrepel, r-magrittr, r-pheatmap, r-rlang, r-rtsne, r-scattermore, and r-tidyr. --- gnu/packages/bioconductor.scm | 19 ++++++++++++++++--- 1 file changed, 16 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 71fa213a87..3388d93ad2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9774,25 +9774,38 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "1.22.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf")))) + "18h7p7g3w9imyd1c93jllgp4kd74z96cs85wcqfhmd26nx18hl82")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) + ("r-colorramps" ,r-colorramps) ("r-consensusclusterplus" ,r-consensusclusterplus) ("r-cytoml" ,r-cytoml) + ("r-dplyr" ,r-dplyr) ("r-flowcore" ,r-flowcore) ("r-flowworkspace" ,r-flowworkspace) + ("r-ggforce" ,r-ggforce) + ("r-ggnewscale" ,r-ggnewscale) + ("r-ggplot2" ,r-ggplot2) + ("r-ggpointdensity" ,r-ggpointdensity) + ("r-ggpubr" ,r-ggpubr) + ("r-ggrepel" ,r-ggrepel) ("r-igraph" ,r-igraph) + ("r-magrittr" ,r-magrittr) + ("r-pheatmap" ,r-pheatmap) ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-tsne" ,r-tsne) + ("r-rlang" ,r-rlang) + ("r-rtsne" ,r-rtsne) + ("r-scattermore" ,r-scattermore) + ("r-tidyr" ,r-tidyr) ("r-xml" ,r-xml))) (home-page "https://bioconductor.org/packages/FlowSOM/") (synopsis "Visualize and interpret cytometry data") -- cgit 1.4.1 From 480dcf3038dd64997f59cbd9f0a7904f88708c63 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:06 +0200 Subject: gnu: r-mixomics: Update to 6.16.0. * gnu/packages/bioconductor.scm (r-mixomics): Update to 6.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3388d93ad2..fd6898b5fe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9817,14 +9817,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.14.1") + (version "6.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "07d1z33bc3bym1jwp1qqfhs18w4v9axk0ycnmldmj6piswvp44wk")))) + "1hri5rrqf8vq3c6pivfamv60yz9mf9rrdpdd5bw2h24lghm2x8rw")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 9c0b691a29b70cd9a12ec0918a340fa494467f66 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:06 +0200 Subject: gnu: r-depecher: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-depecher): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fd6898b5fe..8058b85e6e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9863,14 +9863,14 @@ delete entire rows with missing data.") (define-public r-depecher (package ;Source/Weave error (name "r-depecher") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469")))) + "04vxc43p3kpsx0vksk2nwmy9p56h35z2mc8j9p2wm29zaz1y8j3p")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From f9049add35cdb483fdf90b3552c56d35c481e978 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:06 +0200 Subject: gnu: r-rcistarget: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-rcistarget): Update to 1.12.0. [propagated-inputs]: Add r-arrow, r-dplyr, r-genomeinfodb, r-genomicranges, and r-tibble. --- gnu/packages/bioconductor.scm | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8058b85e6e..a90ff08121 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9909,24 +9909,29 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf")))) + "1yh0l11vnslgr6zsbpgc8mc4aa32zy34f5yrz98hkcdl53iw5y7f")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs - `(("r-aucell" ,r-aucell) + `(("r-arrow" ,r-arrow) + ("r-aucell" ,r-aucell) ("r-biocgenerics" ,r-biocgenerics) ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) ("r-feather" ,r-feather) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) ("r-gseabase" ,r-gseabase) ("r-r-utils" ,r-r-utils) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tibble" ,r-tibble))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://aertslab.org/#scenic") -- cgit 1.4.1 From cec797275909cae7752aabfa77b0e5b4e67d8f56 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:07 +0200 Subject: gnu: r-cicero: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-cicero): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a90ff08121..61f013b572 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9951,14 +9951,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr")))) + "0kw16zf9004d1zlwsswhbcb7p77nabpd1fjagznff3zyan9fpdxf")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) -- cgit 1.4.1 From d37ae38d19ea2a06b68ccdd1d8318d15903a5fb4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:07 +0200 Subject: gnu: r-circrnaprofiler: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-circrnaprofiler): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 61f013b572..90e063fd56 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10018,14 +10018,14 @@ accessibility data.") (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 - "0r1hfm3pc7c71irzmxmdwc27ns9hkymz4vhb4pqbli4xn37q7cg8")))) + "1hif40vfg2lkbyf6abbkxbdm3b1biw6gxnh6ca2sydvi3y5l2ys2")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) -- cgit 1.4.1 From bb3ef4894bffa657eb6784690341a51e3f1c5598 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:07 +0200 Subject: gnu: r-genie3: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-genie3): Update to 1.14.0. [propagated-inputs]: Add r-dplyr. --- gnu/packages/bioconductor.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 90e063fd56..c46a9b795c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10115,17 +10115,19 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5")))) + "1v54dzcz654wfm3npbp8gb55v49im0fm547cz3hvsidq4zhi3l1b")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) - (propagated-inputs `(("r-reshape2" ,r-reshape2))) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-reshape2" ,r-reshape2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/GENIE3") -- cgit 1.4.1 From 125ffdf7886cc66bb33629862ec7645b1d625167 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:07 +0200 Subject: gnu: r-roc: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-roc): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c46a9b795c..3e187c83fb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10140,14 +10140,14 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9")))) + "0ff5rcpyybgjzsfbhaslim0m02n3bksv1r9v7bq0gg0iyzll0rjc")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From d0c36449d2e4fc814479a908867b16cad8edaa9d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:07 +0200 Subject: gnu: r-watermelon: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-watermelon): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3e187c83fb..aa535cf70c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10188,14 +10188,14 @@ data.") (define-public r-watermelon (package (name "r-watermelon") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f")))) + "1qar8z0nf33bqr488swig0bfq8lnvcdjcxvw3q3b0hkkvybn27zw")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 0cc4deb017cad45025f38453cf7cd1e5c7bf55e6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:07 +0200 Subject: gnu: r-gdsfmt: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aa535cf70c..1c50614da0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10225,14 +10225,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.26.1") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "0f5vn8h5fzzazcv92sgrf85hc4xkkizk2wwml9mzjd8ya2fkwg8n")) + "119qdivd7vaaqkjb0nrwidi6g26hh8znhif3g4prqn7x5pl2clvy")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. -- cgit 1.4.1 From 988337d87ba72fed138b09ce997a7cffc1b30b2b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:07 +0200 Subject: gnu: r-bigmelon: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-bigmelon): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1c50614da0..5729c7925e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10284,14 +10284,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7")))) + "061f0hc4m4nvdr6298pg3inpx1z2bpsm9nlxqs3v7n58q15xyzri")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 0615d394c902eec99653cfe56d3497489d374c47 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:07 +0200 Subject: gnu: r-seqbias: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-seqbias): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5729c7925e..dca24cb22b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10312,14 +10312,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2")))) + "06w43plv4x1pafybq633n7adqp9yj3bvaaamq7vylmkfbcx3nl8k")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 66e45a9f1f13af90972ebf2fec23520c394edd11 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:07 +0200 Subject: gnu: r-reqon: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-reqon): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dca24cb22b..8dbc773646 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10376,14 +10376,14 @@ injected in that sequence).") (define-public r-reqon (package (name "r-reqon") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq")))) + "1z13avbxwvvhh03arjfnaipznynifsi8k2hzw4kappz24f7lwmza")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 99496a17f5279a238c89ec00bb96586abe5104b6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:08 +0200 Subject: gnu: r-wavcluster: Update to 2.26.0. * gnu/packages/bioconductor.scm (r-wavcluster): Update to 2.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8dbc773646..ef50992add 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10401,14 +10401,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi")))) + "1sydzrqydfv1ik2h08xkxlx6xrv866bf0if6v5wch9l3krh0sych")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 7a287bc670f52f5bcdc078e9e980c945b36a0e81 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:08 +0200 Subject: gnu: r-timeseriesexperiment: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-timeseriesexperiment): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ef50992add..7d90078406 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10448,14 +10448,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 - "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn")))) + "10xgihjssnc6i03819p9gnzwfc7znanic514ar3yxzl3fhxy3yyy")))) (properties `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) -- cgit 1.4.1 From 27e06000b1e56d59fca44f2aa4feab221e7c4002 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:08 +0200 Subject: gnu: r-variantfiltering: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-variantfiltering): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7d90078406..946fd184c5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10489,14 +10489,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5")))) + "0abhrk53csd9jz9sv4q1qr74jax9mbj2icbz1iilf1123nvnjypd")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) -- cgit 1.4.1 From 2ca9f4fe9b0b0131804ce29b76081faed17f91f4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:08 +0200 Subject: gnu: r-variancepartition: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 946fd184c5..f8958d9dee 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10595,14 +10595,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah")))) + "1pqy2g9pg8pswmkrs2fzlkwwliw2r7f33h05bci5bz41b8ribpzj")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) -- cgit 1.4.1 From 58f2abfbce4540df81a161b305cd1ad12300de02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:08 +0200 Subject: gnu: r-htqpcr: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-htqpcr): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f8958d9dee..f9216b2e22 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10639,14 +10639,14 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji")))) + "1y3ik5a9w66jby6682jfm8mn2883s8yfv4xw8a8v1f6q2d1j938l")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 56ec3a6fb945eba2d34144e8ed30caf8aa031efe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:08 +0200 Subject: gnu: r-unifiedwmwqpcr: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f9216b2e22..449b2c303c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10673,14 +10673,14 @@ features (e.g. genes, microRNAs).") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv")))) + "1clcz610sl3s0mjf84j21xgrmjhkxcc4h292ljwq5yzbkk68g896")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) -- cgit 1.4.1 From e4087ae9c9c30140a1e0c072cf34649ab30855a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:08 +0200 Subject: gnu: r-universalmotif: Update to 1.10.1. * gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.10.1. [propagated-inputs]: Remove r-ggseqlogo and r-rdpack. --- gnu/packages/bioconductor.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 449b2c303c..3bbe5c8a41 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10698,14 +10698,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.8.5") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "07862bs771xldmdnq0zr8926dr299ach8nrgci14p5bbrc88l3ly")))) + "1hwp7802r4pr7yafzir9afqaim9l0vznglm35b0gxaca8k7a3jvy")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) @@ -10720,12 +10720,10 @@ data.") `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) ("r-ggplot2" ,r-ggplot2) - ("r-ggseqlogo" ,r-ggseqlogo) ("r-iranges" ,r-iranges) ("r-mass" ,r-mass) ("r-rcpp" ,r-rcpp) ("r-rcppthread" ,r-rcppthread) - ("r-rdpack" ,r-rdpack) ("r-rlang" ,r-rlang) ("r-s4vectors" ,r-s4vectors) ("r-yaml" ,r-yaml))) -- cgit 1.4.1 From 51d637a32d7d94bc4a57afa836e5ea4926bc6552 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:08 +0200 Subject: gnu: r-bgmix: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-bgmix): Update to 1.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3bbe5c8a41..da95a9db51 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10812,14 +10812,14 @@ cellular organization in health and disease.") (define-public r-bgmix (package (name "r-bgmix") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BGmix" version)) (sha256 (base32 - "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50")))) + "1gp40ddspblpszzm4k4r7ysgx883iwdfqc5ds23p2q1ml9idwgvv")))) (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From bacd432cb13abd2bb6d582f4edc07dc1bda6e720 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:09 +0200 Subject: gnu: r-bgx: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-bgx): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index da95a9db51..438a56455a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10834,14 +10834,14 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im")))) + "18n6j2ihv85rhai5sf5k3mwf9nkc2nl2sinx3rrs6sbl529g4mw4")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 3c64554bbc3acb08db16e95b63d6e4e94d636ddf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:09 +0200 Subject: gnu: r-bhc: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-bhc): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 438a56455a..0889d14195 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10859,14 +10859,14 @@ Affymetrix GeneChips.") (define-public r-bhc (package (name "r-bhc") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 - "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn")))) + "0aaawm7h3ppyyhd7hi14rpynagnxx4730f5vxizj5bpzwbclp6h9")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") -- cgit 1.4.1 From 49403e824162a8171c8d3963720297ca66ec2bcd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:09 +0200 Subject: gnu: r-bicare: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-bicare): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0889d14195..b0d5534851 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10885,14 +10885,14 @@ algorithm which is more efficient for larger data sets.") (define-public r-bicare (package (name "r-bicare") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k")))) + "0j3gs4xcdgaca2c62jf2h86skbbxm1c9g2khs5bsa8fmkskr6vl9")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 58b8ed9f0818674a030bb7844d32e2017eae9cec Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:09 +0200 Subject: gnu: r-bifet: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-bifet): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b0d5534851..e0d52570d7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10909,14 +10909,14 @@ results.") (define-public r-bifet (package (name "r-bifet") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a")))) + "1fwy7ws0bn67557s0kcw8pbln2jg834n6kfbs8297ps07nxr0lpj")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 92f5efa65d548ed69ae77466eb2dc214ff4a0294 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:09 +0200 Subject: gnu: r-rsbml: Update to 2.50.0. * gnu/packages/bioconductor.scm (r-rsbml): Update to 2.50.0. [inputs]: Remove zlib. --- gnu/packages/bioconductor.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e0d52570d7..c01b3964f4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10939,19 +10939,18 @@ the read count and GC content bias.") (define-public r-rsbml (package (name "r-rsbml") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61")))) + "017xwra6ms7kx6sg3ksw1vr9zn23imc2qjgpmjikx7mgbak125xh")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs - `(("libsbml" ,libsbml) - ("zlib" ,zlib))) + `(("libsbml" ,libsbml))) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-graph" ,r-graph))) -- cgit 1.4.1 From d51885812f8a7c5e1d0d11c7d25a36ca8138b223 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:09 +0200 Subject: gnu: r-hypergraph: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-hypergraph): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c01b3964f4..91c5aea6a4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10966,14 +10966,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97")))) + "01knpd964m2g9vwd7c72qnc8g2p2pzhvk7lin4mhvcmb3pvsdlh7")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 302929da31f81d66bbe474c5365917f6d5ecc53e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:09 +0200 Subject: gnu: r-hyperdraw: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-hyperdraw): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 91c5aea6a4..e7c496b0bb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10988,14 +10988,14 @@ manipulating hypergraphs.") (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz")))) + "1qkxixkgvvfha0ii8rwwcbrbjmbbxsy8afv5ymcq01k3hbykx44r")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs `(("graphviz" ,graphviz))) -- cgit 1.4.1 From 90eb7ae1a9ef79f98b04848b01bc9e4bcf1d6b18 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:09 +0200 Subject: gnu: r-biggr: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-biggr): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e7c496b0bb..72786e3722 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11012,14 +11012,14 @@ manipulating hypergraphs.") (define-public r-biggr (package (name "r-biggr") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y")))) + "1y9659pxm65w51zvrz36girb3qvfc64zijjkxmg6xn4pbc8vv1wf")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 8a8f200703b62ac7df5f9119efea50d11112f15b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:10 +0200 Subject: gnu: r-bigpint: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-bigpint): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 72786e3722..bb7406479a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11076,14 +11076,14 @@ a file-backed matrix with factor properties.") (define-public r-bigpint (package (name "r-bigpint") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigPint" version)) (sha256 (base32 - "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis")))) + "0yrg9x1a92zmz7j5hk77cph1jg82mkpr7k7qi9fdr6z5nqq6fgz6")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 02ec364cf62d79ca635ceb130a05e6f925c89091 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:10 +0200 Subject: gnu: r-chemminer: Update to 3.44.0. * gnu/packages/bioconductor.scm (r-chemminer): Update to 3.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bb7406479a..a546532876 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11119,14 +11119,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.42.2") + (version "3.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "10d8h6w24h4s7l02zzv6q46w3yiqsjizip7mf11cvkmd6p7qxfl9")))) + "1z59npqk7hnqzhjdnry6lfqlyxfzwqprp7bmbdzs4rp22pzcv1v8")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 7c990fbcb3aa291189d4e453b92ee1a208dfc5d1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:10 +0200 Subject: gnu: r-bioassayr: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a546532876..4b5259eafc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11160,14 +11160,14 @@ structures.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.28.3") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "03pdb76j7c28b1h1flb40ahq7i9iha22kblq6mkl3x4xmrdgaw5y")))) + "1mlv80w8a7l8cii3dfqvanvh0qdqvcg8c1iiq4xlyvkjxfs64ka1")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From dc2878754cc173e4071e9019c25c80104c2e0dae Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:10 +0200 Subject: gnu: r-biobroom: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-biobroom): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4b5259eafc..90076890eb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11195,14 +11195,14 @@ available bioactivity data.") (define-public r-biobroom (package (name "r-biobroom") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv")))) + "1ybyhmrcvj6k1laxw9bc8jbn533frkzh9k8kl1ibd5pi368rfqzn")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a95a14c0cc3b09c2b59ddbdcd8e951b386bbca50 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:10 +0200 Subject: gnu: r-graphite: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-graphite): Update to 1.38.0. [native-inputs]: Add r-knitr. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 90076890eb..566fa31e1c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11227,14 +11227,14 @@ visualize bioinformatics analyses.") (define-public r-graphite (package (name "r-graphite") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk")))) + "11bgz6951nfygxp3fm0190gf2bb5zplis1bc0am4757liw4qybhf")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs @@ -11243,6 +11243,8 @@ visualize bioinformatics analyses.") ("r-graph" ,r-graph) ("r-httr" ,r-httr) ("r-rappdirs" ,r-rappdirs))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/graphite/") (synopsis "Networks from pathway databases") (description -- cgit 1.4.1 From f218b9b216f790e38cabaeee7671f9933ac95409 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:10 +0200 Subject: gnu: r-reactomepa: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-reactomepa): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 566fa31e1c..ffba2b9017 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11256,14 +11256,14 @@ symbols).") (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m")))) + "1293z89ai766c559axgr7mz5x4564gyl9xqzf6s8s0aj1xb35gqf")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 834a6dbaab486ed17002cd872734118104b43ddf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:10 +0200 Subject: gnu: r-ebarrays: Update to 2.56.0. * gnu/packages/bioconductor.scm (r-ebarrays): Update to 2.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ffba2b9017..14cfe4dd84 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11288,14 +11288,14 @@ enrichment analysis and several functions for visualization.") (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd")))) + "1k1kl0m7wzaqpv7i20pfav2a6jf93bhri4w7qdikmvkf011n9422")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From cd9af2379d68e9236cca2d0349806319c8f96f8e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:10 +0200 Subject: gnu: r-biocgraph: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-biocgraph): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 14cfe4dd84..610b7632fa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11364,14 +11364,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75")))) + "12bmj9kdlylp02cfwviak7y323ndccl2694rvi4cdg4vsx7v3ya3")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 6513592747dc5510ef604c88ffc063234b0edd50 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:10 +0200 Subject: gnu: r-biocstyle: Update to 2.20.0. * gnu/packages/bioconductor.scm (r-biocstyle): Update to 2.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 610b7632fa..255fb6a29c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11389,13 +11389,13 @@ different graph related packages produced by Bioconductor.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.18.1") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp")))) + "062zhy33a2c70ibqghnjxcys0wbqc998aza8nnygk4zmpd4iyy1z")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) -- cgit 1.4.1 From 1e2c0e824cce79c4f4de33129b8b06dcd8cac6f7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:11 +0200 Subject: gnu: r-biocviews: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-biocviews): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 255fb6a29c..cf5624e32c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11417,13 +11417,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.58.1") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4")))) + "0pc5ll59vm8a9s1nrdc7p9wk11a52rrz669fsrrqd8qapa8p6wfd")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) -- cgit 1.4.1 From 28613e1000f44a214220f76c63dd3a063674f02e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:11 +0200 Subject: gnu: r-experimenthub: Update to 2.0.0. * gnu/packages/bioconductor.scm (r-experimenthub): Update to 2.0.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cf5624e32c..50145a9536 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11445,14 +11445,14 @@ also known as views, in a controlled vocabulary.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "1.16.1") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "1iyf052hh2dhlwzwwrj571cwr3hd9wp2j915sqg77x6jn40wjr1g")))) + "1mzmw3100lf33yhz27nbxncrjk5bprlackrjcwf8xdhcaidg40p4")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 37f824c5e72f877dda2aafe2b0f9526ef9f48565 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:11 +0200 Subject: gnu: r-grohmm: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-grohmm): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 50145a9536..edbe0e30b3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11479,14 +11479,14 @@ access.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx")))) + "1h63vg1iskw79ijg5h1b9097ams8pp3kvnlawlfci6xfli07xpkj")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From e7b465e81bfa06c79be2d8814cdacde386016d94 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:11 +0200 Subject: gnu: r-multiassayexperiment: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index edbe0e30b3..bffa0280fe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11506,14 +11506,14 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs")))) + "0l0arf3q1f6zy6pdgsy3h5n523sg1hlilv7lj7snr5814idgdj51")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) -- cgit 1.4.1 From 4faded238efd10c1601ab2b3db6a03c744098771 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:11 +0200 Subject: gnu: r-bioconcotk: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-bioconcotk): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bffa0280fe..65da4528cb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11541,14 +11541,14 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108")))) + "0y396lx2mh9izb07lz83j35wydfj808ihc74jlgras03a3g335p2")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 2023951c8e5b2aab218c824fa80d542dd70a7ca3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:11 +0200 Subject: gnu: r-biocor: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-biocor): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 65da4528cb..e3802a3099 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11586,14 +11586,14 @@ tools for genome-scale analysis of cancer studies.") (define-public r-biocor (package (name "r-biocor") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19")))) + "135rga7mwpzy8ypvriqpbmlh9l5yf61s9s1sa9615qfab14jh06b")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From e9e4f65dc198db5e0001fd8796eb7f6d6038c159 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:11 +0200 Subject: gnu: r-biocpkgtools: Update to 1.10.1. * gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.10.1. [propagated-inputs]: Remove r-rappdirs. --- gnu/packages/bioconductor.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e3802a3099..389b0edca8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11615,14 +11615,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.8.2") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "18m816mh1ic0znp38wax8xppai77lkym3w84x4x30x2mf0vriqfw")))) + "18a9mbzfmkipnv1cc9h3rhn9jxdp7nzywp0bz7hvmsaffv4p4skc")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs @@ -11639,7 +11639,6 @@ gene selection, testing relationships, and so on.") ("r-igraph" ,r-igraph) ("r-jsonlite" ,r-jsonlite) ("r-magrittr" ,r-magrittr) - ("r-rappdirs" ,r-rappdirs) ("r-rbgl" ,r-rbgl) ("r-readr" ,r-readr) ("r-rex" ,r-rex) -- cgit 1.4.1 From e828fa21bb3fd83a7e360db2644fa78d6568db32 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:11 +0200 Subject: gnu: r-biocset: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-biocset): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 389b0edca8..3af5884bef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11664,14 +11664,14 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg")))) + "18zr0r4b4rblfmsiilipqdfxn9fgymx75hlxzx1wk3bm71ryk078")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 36f51f8afe1579214f6d7a0be76235a5ed2ad952 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:12 +0200 Subject: gnu: r-biocworkflowtools: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-biocworkflowtools): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3af5884bef..70122b64d9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11702,14 +11702,14 @@ accessing web references for elements/sets are also available in BiocSet.") (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6")))) + "1a32bwgnxaw0gv2gij2p4rm0a6l06jjhidvfz2v4k900pz1w79av")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) -- cgit 1.4.1 From db46064043cb1d62c98cc5a900d00ea53de8399e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:12 +0200 Subject: gnu: r-biodist: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-biodist): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 70122b64d9..caabdf7cd9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11735,14 +11735,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (define-public r-biodist (package (name "r-biodist") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap")))) + "1y1x9q9aa76gbhsyfn638rxp5icjvq30fv3a4205xh7g5jwlf6yw")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 5d611d3f15e3073a505fe944baf45af7b24d3c02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:12 +0200 Subject: gnu: r-pcatools: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-pcatools): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index caabdf7cd9..5d589ce104 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11758,14 +11758,14 @@ distance measures.") (define-public r-pcatools (package (name "r-pcatools") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PCAtools" version)) (sha256 (base32 - "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb")))) + "11idi9fwvyhkakbm63qxcdhkany8gbskis04z0p5a39lppq8ks31")))) (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 06dd2fd625f81ab7188d4afc4334dcaad3e53326 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:12 +0200 Subject: gnu: r-rgreat: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-rgreat): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5d589ce104..20a3e2832f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11804,14 +11804,14 @@ dimensional mass cytometry data.") (define-public r-rgreat (package (name "r-rgreat") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj")))) + "0ads9c9i8b39wvjih057zlyivj8zpsqjxf6r97yflz4sbi1jmcji")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 3b19239c0fe6987835cdd29578dc46cda8ad2ed5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:12 +0200 Subject: gnu: r-m3c: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-m3c): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 20a3e2832f..8e8fd967f5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11832,14 +11832,14 @@ user's input and automatically retrieving results from GREAT web server.") (define-public r-m3c (package (name "r-m3c") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "M3C" version)) (sha256 (base32 - "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5")))) + "17gj4haa4ywc6bmppm342jzppl3inqa94235yspikij6c098vrmc")))) (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a9f203ba6c4d3cb157ec2f11966c17820c0322b8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:12 +0200 Subject: gnu: r-icens: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-icens): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8e8fd967f5..4253051554 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11865,14 +11865,14 @@ hypothesis @code{K=1}.") (define-public r-icens (package (name "r-icens") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Icens" version)) (sha256 (base32 - "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr")))) + "1rzgwxx4w2bqsaz0xmkhi4w9zsxgms80xf59zg1xp1camyhaihlz")))) (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a78daaa57232d20280ee31d6546882b65d29d267 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:12 +0200 Subject: gnu: r-preprocesscore: Update to 1.54.0. * gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4253051554..cc80c41a7c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11995,14 +11995,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.52.1") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1hz7rlpscaczvvcalky2f5bmr70aii455549m7f6wk10aklp3nll")))) + "17a00blz4kvhmsk92bp5alj9kdpy7h1id7nk4vqxakhkb2jabr20")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) -- cgit 1.4.1 From 5565b8badaff5f6616090498c892a01923c924f8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:12 +0200 Subject: gnu: r-s4vectors: Update to 0.30.0. * gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cc80c41a7c..1637588e81 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12016,13 +12016,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.28.1") + (version "0.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh")))) + "0v5vxmg0a27ivgymmzfl595rcb1m3dz27r2wzbk1j97rlpwy1p4q")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) -- cgit 1.4.1 From 64b03c66adf84be71d50e3f543f47d7399a4c934 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:13 +0200 Subject: gnu: r-rgraphviz: Update to 2.36.0. * gnu/packages/bioconductor.scm (r-rgraphviz): Update to 2.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1637588e81..5580b65865 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12083,14 +12083,14 @@ data manipulation and visualization.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77")))) + "0d0xq1vgr4b165cn4wg7zmfjyc1d9ir4amgs196j4cgrhpmrnl8s")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) (arguments -- cgit 1.4.1 From 914bd41da9fd48af592742ab1427e6a153fa7d11 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:13 +0200 Subject: gnu: r-fithic: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-fithic): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5580b65865..ec49cb7fe7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12121,13 +12121,13 @@ objects from the @code{graph} package.") (define-public r-fithic (package (name "r-fithic") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2")))) + "1p8a6lis5yswaj647bjw89harlarnsxmvjzz63fn1l6gxrwhh8bx")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From dbb929bf4a10635f37a148a46ddae8094336396c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:13 +0200 Subject: gnu: r-hitc: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-hitc): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ec49cb7fe7..6cfc146c7c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12147,13 +12147,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy")))) + "0s3kfqs3zlmq61hxdmxpmi9gfs9w3byckw7xzp1hrhdbsl46yvgq")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 370d020e8831c703c1731d19da81216389f16cb9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:13 +0200 Subject: gnu: r-beachmat: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-beachmat): Update to 2.8.0. [propagated-inputs]: Add r-rcpp. --- gnu/packages/bioconductor.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6cfc146c7c..2e2ad4ab17 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12290,19 +12290,20 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.6.4") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "0vbqdkc52j2v1ghygmhy2cbgqm4l99vmv8930wkzkq1pm73pmjji")))) + "16p6shab4y8sy1adn4qr05ysvwmvs9idliccixafvx9icv5sla86")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix))) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/beachmat") -- cgit 1.4.1 From a92a277873981894186cff98c3da983c08763ddc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:13 +0200 Subject: gnu: r-cner: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-cner): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2e2ad4ab17..4d8a78b265 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12319,13 +12319,13 @@ matrices.") (define-public r-cner (package (name "r-cner") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CNEr" version)) (sha256 - (base32 "0qy4pm23vyy23zwsjkf0mpf2c0p54nq26w9lq7j0ld4bx9l3jc6c")))) + (base32 "13w0gsfm7k29dp5nb0c9sb2ix506ph6dixsjis6xxcz6acq7lg2k")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit 1.4.1 From 0b6b42b6c49288a4ec6c6beb8cda162c6cb2c4a1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:13 +0200 Subject: gnu: r-tfbstools: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-tfbstools): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4d8a78b265..1ab30733c0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12367,14 +12367,14 @@ advanced visualization of sets of conserved noncoding elements.") (define-public r-tfbstools (package (name "r-tfbstools") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TFBSTools" version)) (sha256 (base32 - "0p42hnwhipmcvrsqk3s8qfiian1fvh6izfd9m961bsx99r2clnha")))) + "1avgjv2nyr28cla0z9dvh3v0hr1f561sz2as1k53a42irbjk0var")))) (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 56a2dcfdc7e440e2dde3ec65fe5f620409601d49 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:13 +0200 Subject: gnu: r-motifmatchr: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-motifmatchr): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1ab30733c0..d500bf884a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12413,14 +12413,14 @@ provides a wrapper of de novo motif discovery software.") (define-public r-motifmatchr (package (name "r-motifmatchr") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifmatchr" version)) (sha256 (base32 - "0zrpn0hqdg0hm80ydkfpiqncwyb8y0xp6mlin7g955p8zcpcm67z")))) + "1vif3dp4lv4jz1pxsq0ig791ir8q65jmrlqmkyfxpfxfj5alqnbm")))) (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 71e392966aae0d46d0d92863042755034a98571d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:13 +0200 Subject: gnu: r-chromvar: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-chromvar): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d500bf884a..addf29c6ff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12447,13 +12447,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "0dn04ijgq8fncn2bkvnd0lnabjg2s4mpb91b3kwvv3nkgjgfx819")))) + (base32 "1birmwvcvl2hb5ygbsb3wvbdfayqqs53j1bks46cbkq7ybigfyar")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From b21a73c00b5c2b6d56a79eed1f64dcc51d8eabb6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:14 +0200 Subject: gnu: r-singlecellexperiment: Update to 1.14.1. * gnu/packages/bioconductor.scm (r-singlecellexperiment): Update to 1.14.1. [propagated-inputs]: Add r-delayedarray and r-genomicranges. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index addf29c6ff..e3072e0f96 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12494,19 +12494,21 @@ sequence (@code{DNAse-seq}) experiments.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.12.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2")))) + "1bwdhx0ss0s8f4xdgwd7x48apn849x4dyb5hbyglcz31r5vh1qgz")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) + ("r-delayedarray" ,r-delayedarray) + ("r-genomicranges" ,r-genomicranges) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs -- cgit 1.4.1 From 851894f8daf8e76c62338ce58b4f68c17a84fc7d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:14 +0200 Subject: gnu: r-scuttle: Update to 1.2.0. * gnu/packages/bioconductor.scm (r-scuttle): Update to 1.2.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e3072e0f96..4a15a15580 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12525,14 +12525,14 @@ libraries.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.0.4") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "0vfhxyv81y525qgk0s3bxy1yypj16h1bl7sc1a1jdqx11fxxv2l8")))) + "1vxmgm52n5z2m1a7d4c5ajp5d35rdq7j3hln9qn7188zk9ijjsz5")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From d9755a22f6738b3e3ee65101b33e1bbe666fbd48 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:14 +0200 Subject: gnu: r-scater: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-scater): Update to 1.20.0. [propagated-inputs]: Add r-beachmat, r-rcolorbrewer, and r-rtsne. --- gnu/packages/bioconductor.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4a15a15580..8c660d4b7e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12560,16 +12560,17 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.18.6") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0k1ls5gqv1zsn1w2kszhmbhwfccfjw8khk36s5zbf90rbbkw5609")))) + "0rppbd0mfyi41wb56i499mk3nj2ljhgnv3bv0k2p31bngvmb03j5")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) + `(("r-beachmat" ,r-beachmat) + ("r-biocgenerics" ,r-biocgenerics) ("r-biocneighbors" ,r-biocneighbors) ("r-biocparallel" ,r-biocparallel) ("r-biocsingular" ,r-biocsingular) @@ -12579,7 +12580,9 @@ of other packages.") ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-matrix" ,r-matrix) + ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rlang" ,r-rlang) + ("r-rtsne" ,r-rtsne) ("r-s4vectors" ,r-s4vectors) ("r-scuttle" ,r-scuttle) ("r-singlecellexperiment" ,r-singlecellexperiment) -- cgit 1.4.1 From 015ba64bc0aa04cfe859dd81abed76a3861326a4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:14 +0200 Subject: gnu: r-scran: Update to 1.20.1. * gnu/packages/bioconductor.scm (r-scran): Update to 1.20.1. [propagated-inputs]: Remove r-biocneighbors; add r-metapod. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8c660d4b7e..52cb9f467b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12600,20 +12600,19 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.18.7") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0hsr58b7xj2cqdkyjdpzyifg5wrl1lbylq2h91zbjh5861qjv2n4")))) + "0ilzp6ngw9pq88gk79iic2zxfh5jaic6lnq3xfwc9a269bjylff0")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) ("r-bh" ,r-bh) ("r-biocgenerics" ,r-biocgenerics) - ("r-biocneighbors" ,r-biocneighbors) ("r-biocparallel" ,r-biocparallel) ("r-biocsingular" ,r-biocsingular) ("r-bluster" ,r-bluster) @@ -12624,6 +12623,7 @@ quality control.") ("r-igraph" ,r-igraph) ("r-limma" ,r-limma) ("r-matrix" ,r-matrix) + ("r-metapod" ,r-metapod) ("r-rcpp" ,r-rcpp) ("r-s4vectors" ,r-s4vectors) ("r-scuttle" ,r-scuttle) -- cgit 1.4.1 From 360477c202c26f100fb3a646699371a6c1010771 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:14 +0200 Subject: gnu: r-sparsematrixstats: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-sparsematrixstats): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 52cb9f467b..b4f42ab8f3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12643,14 +12643,14 @@ variable and significantly correlated genes.") (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.2.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "01gnmy9zqd0ygm40vqkmqmiwfqmdawj4m81dysmmcdm7z80rn9ii")))) + "0ilspddfkqpnf2lng9jjs2ahv6vlc6sap69fzkcw314rha59kncr")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) -- cgit 1.4.1 From 47e291df84c3b1a7bafe0f65df1904442098dd46 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:14 +0200 Subject: gnu: r-delayedmatrixstats: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.14.0. [propagated-inputs]: Remove r-biocparallel and r-hdf5array. --- gnu/packages/bioconductor.scm | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b4f42ab8f3..41a57e9376 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12671,21 +12671,19 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.12.3") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1hb8jv5dy3svf7xan6rym7amwdqm5mvl9qx5xhmj1vkb81bizn7h")))) + "02r68rzmc54m353fpw5ampyv26i5622bc7iihfqlpy6p3033lpqk")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-delayedarray" ,r-delayedarray) - ("r-hdf5array" ,r-hdf5array) + `(("r-delayedarray" ,r-delayedarray) ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) ("r-matrixgenerics" ,r-matrixgenerics) -- cgit 1.4.1 From aaf095825b48f497800f351752fda2e0d6bb6f30 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:14 +0200 Subject: gnu: r-mscoreutils: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.4.0. [propagated-inputs]: Add r-clue. --- gnu/packages/bioconductor.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 41a57e9376..bdd1444783 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12707,18 +12707,19 @@ memory usage and processing time is minimized.") (define-public r-mscoreutils (package (name "r-mscoreutils") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 - "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630")))) + "13g8a726vsyjs6m1kd42vf8avdnmhykxhl6z3j2njzkp2jg17pd8")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) + `(("r-clue" ,r-clue) + ("r-mass" ,r-mass) ("r-rcpp" ,r-rcpp) ("r-s4vectors" ,r-s4vectors))) (native-inputs -- cgit 1.4.1 From b5a387745a7320919cb1820641063fb644a0faee Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:15 +0200 Subject: gnu: r-biocio: Update to 1.2.0. * gnu/packages/bioconductor.scm (r-biocio): Update to 1.2.0. [propagated-inputs]: Remove r-genomicranges and r-rcurl. --- gnu/packages/bioconductor.scm | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bdd1444783..1edf5c8c72 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12739,21 +12739,19 @@ within the R for Mass Spectrometry packages.") (define-public r-biocio (package (name "r-biocio") - (version "1.0.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocIO" version)) (sha256 (base32 - "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18")))) + "0skwnpxl6fkqihidpqrfzzh7b05x11j6jwkiinmhggmv0ggjb5ph")))) (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-rcurl" ,r-rcurl) - ("r-s4vectors" ,r-s4vectors))) + `(("r-biocgenerics" ,r-biocgenerics) + ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocIO") -- cgit 1.4.1 From e501608db35b571dabac25995c7a2613ef8853e3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:15 +0200 Subject: gnu: r-msmseda: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-msmseda): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1edf5c8c72..71cee4909e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12773,14 +12773,14 @@ as well as local access. Developers can register a file extension, e.g., (define-public r-msmseda (package (name "r-msmseda") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsEDA" version)) (sha256 (base32 - "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx")))) + "0555a3riyp781mlffmnf93igfq8vl8wjk51pa9qb48qkdn6y8pfc")))) (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 2fe867326332651bcf5c4f0b72215bf2fbb61224 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:15 +0200 Subject: gnu: r-msmstests: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-msmstests): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 71cee4909e..cfa294e461 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12799,14 +12799,14 @@ experiments, and visualize de influence of the involved factors.") (define-public r-msmstests (package (name "r-msmstests") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsTests" version)) (sha256 (base32 - "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j")))) + "11vhy1l6za73dpdj85q4ksaghgd8vb2h8v9iirmsn2vpajqrvgjh")))) (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 8ad54dc134542ac1a9b6806da5e027a603e4653e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:15 +0200 Subject: gnu: r-catalyst: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-catalyst): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cfa294e461..a65b018a93 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12831,14 +12831,14 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "04b5kcvkfiw4ina11x3qf5kwrb7056zihm7xp1919bqm8k7nl3mn")))) + "1lzi3wylx94k3gmfw5lsqh3cvg485ik3n5xd51jllczgavwvki16")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From bd6d0007d9011f0afbfbc1053a101215805463e9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:15 +0200 Subject: gnu: r-erma: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-erma): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a65b018a93..624dbfde27 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12889,14 +12889,14 @@ standards, ii) single-cell deconvolution, and iii) bead-based compensation.") (define-public r-erma (package (name "r-erma") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k")))) + "02a9702sasgighwb0f9ii8n30ngfx1hjnppaay1f5zsigr8vqalz")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From 46b7d19dcc0b65c7b629cfe7a779b1c5ec2383de Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:15 +0200 Subject: gnu: r-ggbio: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-ggbio): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 624dbfde27..664ac9ce2b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12929,14 +12929,14 @@ by Ernst and Kellis.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw")))) + "0k3dxacrwgyrkvm7ggc2s1s1pbfs6c0a7ngykkj7jnc73czvnilx")))) (build-system r-build-system) (arguments `(#:phases -- cgit 1.4.1 From bdfa1178b9869850e6f8f6c8fa72d2a60502e675 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:15 +0200 Subject: gnu: r-gviz: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-gviz): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 664ac9ce2b..4b37858284 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13097,14 +13097,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.34.1") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0bmlfz9ri1gkwyl605a2hqi5b8jdpvynrxwghwmrsd657ip6c7n1")))) + "19vjf4sdz5sxbcdilsqx7m57fq5a8xnxjf354zx2l5mgjrkzkk3h")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From a06d13be0941535265a26e4cdf3afdb50a7b733b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:16 +0200 Subject: gnu: r-gwascat: Update to 2.24.0. * gnu/packages/bioconductor.scm (r-gwascat): Update to 2.24.0. [propagated-inputs]: Add r-annotationhub. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4b37858284..00e1554fe5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13146,17 +13146,18 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna")))) + "0109cxsviq1sk5hfwkjzd0y1kpm934287asjjd0j8jhh4b0ah2b2")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationhub" ,r-annotationhub) ("r-biocfilecache" ,r-biocfilecache) ("r-biostrings" ,r-biostrings) ("r-genomeinfodb" ,r-genomeinfodb) -- cgit 1.4.1 From 2860208c42bf8d6b4e5c8050b7bdb566e30715f8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:16 +0200 Subject: gnu: r-kegggraph: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-kegggraph): Update to 1.52.0. [propagated-inputs]: Add r-rgraphviz. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 00e1554fe5..6ea28e5489 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13180,18 +13180,19 @@ EMBL-EBI GWAS catalog.") (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v")))) + (base32 "0zxdph5hzr3kzj2g1mjqpiviwa189a5sq4bw7wiry6r79fdnklqs")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs `(("r-graph" ,r-graph) ("r-rcurl" ,r-rcurl) + ("r-rgraphviz" ,r-rgraphviz) ("r-xml" ,r-xml))) (home-page "https://bioconductor.org/packages/KEGGgraph") (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor") -- cgit 1.4.1 From b4cea45e7c1d07a932f3ffb1ac0859e91a3b8516 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:16 +0200 Subject: gnu: r-ldblock: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-ldblock): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6ea28e5489..69d629d0b0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13207,14 +13207,14 @@ functionalities including parsing, graph operation, visualization and etc.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm")))) + "075jncvfbn3lydg0jvfhnv5025mnw79saa0k557vpcwdvs9y4p0c")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit 1.4.1 From 8fa5a4d753f0c2f868ec3d5c0418f97323eb4930 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:16 +0200 Subject: gnu: r-pathview: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-pathview): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 69d629d0b0..4f786eca6f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13333,13 +13333,13 @@ other functional sequencing data.") (define-public r-pathview (package (name "r-pathview") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 - (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4")))) + (base32 "1fank0qavv9ikmzxvms8mky2wbzny02rfqkvsqzma26r3vl4r1g1")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 3e2052e7dac115d0795c28e93006df17a562b18b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:16 +0200 Subject: gnu: r-snpstats: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-snpstats): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4f786eca6f..4ffa8694af 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13367,14 +13367,14 @@ large-scale and fully automated analysis.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24")))) + "11vvih5y9kvyjfp2navkfpp4xiyfgwlv4r0x3p52hkj92pc2pg3g")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit 1.4.1 From 3a5642d72e5ef386fb2dca572867eab13998b074 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:16 +0200 Subject: gnu: r-chromstar: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-chromstar): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4ffa8694af..8e0bc500c6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13394,14 +13394,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") (define-public r-chromstar (package (name "r-chromstar") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaR" version)) (sha256 (base32 - "0vgpb7g2cncdn82hia2yzzachyns2zbd7906662g990qjnp2xlm1")))) + "09cqzylci4x4i7wn4ckcqhdlljbzfrp08wdvkkc5vrdldnj9pq5h")))) (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From abe7628a055e0505a625e5e3cd16dd5ed772ce7d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:16 +0200 Subject: gnu: r-guitar: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-guitar): Update to 2.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8e0bc500c6..341d0db13b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13432,14 +13432,14 @@ analyses.") (define-public r-guitar (package (name "r-guitar") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Guitar" version)) (sha256 (base32 - "0lvfrpgrvmrz4f4qmsii70hw10h72zh1g1alv2sf6a6ixhndm0mz")))) + "1q4m6c5181dw12lvdp324jlk78c9jgcsg6b9hk87zjadp6j0gfr6")))) (properties `((upstream-name . "Guitar"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 8f12002f6e720bf02ed455a32bc8fc39ff379a2f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 08:50:16 +0200 Subject: gnu: r-sushi: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-sushi): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 341d0db13b..d84481bdb8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13464,13 +13464,13 @@ starting site, start codon, stop codon and transcription ending site.") (define-public r-sushi (package (name "r-sushi") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p")))) + "1m5l0nflhcynb3gz7b8qzvknb0s6xhds8z1yl3mbv8ic9qn2knv4")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From c128d4f931dfe4c6d867fa64e3ab95264329c83e Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 5 Jun 2021 09:21:26 +0200 Subject: gnu: sbcl-cmd: Update to 20210531. * gnu/packages/lisp-xyz.scm (sbcl-cmd): Update to 20210531. --- gnu/packages/lisp-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 04954647fc..b61356d46a 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -14470,10 +14470,10 @@ standard library.") (sbcl-package->cl-source-package sbcl-shlex)) (define-public sbcl-cmd - (let ((commit "bc5a3bee8f22917126e4c3d05b33f766e562dbd8")) + (let ((commit "8ace7fb45f2ecf0eefae28583ee36c941d142179")) (package (name "sbcl-cmd") - (version (git-version "0.0.1" "3" commit)) + (version (git-version "0.0.1" "4" commit)) (source (origin (method git-fetch) @@ -14482,7 +14482,7 @@ standard library.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "1sjlabrknw1kjb2y89vssjhcqh3slgly8wnr3152zgis8lsj2yc7")))) + (base32 "1da8sa0fsvsdivnx2s9m6jbb7yszrnkqqcxrn1sszp7k6iwnnkgi")))) (build-system asdf-build-system/sbcl) (inputs `(("alexandria" ,sbcl-alexandria) -- cgit 1.4.1 From c2b6d36b66c1c9ca5b1f7a5bf6416f1713cd76a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 09:20:50 +0200 Subject: gnu: pari-gp: Use patched texlive-amsfonts. * gnu/packages/algebra.scm (pari-gp)[native-inputs]: Use texlive-amsfonts/patched. --- gnu/packages/algebra.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 573688d43c..a39eb4d12c 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -247,7 +247,7 @@ the real span of the lattice.") (build-system gnu-build-system) (native-inputs `(("texlive" ,(texlive-union - (list texlive-amsfonts))))) + (list texlive-amsfonts/patched))))) (inputs `(("gmp" ,gmp) ("libx11" ,libx11) ("perl" ,perl) -- cgit 1.4.1 From 701a11553365a859079c591eaf30a07daa485869 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 09:21:21 +0200 Subject: gnu: dblatex: Use patched texlive-amsfonts. * gnu/packages/docbook.scm (dblatex)[inputs]: Use texlive-amsfonts/patched. --- gnu/packages/docbook.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/docbook.scm b/gnu/packages/docbook.scm index e348fb1a5b..1945fb6a4b 100644 --- a/gnu/packages/docbook.scm +++ b/gnu/packages/docbook.scm @@ -394,7 +394,7 @@ the in DocBook SGML DTDs.") (build-system python-build-system) ;; TODO: Add xfig/transfig for fig2dev utility (inputs - `(("texlive" ,(texlive-union (list texlive-amsfonts + `(("texlive" ,(texlive-union (list texlive-amsfonts/patched texlive-latex-anysize texlive-latex-appendix texlive-latex-changebar -- cgit 1.4.1 From 11caa5f68abf3a9f8184afcf90f5db9cd76d2ccb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 09:21:44 +0200 Subject: gnu: emacs-auctex: Use patched texlive-amsfonts. * gnu/packages/emacs-xyz.scm (emacs-auctex)[inputs]: Use texlive-amsfonts/patched. --- gnu/packages/emacs-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 9a14e71c7c..e8e02de1b2 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -2454,7 +2454,7 @@ as a library for other Emacs packages.") `(("perl" ,perl))) (inputs `(("ghostscript" ,ghostscript) - ("texlive" ,(texlive-union (list texlive-amsfonts))))) + ("texlive" ,(texlive-union (list texlive-amsfonts/patched))))) (home-page "https://www.gnu.org/software/auctex/") (synopsis "Integrated environment for TeX") (description -- cgit 1.4.1 From 41bbbd53d2a4b8ad059c9a943e28fe7dda479149 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 09:22:16 +0200 Subject: gnu: asymptote: Use patched texlive-amsfonts. Fixes . * gnu/packages/plotutils.scm (asymptote)[native-inputs]: Use texlive-amsfonts/patched. --- gnu/packages/plotutils.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/plotutils.scm b/gnu/packages/plotutils.scm index 7f59bae770..4b89ddafd1 100644 --- a/gnu/packages/plotutils.scm +++ b/gnu/packages/plotutils.scm @@ -224,7 +224,7 @@ colors, styles, options and details.") ("perl" ,perl) ("texinfo" ,texinfo) ;For generating documentation ;; For the manual and the tests. - ("texlive" ,(texlive-union (list texlive-amsfonts + ("texlive" ,(texlive-union (list texlive-amsfonts/patched texlive-epsf texlive-etoolbox texlive-latex-base -- cgit 1.4.1 From 232bdb900de520333fb776b40ac2bf8933d7f293 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 09:23:30 +0200 Subject: gnu: gnuradio: Use patched texlive-amsfonts. * gnu/packages/radio.scm (gnuradio)[native-inputs]: Use texlive-amsfonts/patched. --- gnu/packages/radio.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 6a9d2db084..cafc6428ba 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -350,7 +350,7 @@ used by RDS Spy, and audio files containing @dfn{multiplex} signals (MPX).") ("python-pyzmq" ,python-pyzmq) ("python-scipy" ,python-scipy) ("python-sphinx" ,python-sphinx) - ("texlive" ,(texlive-union (list texlive-amsfonts + ("texlive" ,(texlive-union (list texlive-amsfonts/patched texlive-latex-amsmath ;; TODO: Add newunicodechar. texlive-latex-graphics))) -- cgit 1.4.1 From af8a5285d2295fff342338dbc3a6157e25a4326a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 09:23:55 +0200 Subject: gnu: libosmo-dsp: Use patched texlive-amsfonts. * gnu/packages/radio.scm (libosmo-dsp)[native-inputs]: Use texlive-amsfonts/patched. --- gnu/packages/radio.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index cafc6428ba..c511fd7e8c 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -553,7 +553,7 @@ to access different radio hardware.") ("doxygen" ,doxygen) ("libtool" ,libtool) ("pkg-config" ,pkg-config) - ("texlive" ,(texlive-union (list texlive-amsfonts + ("texlive" ,(texlive-union (list texlive-amsfonts/patched texlive-latex-amsmath ;; TODO: Add newunicodechar. texlive-latex-graphics))))) -- cgit 1.4.1 From d71751526f330f5dcfce6e50e00fbddce0676811 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 09:24:24 +0200 Subject: gnu: python-numpy-documentation: Use patched texlive-amsfonts. * gnu/packages/python-xyz.scm (python-numpy-documentation)[native-inputs]: Use texlive-amsfonts/patched. --- gnu/packages/python-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f3404178ba..8a1aabdca8 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5203,7 +5203,7 @@ color scales, and color space conversion easy. It has support for: texlive-fonts-ec texlive-generic-ifxetex texlive-generic-pdftex - texlive-amsfonts + texlive-amsfonts/patched texlive-latex-capt-of texlive-latex-cmap texlive-latex-environ -- cgit 1.4.1 From ace97406f2ba198b8f866f37fd17ebbee73739bc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 09:24:54 +0200 Subject: gnu: python-matplotlib-documentation: Use patched texlive-amsfonts. * gnu/packages/python-xyz.scm (python-matplotlib-documentation)[native-inputs]: Use texlive-amsfonts/patched. --- gnu/packages/python-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8a1aabdca8..e28fb648b0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5743,7 +5743,7 @@ toolkits.") ("python-ipykernel" ,python-ipykernel) ("python-mock" ,python-mock) ("graphviz" ,graphviz) - ("texlive" ,(texlive-union (list texlive-amsfonts + ("texlive" ,(texlive-union (list texlive-amsfonts/patched texlive-latex-amsmath texlive-latex-enumitem texlive-latex-expdlist -- cgit 1.4.1 From 45aae518e77eedde534c6017363a275d9c4e0eb8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 09:25:22 +0200 Subject: gnu: python-ipython-documentation: Use patched texlive-amsfonts. * gnu/packages/python-xyz.scm (python-ipython-documentation)[native-inputs]: Use texlive-amsfonts/patched. --- gnu/packages/python-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e28fb648b0..dfbeeabe59 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8107,7 +8107,7 @@ computing.") `(("python-sphinx" ,python-sphinx) ("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme) ;; FIXME: It's possible that a smaller union would work just as well. - ("texlive" ,(texlive-union (list texlive-amsfonts + ("texlive" ,(texlive-union (list texlive-amsfonts/patched texlive-fonts-ec texlive-generic-ifxetex texlive-generic-pdftex -- cgit 1.4.1 From f9ef881e4dea6f7fdbe5c4be59d54b34f2b62f36 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 09:25:43 +0200 Subject: gnu: python-pypandoc: Use patched texlive-amsfonts. * gnu/packages/python-xyz.scm (python-pypandoc)[native-inputs]: Use texlive-amsfonts/patched. --- gnu/packages/python-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index dfbeeabe59..b63c2852d5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -24844,7 +24844,7 @@ By default it uses the open Python vulnerability database Safety DB.") (propagated-inputs `(("wheel" ,python-wheel))) (native-inputs - `(("texlive" ,(texlive-union (list texlive-amsfonts + `(("texlive" ,(texlive-union (list texlive-amsfonts/patched texlive-fonts-ec texlive-latex-hyperref texlive-latex-oberdiek -- cgit 1.4.1 From ba9cbb66126df73363ac3a3ccc8e2843f1753168 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Sat, 5 Jun 2021 11:23:10 +0200 Subject: gnu: Add libfec. * gnu/packages/radio.scm (libfec): New variable. --- gnu/packages/radio.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index c511fd7e8c..dd3771d786 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -94,6 +94,34 @@ #:use-module (guix build-system python) #:use-module (guix build-system qt)) +(define-public libfec + ;; Use commit to get compilation fixes that are not in a release yet. + (let ((commit "9750ca0a6d0a786b506e44692776b541f90daa91") + (revision "1")) + (package + (name "libfec") + (version (git-version "1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/quiet/libfec") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0i6jhrdswr1wglyb9h39idpz5v9z13yhidvlbj34vxpyngrkhlvs")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON") + #:test-target "test_all")) + (home-page "https://github.com/quiet/libfec") + (synopsis "Forward error correction algorithms library") + (description + "This package provides a set of functions that implement several popular +@dfn{forward error correction} (FEC) algorithms and several low-level routines +useful in modems implemented with @dfn{digital signal processing} (DSP).") + (license license:lgpl2.1)))) + (define-public liquid-dsp (package (name "liquid-dsp") -- cgit 1.4.1 From 573f777495eee94c62bd5f80dd71f2a787d63018 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Sat, 5 Jun 2021 11:38:09 +0200 Subject: gnu: liquid-dsp: Add support for more error correction codes. * gnu/packages/radio.scm (liquid-dsp)[inputs]: Add libfec. --- gnu/packages/radio.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index dd3771d786..2b13c062d7 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -139,7 +139,8 @@ useful in modems implemented with @dfn{digital signal processing} (DSP).") `(("autoconf" ,autoconf))) (inputs `(("fftw" ,fftw) - ("fftwf" ,fftwf))) + ("fftwf" ,fftwf) + ("libfec" ,libfec))) (home-page "https://liquidsdr.org") (synopsis "Signal processing library for software-defined radios") (description -- cgit 1.4.1 From 3a8d0eff9ef4037b0234fc2508039ab48af8d633 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Sat, 5 Jun 2021 11:43:00 +0200 Subject: gnu: liquid-dsp: Remove static library. * gnu/packages/radio.scm (liquid-dsp)[arguments]: Add 'delete-static-library' phase. --- gnu/packages/radio.scm | 7 +++++++ 1 file changed, 7 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 2b13c062d7..6d2ab5ff1c 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -141,6 +141,13 @@ useful in modems implemented with @dfn{digital signal processing} (DSP).") `(("fftw" ,fftw) ("fftwf" ,fftwf) ("libfec" ,libfec))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'install 'delete-static-library + (lambda* (#:key outputs #:allow-other-keys) + (delete-file (string-append (assoc-ref outputs "out") + "/lib/libliquid.a"))))))) (home-page "https://liquidsdr.org") (synopsis "Signal processing library for software-defined radios") (description -- cgit 1.4.1 From f9a7a365ed5af80f0645779d3352555271ea1c8f Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Sat, 5 Jun 2021 11:45:47 +0200 Subject: gnu: liquid-dsp: Remove unused input. * gnu/packages/radio.scm (liquid-dsp)[inputs]: Remove fftw. --- gnu/packages/radio.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 6d2ab5ff1c..5fbddc102b 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -138,8 +138,7 @@ useful in modems implemented with @dfn{digital signal processing} (DSP).") (native-inputs `(("autoconf" ,autoconf))) (inputs - `(("fftw" ,fftw) - ("fftwf" ,fftwf) + `(("fftwf" ,fftwf) ("libfec" ,libfec))) (arguments `(#:phases -- cgit 1.4.1 From ac9da35707549156bc83da7dded1ed9ad3715347 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 5 Jun 2021 11:12:13 +0200 Subject: gnu: emacs-webfeeder: Update to 1.1.2. * gnu/packages/emacs-xyz.scm (emacs-webfeeder): Update to 1.1.2. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index e8e02de1b2..1c4d8c6c1a 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -24359,7 +24359,7 @@ and article extracts for Wikipedia.") (define-public emacs-webfeeder (package (name "emacs-webfeeder") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) @@ -24369,7 +24369,7 @@ and article extracts for Wikipedia.") ".tar")) (sha256 (base32 - "09caj12hfdfhlbcsmjyhw728w1f7yq13hdslh793yvfqv83ipvc4")))) + "1l128q424qsq9jv2wk8cv4zli71rk34q5kgwa9axdz0d27p9l6v4")))) (build-system emacs-build-system) (home-page "https://gitlab.com/Ambrevar/emacs-webfeeder") (synopsis "Build RSS and Atom webfeeds from HTML files") -- cgit 1.4.1 From bbf54272c6eb7da5ba2b072bc93ddc0928e87208 Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Wed, 2 Jun 2021 23:00:31 +0200 Subject: gnu: Add emacs-hgignore-mode. * gnu/packages/emacs-xyz.scm (emacs-hgignore-mode): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 1c4d8c6c1a..704d9c9fb0 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -425,6 +425,32 @@ repositories through the server}. The main advantage compared to @code{vc-hg} is speed.") (license license:gpl3+))) +(define-public emacs-hgignore-mode + ;; From 2021-03-14. + ;; No releases available. + (let ((commit "2c5aa4c238848f5b4f2955afcfb5f21ea513653b") + (revision "0")) + (package + (name "emacs-hgignore-mode") + ;; `Version:' header says 0.1.20150329 + (version (git-version "0.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/omajid/hgignore-mode") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0jn9rzhrmmv4lf7rdapdjclk6623d1mir2lq3c46428skhzjlph7")))) + (build-system emacs-build-system) + (home-page "https://github.com/omajid/hgignore-mode") + (synopsis "Major mode for editing @file{hgignore} files") + (description "This package provides a basic major mode for +editing @file{.hgignore} files used by the Mercurial version control +system.") + (license license:gpl3+)))) + (define-public emacs-hyperbole (package (name "emacs-hyperbole") -- cgit 1.4.1 From 612e5b8528e1f4f9c1c03ba7fa01997ca16f4250 Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Wed, 2 Jun 2021 23:08:33 +0200 Subject: gnu: Add emacs-hg-histedit. * gnu/packages/emacs-xyz.scm (emacs-hg-histedit): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 704d9c9fb0..63de8bea05 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -506,6 +506,32 @@ outlines, manage all your contacts, your windows and frames, and search across buffers, directory trees, or the web.") (license license:gpl3+))) +(define-public emacs-hg-histedit + ;; From 2021-03-02. + ;; No releases available. + (let ((commit "a05149483b9c5f7848ece0ba6028c900595a6a25") + (revision "0")) + (package + (name "emacs-hg-histedit") + (version (git-version "0.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jojojames/hg-histedit") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "04zps0d4s99f5a8ahrpyf8b6qw0c1y7rd1bsaq9nc6m4qblsvwc8")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-with-editor" ,emacs-with-editor))) + (home-page "https://github.com/jojojames/hg-histedit") + (synopsis "Emacs interface to @command{hg histedit}") + (description "This package provides an Emacs interface to +@command{hg histedit} for editing the commit history.") + (license license:gpl3+)))) + (define-public emacs-paredit (package (name "emacs-paredit") -- cgit 1.4.1 From b61ee34c9d7b679cb772e6e8ff0c0876ccf087b1 Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Thu, 3 Jun 2021 22:12:52 +0200 Subject: gnu: Add emacs-djvu3. * gnu/packages/emacs-xyz.scm (emacs-djvu3): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 63de8bea05..676b3d35e9 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -3105,6 +3105,46 @@ filters, new key bindings and faces. It can be enabled by DjVuLibre, see @url{http://djvu.sourceforge.net/}.") (license license:gpl3+))) +(define-public emacs-djvu3 + ;; Commit from 2021-06-03. + (let ((commit "37b675be1d4d436cdd0c3b5d3f13e88b59a7bf18") + (revision "0")) + (package + (name "emacs-djvu3") + ;; `Version:' header says 1.0 + (version (git-version "1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dalanicolai/djvu3") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0p0izjrgbayx5ybk1n6db5hbrjv9d4kpn57w4iyxdm3h96sp9cmr")))) + (propagated-inputs + `(("emacs-djvu" ,emacs-djvu) + ("emacs-tablist" ,emacs-tablist))) + (build-system emacs-build-system) + (home-page "https://github.com/dalanicolai/djvu3") + (synopsis "Extend djvu.el to display annotations and more") + (description "This package extends @code{emacs-djvu} with annotation +rendering features and a fast occur search feature using @code{svg.el}. + +Other features include: + +@itemize +@item clickable links +@item marker extension to @code{svg.el} for providing arrowheads (or other +types of markers) +@item a quite fancy keyboard annotation function +@item an @code{imenu} index function to enable imenu navigation +@item document restore function to open the document at the last location of +the previous session +@end itemize") + (license license:gpl3+)))) + (define-public emacs-pabbrev (package (name "emacs-pabbrev") -- cgit 1.4.1 From fec881eac3b6ad1d3a757544244e6aaff6113706 Mon Sep 17 00:00:00 2001 From: Alexandr Vityazev Date: Thu, 3 Jun 2021 20:39:32 +0000 Subject: gnu: Add emacs-kibit-helper. * gnu/packages/emacs-xyz.scm (emacs-kibit-helper): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 676b3d35e9..b4a96b28be 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -28336,3 +28336,26 @@ shorter than usual, using mostly unprefixed keys.") (description "@code{emacs-multitran} is a zero-dependency Emacs interface to the https://multitran.com online dictionary.") (license license:gpl3+))) + +(define-public emacs-kibit-helper + (package + (name "emacs-kibit-helper") + (version "0.1.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/brunchboy/kibit-helper") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ky167xh1hrmqsldybzjhyqjizgjzs1grn5mf8sm2j9qwcvjw2zv")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-s" ,emacs-s))) + (home-page "http://www.github.com/brunchboy/kibit-helper") + (synopsis "Use the Kibit Leiningen plugin from Emacs") + (description + "Kibit Helper provides functions to work with the Kibit Leiningen plugin +for detecting and improve non-idiomatic Clojure source code.") + (license license:gpl3+))) -- cgit 1.4.1 From c6d4f974bcb38433bf559301c87e07ca713b8023 Mon Sep 17 00:00:00 2001 From: Alexandr Vityazev Date: Sat, 5 Jun 2021 14:00:42 +0200 Subject: gnu: Add emacs-clojure-snippets. * gnu/packages/emacs-xyz.scm (emacs-clojure-snippets): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index b4a96b28be..e13ca415d2 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -8938,6 +8938,35 @@ refactoring for the @uref{http://clojure.org, Clojure programming language}. It is recommended to use @code{clojure-mode} with Paredit or Smartparens.") (license license:gpl3+))) +(define-public emacs-clojure-snippets + ;; Use latest commit (2018) since latest tagged release is too old and is + ;; missing important changes. + (let ((version "1.0.1") + (revision "0") + (commit "6068dca90467a0f4ebc2cd39338a173d6f5ddc04")) + (package + (name "emacs-clojure-snippets") + (version (git-version version revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mpenet/clojure-snippets") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0vvadcydpsz4b17dlm1jd4fbddzfqibh3mlzv3k4gvp67vv10cqy")))) + (build-system emacs-build-system) + (arguments + `(#:include (cons* "^.*\\/" %default-include))) + (propagated-inputs + `(("emacs-yasnippet" ,emacs-yasnippet))) + (home-page "https://github.com/mpenet/clojure-snippets") + (synopsis "Yasnippets for Clojure") + (description + "This package provides Yasnippets snippets for Clojure.") + (license license:gpl3+)))) + (define-public emacs-epl (package (name "emacs-epl") @@ -28359,3 +28388,4 @@ to the https://multitran.com online dictionary.") "Kibit Helper provides functions to work with the Kibit Leiningen plugin for detecting and improve non-idiomatic Clojure source code.") (license license:gpl3+))) + -- cgit 1.4.1 From 0a4b2da0ed817f95a55e57d5756b389cf71f90b5 Mon Sep 17 00:00:00 2001 From: Alexandr Vityazev Date: Sat, 5 Jun 2021 14:10:54 +0200 Subject: gnu: Add emacs-anakondo. * gnu/packages/emacs-xyz.scm (emacs-anakondo): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index e13ca415d2..0a96d95d95 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -8967,6 +8967,31 @@ It is recommended to use @code{clojure-mode} with Paredit or Smartparens.") "This package provides Yasnippets snippets for Clojure.") (license license:gpl3+)))) +(define-public emacs-anakondo + ;; This particular commit introduces bug fixes above latest release. + (let ((version "0.2.1") + (revision "0") + (commit "c48518560815c49d8d78fb9069906d17e883385e")) + (package + (name "emacs-anakondo") + (version (git-version version revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/didibus/anakondo") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1fzsqd150gpmrj8kz3zy9cd78x9vank7ra720mljhyf04z0h1mj6")))) + (build-system emacs-build-system) + (home-page "https://github.com/didibus/anakondo") + (synopsis "clj-kondo based Clojure[Script] editing facilities") + (description + "This package makes use of clj-kondo's analysis data to provide code +editing facilities related to Clojure, ClojureScript and cljc source.") + (license license:expat)))) + (define-public emacs-epl (package (name "emacs-epl") -- cgit 1.4.1 From 00f8451ea1a52bd9e70fa77c292ab840c639c449 Mon Sep 17 00:00:00 2001 From: Alexandr Vityazev Date: Sat, 5 Jun 2021 14:23:28 +0200 Subject: gnu: Add emacs-flymake-quickdef. * gnu/packages/emacs-xyz.scm (emacs-flymake-quickdef): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 0a96d95d95..eee31f1861 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1503,6 +1503,31 @@ different tools. It highlights errors and warnings inline in the buffer, and provides an optional IDE-like error list.") (license license:gpl3+)))) ;+GFDLv1.3+ for the manual +(define-public emacs-flymake-quickdef + ;; This particular commit includes bug fixes on top of 1.0.0 release. + (let ((version "1.0.0") + (revision "0") + (commit "150c5839768a3d32f988f9dc08052978a68f2ad7")) + (package + (name "emacs-flymake-quickdef") + (version (git-version version revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/karlotness/flymake-quickdef") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "19gfd539l97j8xbrq1fw83b54mxbcamlz9m896088d3p01zf8b0g")))) + (build-system emacs-build-system) + (home-page "https://github.com/karlotness/flymake-quickdef") + (synopsis "Quickly define a new Flymake backend") + (description + "This package mainly defines a macro which helps remove some of the +boilerplate code from defining new Flymake backend functions.") + (license license:gpl3+)))) + (define-public emacs-flymake-shellcheck ;; No tag, version grabbed from source .el file. (let ((commit "ac534e9ef15c82ac86ae65fe5004d29dbc8c92c7") -- cgit 1.4.1 From 087fbcfe48e079d088a38714b0e5fc3c6bbac5d8 Mon Sep 17 00:00:00 2001 From: Alexandr Vityazev Date: Sat, 5 Jun 2021 14:25:30 +0200 Subject: gnu: Add emacs-flymake-kondor. * gnu/packages/emacs-xyz.scm (emacs-flymake-kondor): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index eee31f1861..872d821593 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1528,6 +1528,27 @@ provides an optional IDE-like error list.") boilerplate code from defining new Flymake backend functions.") (license license:gpl3+)))) +(define-public emacs-flymake-kondor + (package + (name "emacs-flymake-kondor") + (version "0.0.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/turbo-cafe/flymake-kondor") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0h8dqk35r10pxx2w4swb3kij4y2vi17j9wfk978x8lf0wd3h3hsy")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-flymake-quickdef" ,emacs-flymake-quickdef))) + (home-page "https://github.com/turbo-cafe/flymake-kondor") + (synopsis "Linter with clj-kondo") + (description "This package adds Clojure syntax checker clj-kondo.") + (license license:gpl3+))) + (define-public emacs-flymake-shellcheck ;; No tag, version grabbed from source .el file. (let ((commit "ac534e9ef15c82ac86ae65fe5004d29dbc8c92c7") -- cgit 1.4.1 From 11f18341db9929f1af4483fd49a0e65d530e3991 Mon Sep 17 00:00:00 2001 From: Adam Kandur Date: Sat, 5 Jun 2021 15:47:52 +0200 Subject: gnu: Add emacs-vscode-dark-plus. * gnu/packages/emacs-xyz.scm (emacs-vscode-dark-plus): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 872d821593..cf595786b3 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -968,6 +968,27 @@ theme and apply them to the rest of Linux with Pywal. Pywal only applies your theme to the current session.") (license license:gpl3+)))) +(define-public emacs-vscode-dark-plus + (package + (name "emacs-vscode-dark-plus") + (version "2.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ianyepan/vscode-dark-plus-emacs-theme") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1vcaqvhdgr91pr7kqskbscs8awm8jp6dkh79h6w36i9ipmc4l4hl")))) + (build-system emacs-build-system) + (home-page "https://github.com/ianyepan/vscode-dark-plus-emacs-theme") + (synopsis "Emacs port of the default VS Code Dark+ theme") + (description + "This theme aims to be as identical as possible to the default Dark+ +color scheme used by Visual Studio Code.") + (license license:gpl3+))) + (define-public emacs-theme-sorcery (let ((revision "0") (commit "5a1c4445b9e6e09589a299a9962a6973272a0c2f")) -- cgit 1.4.1 From fb41cc6c41378a37d84362e133e3e2066be05fe8 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 5 Jun 2021 15:52:52 +0200 Subject: gnu: emacs-leaf: Update to 4.4.8. * gnu/packages/emacs-xyz.scm (emacs-leaf): Update to 4.4.8. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index cf595786b3..d18770f6ff 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -12949,14 +12949,14 @@ performance-oriented and tidy.") (define-public emacs-leaf (package (name "emacs-leaf") - (version "4.4.4") + (version "4.4.8") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "leaf-" version ".tar")) (sha256 - (base32 "1npg06zmy21kg2qsqgfm03l7vjib697i96awypcdb0hw5mvmc1a1")))) + (base32 "0h0ksmgrhn29ci6z8y54dbbzcqlvfs1ra0kmf226gz0dqzk45vb3")))) (build-system emacs-build-system) (home-page "https://github.com/conao3/leaf.el") (synopsis "Simplify your init.el configuration, extended use-package") -- cgit 1.4.1 From bdab742322a84803caa2333e7e949d2b8fdb9904 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 5 Jun 2021 15:56:20 +0200 Subject: gnu: emacs-all-the-icons: Update to 5.0.0. * gnu/packages/emacs-xyz.scm (emacs-all-the-icons): Update to 5.0.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index d18770f6ff..3c97d65051 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -21335,7 +21335,7 @@ files are easily readable and they work nicely with version control systems.") (define-public emacs-all-the-icons (package (name "emacs-all-the-icons") - (version "4.0.1") + (version "5.0.0") (source (origin (method git-fetch) @@ -21344,7 +21344,7 @@ files are easily readable and they work nicely with version control systems.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0yh7gnv9xfqn8q4rzaa6wpyn9575vyfxy7d3afly2mqsb367fgm5")))) + (base32 "0lwgvgnqf7vihglm0c5bwsxbl4x7f641289cji5s7jwy2dbsqk7g")))) (build-system emacs-build-system) (arguments `(#:include '("\\.el$" "^data/" "^fonts/") -- cgit 1.4.1 From bb7706dcdd6cbfa7a2f1e794fe3797b694075172 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 5 Jun 2021 15:57:59 +0200 Subject: gnu: emacs-undercover: Update to 0.8.1. * gnu/packages/emacs-xyz.scm (emacs-undercover): Update to 0.8.1. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 3c97d65051..773e484953 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -4512,7 +4512,7 @@ Emacs shell script.") (define-public emacs-undercover (package (name "emacs-undercover") - (version "0.8.0") + (version "0.8.1") (source (origin (method git-fetch) @@ -4521,7 +4521,7 @@ Emacs shell script.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "19d3373fy635vbfwr1yhxirwqn68qzny9byv74smxws4ly04mr02")))) + (base32 "0qmvyy3xg5qi7ws8zcs934d6afsappr1a6pgfp796xpa9vdr4y6j")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-dash" ,emacs-dash) -- cgit 1.4.1 From 9da90938c63208b7721276f8cefcdac82ba765f2 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 5 Jun 2021 16:08:34 +0200 Subject: gnu: rosegarden: Update to 21.06. * gnu/packages/music.scm (rosegarden): Update to 21.06. --- gnu/packages/music.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index cc9076e763..68d48a2937 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -4981,14 +4981,14 @@ specification and header.") (define-public rosegarden (package (name "rosegarden") - (version "20.12") + (version "21.06") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/rosegarden/rosegarden/" version "/rosegarden-" version ".tar.bz2")) (sha256 - (base32 "0nqw2caxmv6mqh485wzvywa024yvi18q87sd4dw9b2l5qnpq8rl8")))) + (base32 "0rhbmygzh62hc3mkq60lh9r28wvfkhzzd5kspl1ll0h1ipjgvr6d")))) (build-system cmake-build-system) (arguments `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release") -- cgit 1.4.1 From 20d9535e1bf981a37f39f171ad72f67cdb1e6919 Mon Sep 17 00:00:00 2001 From: Carl Dong Date: Sat, 29 May 2021 01:28:10 -0400 Subject: gnu: nsis: Respect SOURCE-DATE-EPOCH for reproducibility * gnu/packages/patches/nsis-source-date-epoch.patch: New patch. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/installers.scm (make-nsis)[source]: Apply it. --- gnu/local.mk | 1 + gnu/packages/installers.scm | 3 ++- gnu/packages/patches/nsis-source-date-epoch.patch | 23 +++++++++++++++++++++++ 3 files changed, 26 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/nsis-source-date-epoch.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 8c235f50c8..870769cffc 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1468,6 +1468,7 @@ dist_patch_DATA = \ %D%/packages/patches/network-manager-plugin-path.patch \ %D%/packages/patches/nginx-socket-cloexec.patch \ %D%/packages/patches/nsis-env-passthru.patch \ + %D%/packages/patches/nsis-source-date-epoch.patch \ %D%/packages/patches/nss-increase-test-timeout.patch \ %D%/packages/patches/nss-3.56-pkgconfig.patch \ %D%/packages/patches/ntfs-3g-CVE-2019-9755.patch \ diff --git a/gnu/packages/installers.scm b/gnu/packages/installers.scm index 775b91f0f7..c768a367aa 100644 --- a/gnu/packages/installers.scm +++ b/gnu/packages/installers.scm @@ -42,7 +42,8 @@ (sha256 (base32 "1sbwx5vzpddharkb7nj4q5z3i5fbg4lan63ng738cw4hmc4v7qdn")) - (patches (search-patches "nsis-env-passthru.patch")))) + (patches (search-patches "nsis-env-passthru.patch" + "nsis-source-date-epoch.patch")))) (build-system scons-build-system) (native-inputs `(("xgcc" ,xgcc) ("xbinutils" ,xbinutils) diff --git a/gnu/packages/patches/nsis-source-date-epoch.patch b/gnu/packages/patches/nsis-source-date-epoch.patch new file mode 100644 index 0000000000..744c2a8011 --- /dev/null +++ b/gnu/packages/patches/nsis-source-date-epoch.patch @@ -0,0 +1,23 @@ +Honour SOURCE_DATE_EPOCH for VERSION default + +Merged upstream as cd3f1024a37a332f1d4fa96a817ca80dfa2a478c, but not yet in a +release. GitHub PR: https://github.com/kichik/nsis/pull/13 + +Python snippet from: https://reproducible-builds.org/docs/source-date-epoch/#python + + +diff --git a/SConstruct b/SConstruct +index e8252c9..41786f2 100755 +--- a/SConstruct ++++ b/SConstruct +@@ -95,8 +95,8 @@ default_doctype = 'html' + if defenv.WhereIs('hhc', os.environ['PATH']): + default_doctype = 'chm' + +-from time import strftime, gmtime +-cvs_version = strftime('%d-%b-%Y.cvs', gmtime()) ++import time ++cvs_version = time.strftime('%d-%b-%Y.cvs', time.gmtime(int(os.environ.get('SOURCE_DATE_EPOCH', time.time())))) + + opts = Variables() + -- cgit 1.4.1 From 38eaba9a8e65ee286a5c6688e084fa618c329f82 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 5 Jun 2021 17:24:13 +0200 Subject: gnu: giac: Update to 1.7.0-11. * gnu/packages/algebra.scm (giac): Update to 1.7.0-11. --- gnu/packages/algebra.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index a39eb4d12c..ce8dc34fb1 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -341,7 +341,7 @@ precision.") (define-public giac (package (name "giac") - (version "1.7.0-9") + (version "1.7.0-11") (source (origin (method url-fetch) @@ -353,7 +353,7 @@ precision.") "~parisse/debian/dists/stable/main/source/" "giac_" version ".tar.gz")) (sha256 - (base32 "0yl5h13rnis8gqg48g9z719d5xfgxjcxz7bwbdqlwsvdy42crrim")))) + (base32 "12njy2akcc3sj1fmq52v19m4qd1ysrdcpc9a3zslkxsnidjix81m")))) (build-system gnu-build-system) (arguments `(#:modules ((ice-9 ftw) -- cgit 1.4.1 From de1b8f71431a8878d718badda812122235f24e6f Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 5 Jun 2021 17:48:42 +0200 Subject: gnu: wireshark: Update to 3.4.6. * gnu/packages/networking.scm (wireshark): Update to 3.4.6. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 1be47e6102..fc09429b57 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1458,14 +1458,14 @@ of the same name.") (define-public wireshark (package (name "wireshark") - (version "3.4.5") + (version "3.4.6") (source (origin (method url-fetch) (uri (string-append "https://www.wireshark.org/download/src/wireshark-" version ".tar.xz")) (sha256 - (base32 "0cyk8nqws9gp8p2ywszbynh8vawivnbhw60dhmy21qd1038sy6ny")))) + (base32 "0a26kcj3n1a2kw1f3fc6s1x3rw3f3bj2cq6rp7k0kc4ciwh7i9hj")))) (build-system cmake-build-system) (arguments `(#:phases -- cgit 1.4.1 From 9412762f9b092a89bf63054540909f84a577c1dd Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 5 Jun 2021 13:38:32 +0200 Subject: gnu: thermald: Update to 2.4.5. * gnu/packages/admin.scm (thermald): Update to 2.4.5. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 8bc02f5ee3..551cd3666c 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -3637,7 +3637,7 @@ make it a perfect utility on modern distros.") (define-public thermald (package (name "thermald") - (version "2.4.4") + (version "2.4.5") (source (origin (method git-fetch) @@ -3646,7 +3646,7 @@ make it a perfect utility on modern distros.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1k0r2c13fihjndwfh0byw0i8ni4lzsjgwz874pvpj1l1nvjj0ajx")))) + (base32 "1y8s0cpjm01bz4isp3ksvnrbhpp3phivdhsb0w2kxhv09sfxkc5g")))) (build-system gnu-build-system) (arguments `(#:configure-flags -- cgit 1.4.1 From ddd871c18ab2d853503c167fd306fa8d84e99421 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 5 Jun 2021 13:39:15 +0200 Subject: gnu: thermald: Compile with -Werror again. * gnu/packages/admin.scm (thermald)[arguments]: Remove substitution, and a #t whilst we're here. --- gnu/packages/admin.scm | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 551cd3666c..9bade4a850 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -3660,13 +3660,7 @@ make it a perfect utility on modern distros.") (modify-phases %standard-phases (add-before 'bootstrap 'no-early-./configure (lambda _ - (setenv "NO_CONFIGURE" "yet") - ;; XXX thd_trip_point.h redefines "__STDC_LIMIT_MACROS" after - ;; /include/lzma.h. ./configure forcibly appends -Werror - ;; to CXXFLAGS, overriding any -Wno-error we'd add. - (substitute* "configure.ac" - (("-Werror") "")) - #t))))) + (setenv "NO_CONFIGURE" "yet")))))) (native-inputs `(("autoconf" ,autoconf) ("autoconf-archive" ,autoconf-archive) -- cgit 1.4.1 From 1e1a274ffd5fdeb41b4c65a99cb333712c95b3f4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 5 Jun 2021 13:49:43 +0200 Subject: gnu: nnn: Update to 4.1.1. * gnu/packages/admin.scm (nnn): Update to 4.1.1. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 9bade4a850..83e52963f1 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -3596,14 +3596,14 @@ information tool.") (define-public nnn (package (name "nnn") - (version "4.0") + (version "4.1.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/jarun/nnn/releases/download/v" version "/nnn-v" version ".tar.gz")) (sha256 - (base32 "0m07nh1cdfikn4bkpni29j61hr9jdwbl0n5fmlm53l1xmn7yq6d2")))) + (base32 "1fnf35s3b2nfp18s712n5vhg6idx4rfgwdfv74nc2933v9l2dq7h")))) (build-system gnu-build-system) (inputs `(("ncurses" ,ncurses) -- cgit 1.4.1 From 49dd606f574b3e7aadea8d93818bfdc6f3de71cc Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 5 Jun 2021 13:51:37 +0200 Subject: gnu: nnn: Use #:make-flags over Makefile patching. * gnu/packages/admin.scm (nnn)[arguments]: Remove 'patch-pkg-config phase. Set PKG_CONFIG in #:make-flags instead. --- gnu/packages/admin.scm | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 83e52963f1..a2e013ed03 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -3614,17 +3614,13 @@ information tool.") `(#:tests? #f ; no tests #:phases (modify-phases %standard-phases - (delete 'configure) ; no configure script - (add-after 'unpack 'patch-pkg-config - (lambda _ - (substitute* "Makefile" - (("pkg-config") - ,(pkg-config-for-target)))))) + (delete 'configure)) ; no configure script #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")) - (string-append "CC=" ,(cc-for-target))))) + (string-append "CC=" ,(cc-for-target)) + (string-append "PKG_CONFIG=" ,(pkg-config-for-target))))) (home-page "https://github.com/jarun/nnn") (synopsis "Terminal file browser") (description "@command{nnn} is a fork of @command{noice}, a blazing-fast -- cgit 1.4.1 From 605a40b3857ffb705649aa0857a0ef0d065aa7a7 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 5 Jun 2021 13:52:43 +0200 Subject: gnu: nnn: Remove marketing hyperbole. * gnu/packages/admin.scm (nnn)[description]: Gush less. --- gnu/packages/admin.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index a2e013ed03..661e5e131d 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -3623,11 +3623,11 @@ information tool.") (string-append "PKG_CONFIG=" ,(pkg-config-for-target))))) (home-page "https://github.com/jarun/nnn") (synopsis "Terminal file browser") - (description "@command{nnn} is a fork of @command{noice}, a blazing-fast -lightweight terminal file browser with easy keyboard shortcuts for -navigation, opening files and running tasks. There is no config file and -mime associations are hard-coded. The incredible user-friendliness and speed -make it a perfect utility on modern distros.") + (description + "@command{nnn} is a fork of @command{noice}, a fast and minimal text +terminal file browser with keyboard shortcuts for navigation, opening files and +running tasks. There is no configuration file and MIME associations are +hard-coded.") (license license:bsd-2))) (define-public thermald -- cgit 1.4.1 From c6e36ee2dc570ee5c636ebee0561f989c66912e0 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 5 Jun 2021 14:11:32 +0200 Subject: gnu: ispell: Update to 3.4.04. * gnu/packages/aspell.scm (ispell): Update to 3.4.04. --- gnu/packages/aspell.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/aspell.scm b/gnu/packages/aspell.scm index 4821e08432..a86984b28c 100644 --- a/gnu/packages/aspell.scm +++ b/gnu/packages/aspell.scm @@ -489,14 +489,14 @@ under permissive licensing terms. See the 'Copyright' file.")))) (define-public ispell (package (name "ispell") - (version "3.4.03") + (version "3.4.04") (source (origin (method url-fetch) (uri (string-append "https://www.cs.hmc.edu/~geoff/tars/ispell-" version ".tar.gz")) (sha256 - (base32 "040wvf81ihq2sdacvi4kk1n6f19fjdn44hb1ydz0l5lj1sz6mrxs")))) + (base32 "0gp1rwn8grkvz28wgisc2j9w9svldnaiahl3lyis118xabqddg47")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f -- cgit 1.4.1 From d22b1b21f685fe289901d0ec29579421a3a2bda0 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 5 Jun 2021 14:30:06 +0200 Subject: gnu: iperf: Update to 3.10.1. * gnu/packages/networking.scm (iperf): Update to 3.10.1. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index fc09429b57..1912e63585 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2380,7 +2380,7 @@ that block port 22.") (define-public iperf (package (name "iperf") - (version "3.10") + (version "3.10.1") (source (origin (method git-fetch) @@ -2389,7 +2389,7 @@ that block port 22.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "102wcyl4j7c7lj7z87b5xlhj1ark88v4f3q9pmmljw8ksn2w1m2g")))) + (base32 "0svkrmxki6ckn2a8xysh5x0bw68mqnvl3w64j6d45fxs97dca2vq")))) (build-system gnu-build-system) (arguments `(#:configure-flags -- cgit 1.4.1 From debcc760e892a6cfbc3b936e4557ac3807253fb2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 5 Jun 2021 17:10:36 +0200 Subject: gnu: qca: Update to 2.3.3. * gnu/packages/kde.scm (qca): Update to 2.3.3. --- gnu/packages/kde.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index 2af02615c0..3b112324bf 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -619,14 +619,14 @@ used in KDE development tools Kompare and KDevelop.") (define-public qca (package (name "qca") - (version "2.3.2") + (version "2.3.3") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/qca/" version "/qca-" version ".tar.xz")) (sha256 - (base32 "0vb0kwm4vpf71vczadg6h1ib09sgca0crll7ksbkmg646w1615s6")))) + (base32 "0rvvf97la95lah67jcj0p06n4br0pc2mri0q1hn4x522hndqybjn")))) (build-system cmake-build-system) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit 1.4.1 From 0339829a633ffd46295e3ce8f30d8bd5f2b56b57 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 5 Jun 2021 18:07:23 +0200 Subject: gnu: wireshark: Support more compression algorithms. * gnu/packages/networking.scm (wireshark)[inputs]: Add google-brotli, minizip, and zstd:lib. --- gnu/packages/networking.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 1912e63585..60d9cfa241 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1496,6 +1496,7 @@ of the same name.") `(("c-ares" ,c-ares) ("glib" ,glib) ("gnutls" ,gnutls) + ("google-brotli" ,google-brotli) ("libcap" ,libcap) ("libgcrypt" ,libgcrypt) ("libnl" ,libnl) @@ -1505,12 +1506,14 @@ of the same name.") ("lz4" ,lz4) ("lua" ,lua-5.2) ;Lua 5.3 unsupported ("krb5" ,mit-krb5) + ("minizip" ,minizip) ("qtbase" ,qtbase) ("qtmultimedia" ,qtmultimedia) ("qtsvg" ,qtsvg) ("sbc" ,sbc) ("snappy" ,snappy) - ("zlib" ,zlib))) + ("zlib" ,zlib) + ("zstd:lib" ,zstd "lib"))) (native-inputs `(("bison" ,bison) ("doxygen" ,doxygen) -- cgit 1.4.1 From f1a4b85af1db7f9f8ffcd96b6db410a88620b17a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 5 Jun 2021 18:08:30 +0200 Subject: gnu: wireshark: Inspect HTTP/2 headers. * gnu/packages/networking.scm (wireshark)[inputs]: Add nghttp2:lib. --- gnu/packages/networking.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 60d9cfa241..804a951eb7 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1506,6 +1506,7 @@ of the same name.") ("lz4" ,lz4) ("lua" ,lua-5.2) ;Lua 5.3 unsupported ("krb5" ,mit-krb5) + ("nghttp2:lib" ,nghttp2 "lib") ("minizip" ,minizip) ("qtbase" ,qtbase) ("qtmultimedia" ,qtmultimedia) -- cgit 1.4.1 From ddc9da2ba99e65e2bcc29683b2312c0a6afc0b5b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 5 Jun 2021 18:08:39 +0200 Subject: gnu: faudio: Update to 21.06. * gnu/packages/audio.scm (faudio): Update to 21.06. --- gnu/packages/audio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index f905a2827c..662d1f6068 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -4472,7 +4472,7 @@ library.") (define-public faudio (package (name "faudio") - (version "21.05") + (version "21.06") (source (origin (method git-fetch) @@ -4481,7 +4481,7 @@ library.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0lzvfx5gg5m6jbdzqwkjl4wq4fdg5n98fxn5x8n65vgvrj95sx6z")))) + (base32 "1nnx4l1r5hwdaw824d4fmd558qsqa22qzpvnkhs8nkjr40cnidkr")))) (arguments '(#:tests? #f ; No tests. #:configure-flags '("-DGSTREAMER=ON"))) -- cgit 1.4.1 From cd6c61f8c8a411a53047714256eacde63635f9a2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 5 Jun 2021 18:44:33 +0200 Subject: gnu: nzbget: Update to 21.1. * gnu/packages/networking.scm (nzbget): Update to 21.1. [source]: Remove upstreamed snippet. --- gnu/packages/networking.scm | 13 ++----------- 1 file changed, 2 insertions(+), 11 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 804a951eb7..ff28ad7233 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2451,7 +2451,7 @@ gone wild and are suddenly taking up your bandwidth.") (define-public nzbget (package (name "nzbget") - (version "21.0") + (version "21.1") (source (origin (method url-fetch) @@ -2459,16 +2459,7 @@ gone wild and are suddenly taking up your bandwidth.") "/download/v" version "/nzbget-" version "-src.tar.gz")) (sha256 - (base32 - "0lwd0pfrs4a5ms193hgz2qiyf7grrc925dw6y0nfc0gkp27db9b5")) - (modules '((guix build utils))) - (snippet - ;; Reported upstream as . - '(begin - (substitute* "daemon/connect/TlsSocket.cpp" - (("gnutls_certificate-verification_status_print") - "gnutls_certificate_verification_status_print")) - #t)))) + (base32 "09900x1k0yf4yi2cc0k093advvadyhrkm8rnd8nszhhdp2zc33sf")))) (arguments `(#:configure-flags (list -- cgit 1.4.1 From a80cde0326428c453218e7b9f6965d65c932fa7a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 5 Jun 2021 18:51:33 +0200 Subject: gnu: console-setup: Update to 1.203. * gnu/packages/xorg.scm (console-setup): Update to 1.203. --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 1b9dfed34b..34d7997550 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -6662,7 +6662,7 @@ output.") (define-public console-setup (package (name "console-setup") - (version "1.201") + (version "1.203") (source (origin (method git-fetch) @@ -6670,7 +6670,7 @@ output.") (url "https://salsa.debian.org/installer-team/console-setup.git") (commit version))) (sha256 - (base32 "0xkynb8d1813wph3p0sdvbpimx7zqkzh4c3mmqymp3pibcg7af5a")) + (base32 "1bavb8h4j1za2h7mxr109imicjmh7fp4099lvzfgavhjr3l3vsab")) (file-name (git-file-name name version)))) (build-system gnu-build-system) (arguments -- cgit 1.4.1 From c107a30bb48cda91fba502e862a1b426d475cb19 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 5 Jun 2021 19:07:07 +0200 Subject: gnu: wgetpaste: Don't install LICENSE file twice. * gnu/packages/wget.scm (wgetpaste)[arguments]: Leave LICENSE file installation to the aptly-named 'install-license-files default phase. --- gnu/packages/wget.scm | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/wget.scm b/gnu/packages/wget.scm index 1092237a03..70022f6c90 100644 --- a/gnu/packages/wget.scm +++ b/gnu/packages/wget.scm @@ -106,11 +106,9 @@ in downloaded documents to relative links.") (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin")) - (zsh (string-append out "/share/zsh/site-functions")) - (doc (string-append out "/share/doc/" ,name "-" ,version))) + (zsh (string-append out "/share/zsh/site-functions"))) (install-file "wgetpaste" bin) (install-file "_wgetpaste" zsh) - (install-file "LICENSE" doc) #t))) (add-after 'install 'wrap-program ;; /bin/wgetpaste prides itself on relying only on the following -- cgit 1.4.1 From 2e97761efe4816df4604870c2c85c90725969de2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 5 Jun 2021 19:11:33 +0200 Subject: gnu: wgetpaste: Build from Git. * gnu/packages/wget.scm (wgetpaste)[source]: Use GIT-FETCH and GIT-FILE-NAME. --- gnu/packages/wget.scm | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/wget.scm b/gnu/packages/wget.scm index 70022f6c90..3d7f266dd7 100644 --- a/gnu/packages/wget.scm +++ b/gnu/packages/wget.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2014, 2015, 2017, 2018 Ludovic Courtès ;;; Copyright © 2016, 2017, 2019, 2020 Efraim Flashner ;;; Copyright © 2017 Rutger Helling -;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice +;;; Copyright © 2018–2021 Tobias Geerinckx-Rice ;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen ;;; ;;; This file is part of GNU Guix. @@ -39,6 +39,7 @@ #:use-module (gnu packages xdisorg) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix build-system gnu)) (define-public wget @@ -80,11 +81,13 @@ in downloaded documents to relative links.") (version "2.30") (source (origin - (method url-fetch) - (uri (string-append "https://wgetpaste.zlin.dk/wgetpaste-" - version ".tar.bz2")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/zlin/wgetpaste") + (commit version))) + (file-name (git-file-name name version)) (sha256 - (base32 "14k5i6j6f34hcf9gdb9cnvfwscn0ys2dgd73ci421wj9zzqkbv73")) + (base32 "0fhm0qxdsm4k1m24z4bbb7mdv1x1iaqzgsnwkax6vb8bx9yd1ysi")) (patches (search-patches "wgetpaste-update-bpaste.patch")))) (build-system gnu-build-system) (arguments -- cgit 1.4.1 From bdd2970c087eba1027123f45e358bf4eac295572 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 5 Jun 2021 19:13:39 +0200 Subject: gnu: wgetpaste: Update to 2.32. * gnu/packages/wget.scm (wgetpaste): Update to 2.32. [source]: Remove patch. * gnu/packages/patches/wgetpaste-update-bpaste.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/patches/wgetpaste-update-bpaste.patch | 27 ---------------------- gnu/packages/wget.scm | 5 ++-- 3 files changed, 2 insertions(+), 31 deletions(-) delete mode 100644 gnu/packages/patches/wgetpaste-update-bpaste.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 870769cffc..1c692e0ce4 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1805,7 +1805,6 @@ dist_patch_DATA = \ %D%/packages/patches/webkitgtk-share-store.patch \ %D%/packages/patches/webkitgtk-bind-all-fonts.patch \ %D%/packages/patches/websocketpp-fix-for-cmake-3.15.patch \ - %D%/packages/patches/wgetpaste-update-bpaste.patch \ %D%/packages/patches/wicd-bitrate-none-fix.patch \ %D%/packages/patches/wicd-get-selected-profile-fix.patch \ %D%/packages/patches/wicd-urwid-1.3.patch \ diff --git a/gnu/packages/patches/wgetpaste-update-bpaste.patch b/gnu/packages/patches/wgetpaste-update-bpaste.patch deleted file mode 100644 index f92a0c17ed..0000000000 --- a/gnu/packages/patches/wgetpaste-update-bpaste.patch +++ /dev/null @@ -1,27 +0,0 @@ -From: Tobias Geerinckx-Rice -Date: Tue, 01 Sep 2020 04:23:25 +0200 -Subject: [PATCH] Update bpaste URL & regular expressions. - -diff -Naur wgetpaste-2.30/wgetpaste wgetpaste-2.30a/wgetpaste ---- wgetpaste-2.30/wgetpaste 2020-07-31 23:56:05.000000000 +0200 -+++ wgetpaste-2.30a/wgetpaste 2020-09-01 04:22:37.499898403 +0200 -@@ -16,7 +16,7 @@ - SERVICES="codepad bpaste dpaste gists snippets" - # bpaste - ENGINE_bpaste=pinnwand --URL_bpaste="https://bpaste.net/" -+URL_bpaste="https://bpa.st/" - DEFAULT_EXPIRATION_bpaste="1week" - DEFAULT_LANGUAGE_bpaste="text" - # codepad -@@ -194,8 +194,8 @@ - xml+velocity xml xquery xslt xtend yaml" - EXPIRATIONS_pinnwand="1day 1week 1month never" - POST_pinnwand="submit=Paste! % % lexer expiry % code" --REGEX_LOC_pinnwand="\(/show/[^ ]*\).*$|https://bpaste.net\1" --REGEX_RAW_pinnwand='s|^\(https\?://[^/]*/\)show\(/[^ ]*/\?\)$|\1raw\2|' -+REGEX_LOC_pinnwand="\(/[^ ]*\).*$|https://bpa.st\1" -+REGEX_RAW_pinnwand='s|^\(https\?://[^/]*\)\(/[^ ]*/\?\)$|\1/raw\2|' - - ### errors - die() { diff --git a/gnu/packages/wget.scm b/gnu/packages/wget.scm index 3d7f266dd7..8891170e10 100644 --- a/gnu/packages/wget.scm +++ b/gnu/packages/wget.scm @@ -78,7 +78,7 @@ in downloaded documents to relative links.") (define-public wgetpaste (package (name "wgetpaste") - (version "2.30") + (version "2.32") (source (origin (method git-fetch) @@ -87,8 +87,7 @@ in downloaded documents to relative links.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0fhm0qxdsm4k1m24z4bbb7mdv1x1iaqzgsnwkax6vb8bx9yd1ysi")) - (patches (search-patches "wgetpaste-update-bpaste.patch")))) + (base32 "13zdqfnbpymwz2f04icw92flj50227n5r0dcms84qxswfxrarnas")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build gnu-build-system) -- cgit 1.4.1 From febfd4ce0d86aa44b3b57c2a661a467178a8323b Mon Sep 17 00:00:00 2001 From: Antero Mejr Date: Mon, 31 May 2021 19:55:35 -0400 Subject: gnu: rust-structopt-derive-0.4: Update to 0.4.14. * gnu/packages/crates-io.scm (rust-structopt-derive-0.4): Update to 0.4.14. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 50 +++++++++++++++++++++++----------------------- 1 file changed, 25 insertions(+), 25 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 398c7084ed..af7c1fa410 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -40794,31 +40794,31 @@ and Jaro-Winkler.") (define-public rust-structopt-derive-0.4 (package - (name "rust-structopt-derive") - (version "0.4.5") - (source - (origin - (method url-fetch) - (uri (crate-uri "structopt-derive" version)) - (file-name - (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "0c04bbzc5bmr2ns6qy35yz55nn3xvlq4dpwxdynnljb9ikhvi21z")))) - (build-system cargo-build-system) - (arguments - `(#:skip-build? #t - #:cargo-inputs - (("rust-heck" ,rust-heck-0.3) - ("rust-proc-macro-error" ,rust-proc-macro-error-0.4) - ("rust-proc-macro2" ,rust-proc-macro2-1) - ("rust-syn" ,rust-syn-1) - ("rust-quote" ,rust-quote-1)))) - (home-page "https://github.com/TeXitoi/structopt") - (synopsis "Parse command line argument by defining a struct, derive crate") - (description - "Parse command line argument by defining a struct, derive crate.") - (license (list license:asl2.0 license:expat)))) + (name "rust-structopt-derive") + (version "0.4.14") + (source + (origin + (method url-fetch) + (uri (crate-uri "structopt-derive" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "143gjwvz3s86hwp070km83y25n8kqp5f01kb1dr19f4ilkywvaav")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-heck" ,rust-heck-0.3) + ("rust-proc-macro-error" ,rust-proc-macro-error-1) + ("rust-proc-macro2" ,rust-proc-macro2-1) + ("rust-syn" ,rust-syn-1) + ("rust-quote" ,rust-quote-1)))) + (home-page "https://github.com/TeXitoi/structopt") + (synopsis "Parse command line argument by defining a struct, derive crate") + (description + "This package provides the derive Rust crate for the structopt crate.") + (license license:asl2.0))) (define-public rust-structopt-derive-0.2 (package -- cgit 1.4.1 From 38233e745ed4b4cf0904894c3a0877aef4ac5cdc Mon Sep 17 00:00:00 2001 From: Antero Mejr Date: Mon, 31 May 2021 19:55:36 -0400 Subject: gnu: rust-structopt-0.3: Update to 0.3.21. * gnu/packages/crates-io.scm (rust-structopt-0.3): Update to 0.3.21. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index af7c1fa410..f0489f7d09 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -40745,16 +40745,16 @@ and Jaro-Winkler.") (define-public rust-structopt-0.3 (package (name "rust-structopt") - (version "0.3.12") + (version "0.3.21") (source - (origin - (method url-fetch) - (uri (crate-uri "structopt" version)) - (file-name - (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "178m7wxnjyy9a8a961z74nazjsg79rfv3gv9g3bykfrrjmqs5yn8")))) + (origin + (method url-fetch) + (uri (crate-uri "structopt" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "136j0lvjmpv5syi751vxg8vb30gfyv4k81x8d18kxrj6xvbsqxsj")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t @@ -40765,7 +40765,8 @@ and Jaro-Winkler.") (home-page "https://github.com/TeXitoi/structopt") (synopsis "Parse command line argument by defining a struct") (description - "Parse command line argument by defining a struct.") + "This package parses command lines arguments by defining a Rust +struct.") (license (list license:asl2.0 license:expat)))) (define-public rust-structopt-0.2 -- cgit 1.4.1 From 51f5292014ce85f4b2918ed60b363820b06faf52 Mon Sep 17 00:00:00 2001 From: Antero Mejr Date: Mon, 31 May 2021 19:55:37 -0400 Subject: gnu: Add rust-progressing-3. * gnu/packages/crates-io.scm (rust-progressing-3): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index f0489f7d09..f05a5ac681 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -30515,6 +30515,29 @@ macro use case.") @code{proc_macro_derive} pretend to be @code{proc_macro}.") (license (list license:expat license:asl2.0)))) +(define-public rust-progressing-3 + (package + (name "rust-progressing") + (version "3.0.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "progressing" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "06sb1cxpkc8lx56s76c95cfljs0513nsnn35wd6w79sblwcxpdwp")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("log" ,rust-log-0.4)))) + (home-page "https://github.com/dominicparga/progressing") + (synopsis "Counting progress-bar for Rust") + (description + "This package provides a set of text-based, counting +progress-bars for Rust.") + (license license:asl2.0))) + (define-public rust-progrs-0.1 (package (name "rust-progrs") -- cgit 1.4.1 From ed300014723e88c9cda21595274e628cfecc6e6c Mon Sep 17 00:00:00 2001 From: Antero Mejr Date: Mon, 31 May 2021 19:55:38 -0400 Subject: gnu: Add rust-nitrokey-0.9. * gnu/packages/crates-io.scm (rust-nitrokey-0.9): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 90 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 90 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index f05a5ac681..a548204b86 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -25378,6 +25378,96 @@ selectors. You can use the jQuery-like syntax to query and manipulate an HTML document quickly.") (license (list license:expat license:asl2.0)))) +(define-public rust-nitrokey-0.9 + (package + (name "rust-nitrokey") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "nitrokey" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0c8mj52ckvy1311vwxs6jpw16b2bihp5cc811isb96j9slcjvsyx")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-lazy_static" ,rust-lazy-static-1) + ("rust-libc" ,rust-libc-0.2) + ("rust-nitrokey-sys" ,rust-nitrokey-sys-3) + ("rust-rand_core" ,rust-rand-core-0.5)))) + (home-page "https://git.sr.ht/~ireas/nitrokey-rs") + (synopsis "Rust bindings to libnitrokey") + (description + "This package provides bindings to libnitrokey for communication +with Nitrokey devices.") + (license license:expat))) + +(define-public rust-nitrokey-sys-3 + (package + (name "rust-nitrokey-sys") + (version "3.6.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "nitrokey-sys" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "08c3lnb8iqx000jd5rzvrdvv4ihjyw3x3s8q11dw56is0nmjyvws")))) + (build-system cargo-build-system) + (home-page "https://git.sr.ht/~ireas/nitrokey-sys-rs") + (synopsis "Low-level Rust bindings for libnitrokey") + (description + "This package provides low-level bindings to libnitrokey for +communication with Nitrokey devices.") + (license license:lgpl3))) + +(define-public rust-nitrokey-test-0.5 + (package + (name "rust-nitrokey-test") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "nitrokey-test" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "197j9r2s4ydzbqfydza6v31mgcsgd29jpidz4psqawjdm49f8lg6")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-proc-macro2" ,rust-proc-macro2-1) + ("quote" ,rust-quote-1) + ("syn" ,rust-syn-1)))) + (home-page "https://github.com/d-e-s-o/nitrokey-test") + (synopsis "Supporting test infrastructure for the nitrokey crate") + (description + "This package provides supporting test infrastructure for the +nitrokey crate and others using it.") + (license license:gpl3+))) + +(define-public rust-nitrokey-test-state-0.1 + (package + (name "rust-nitrokey-test-state") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "nitrokey-test-state" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "00w817kl8q3sna924pzl72ybqljny14rdv1ixlj288fmsqp776x5")))) + (build-system cargo-build-system) + (home-page "https://github.com/d-e-s-o/nitrokey-test") + (synopsis "State required and used by the nitrokey-test crate") + (description "This package provides state required and used by the +nitrokey-test crate.") + (license license:gpl3+))) + (define-public rust-nix-0.20 (package (name "rust-nix") -- cgit 1.4.1 From 9c92fb862d0874e332d7be50b49ecb507082f770 Mon Sep 17 00:00:00 2001 From: Antero Mejr Date: Sat, 5 Jun 2021 22:05:28 +0200 Subject: gnu: Add rust-merge-derive-0.1. * gnu/packages/crates-io.scm (rust-merge-derive-0.1): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index a548204b86..b5a7720831 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -23661,6 +23661,24 @@ for Rust structs.") (sha256 (base32 "13ir50j549gdz94pds1i7ljnk14d66q5x91s11hncm1pih7jif8c")))))) +(define-public rust-merge-derive-0.1 + (package + (name "rust-merge-derive") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "merge_derive" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "01wxhi7mqmp34l540wcfb24hb13vcbps4wlynas66bnsfra0g790")))) + (build-system cargo-build-system) + (home-page "https://sr.ht/~ireas/merge-rs") + (synopsis "Derive macro for the merge crate") + (description "This crate provides a derive macro for the +@code{merge::Merge} crate.") + (license (list license:asl2.0 license:expat)))) + (define-public rust-merlin-2 (package (name "rust-merlin") -- cgit 1.4.1 From 7b5f5aa82baa1117c0ff10d1208154e5cbb3ce6f Mon Sep 17 00:00:00 2001 From: Antero Mejr Date: Sat, 5 Jun 2021 22:17:39 +0200 Subject: gnu: Add rust-merge-0.1. * gnu/packages/crates-io.scm (rust-merge-0.1): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index b5a7720831..bf9082c3f1 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -23679,6 +23679,29 @@ for Rust structs.") @code{merge::Merge} crate.") (license (list license:asl2.0 license:expat)))) +(define-public rust-merge-0.1 + (package + (name "rust-merge") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "merge" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1sck0vhi9lk8a6mgky0rgn842fj7yspywidwbd963nmimf9yzfqh")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-merge-derive" ,rust-merge-derive-0.1) + ("rust-num-traits" ,rust-num-traits-0.2)))) + (home-page "https://sr.ht/~ireas/merge-rs") + (synopsis "Rust trait for objects that can be merged") + (description "This package provides a merge trait that can be used +to merge two objects of the same type into one.") + (license (list license:asl2.0 license:expat)))) + (define-public rust-merlin-2 (package (name "rust-merlin") -- cgit 1.4.1 From add0c5f2b1abae743d76db0b1eaee6affab6a3f3 Mon Sep 17 00:00:00 2001 From: Antero Mejr Date: Mon, 31 May 2021 19:55:41 -0400 Subject: gnu: Add rust-envy-0.4. * gnu/packages/crates-io.scm (rust-envy-0.4): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index bf9082c3f1..26514a6319 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -13511,6 +13511,30 @@ variables.") "Environment variables utility functions.") (license license:asl2.0))) +(define-public rust-envy-0.4 + (package + (name "rust-envy") + (version "0.4.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "envy" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0rar459p7pl19v6pbx98q3hi2hxfl8q1ndxxw5d4zd9cgway0irz")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-serde" ,rust-serde-1)))) + (home-page "https://github.com/softprops/envy") + (synopsis "Deserialize environment variables into Rust structs") + (description + "This package provides access to typesafe config structs +deserialized from environment variables.") + (license license:expat))) + (define-public rust-erased-serde-0.3 (package (name "rust-erased-serde") -- cgit 1.4.1 From 3463559d5528179111852ba1e02cbdda97a8aed5 Mon Sep 17 00:00:00 2001 From: Antero Mejr Date: Mon, 31 May 2021 19:55:42 -0400 Subject: gnu: Add rust-base32-0.4. * gnu/packages/crates-io.scm (rust-base32-0.4): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 26514a6319..cc5dbc4252 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -15,6 +15,7 @@ ;;; Copyright © 2021 aecepoglu ;;; Copyright © 2021 Zheng Junjie <873216071@qq.com> ;;; Copyright © 2021 Alexandru-Sergiu Marton +;;; Copyright © 2021 Antero Mejr ;;; ;;; This file is part of GNU Guix. ;;; @@ -3816,6 +3817,25 @@ trace (backtrace) at runtime in a Rust program.") (license (list license:asl2.0 license:expat)))) +(define-public rust-base32-0.4 + (package + (name "rust-base32") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "base32" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1ykwx8jhksqxghfgyw2pzikzjf4n9wqm1x2ww5wqyn68ssf6dki3")))) + (build-system cargo-build-system) + (home-page "https://github.com/andreasots/base32") + (synopsis "Base32 encoder/decoder for Rust") + (description "This library lets you encode and decode in either +RFC4648 Base32 or in Crockford Base32.") + (license (list license:asl2.0 license:expat)))) + (define-public rust-base58-0.1 (package (name "rust-base58") -- cgit 1.4.1 From 7905b901a299facd220d01dbf72aa70923cdbc87 Mon Sep 17 00:00:00 2001 From: Antero Mejr Date: Mon, 31 May 2021 19:55:34 -0400 Subject: gnu: Add nitrocli. * gnu/packages/security-token.scm (nitrocli): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/security-token.scm | 46 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/security-token.scm b/gnu/packages/security-token.scm index dfa43bb2bf..89783de965 100644 --- a/gnu/packages/security-token.scm +++ b/gnu/packages/security-token.scm @@ -9,6 +9,7 @@ ;;; Copyright © 2018, 2019 Chris Marusich ;;; Copyright © 2018 Arun Isaac ;;; Copyright © 2020 Raphaël Mélotte +;;; Copyright © 2021 Antero Mejr ;;; ;;; This file is part of GNU Guix. ;;; @@ -32,6 +33,7 @@ #:use-module (guix download) #:use-module (guix gexp) #:use-module (guix git-download) + #:use-module (guix build-system cargo) #:use-module (guix build-system gnu) #:use-module (guix build-system glib-or-gtk) #:use-module (guix build-system python) @@ -39,6 +41,7 @@ #:use-module (gnu packages base) #:use-module (gnu packages curl) #:use-module (gnu packages check) + #:use-module (gnu packages crates-io) #:use-module (gnu packages docbook) #:use-module (gnu packages documentation) #:use-module (gnu packages dns) @@ -674,3 +677,46 @@ that after installing this package, you might still need to add appropriate udev rules to your system configuration to be able to configure the YubiKey as an unprivileged user.") (license license:bsd-2))) + +(define-public nitrocli + (package + (name "nitrocli") + (version "0.4.1") + (source (origin + (method url-fetch) + (uri (crate-uri "nitrocli" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1djspfvcqjipg17v8hkph8xrhkdg1xqjhq5jk1sr8vr750yavidy")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ;; 2/164 tests fail, nitrocli-ext tests failing + #:cargo-inputs + (("rust-anyhow" ,rust-anyhow-1) + ("rust-base32" ,rust-base32-0.4) + ("rust-directories" ,rust-directories-3) + ("rust-envy" ,rust-envy-0.4) + ("rust-libc-0.2" ,rust-libc-0.2) + ("rust-merge" ,rust-merge-0.1) + ("rust-nitrokey" ,rust-nitrokey-0.9) + ("rust-progressing" ,rust-progressing-3) + ("rust-serde" ,rust-serde-1) + ("rust-structopt" ,rust-structopt-0.3) + ("rust-termion" ,rust-termion-1) + ("rust-toml" ,rust-toml-0.5)) + #:cargo-development-inputs + (("rust-nitrokey-test" ,rust-nitrokey-test-0.5) + ("rust-nitrokey-test-state" ,rust-nitrokey-test-state-0.1) + ("rust-regex" ,rust-regex-1) + ("rust-tempfile" ,rust-tempfile-3)))) + (inputs + `(("hidapi" ,hidapi) + ("gnupg" ,gnupg))) + (home-page "https://github.com/d-e-s-o/nitrocli") + (synopsis "Command line tool for Nitrokey devices") + (description + "nitrocli is a program that provides a command line interface +for interaction with Nitrokey Pro, Nitrokey Storage, and Librem Key +devices.") + (license license:gpl3+))) -- cgit 1.4.1 From f1e0e5fde34ff0e882247498ecf78106c73284d6 Mon Sep 17 00:00:00 2001 From: Jonathan Brielmaier Date: Sat, 5 Jun 2021 20:36:45 +0200 Subject: gnu: icedove: Update to 78.11.0 [fixes CVE-2021-29967]. * gnu/packages/gnuzilla.scm (icedove): Update to 78.11.0. --- gnu/packages/gnuzilla.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index cc65b1ccfb..ab4c9ac193 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -1302,11 +1302,11 @@ standards of the IceCat project.") (cpe-version . ,(first (string-split version #\-))))))) ;; Update this together with icecat! -(define %icedove-build-id "20210504000000") ;must be of the form YYYYMMDDhhmmss +(define %icedove-build-id "20210601000000") ;must be of the form YYYYMMDDhhmmss (define-public icedove (package (name "icedove") - (version "78.10.1") + (version "78.11.0") (source icecat-source) (properties `((cpe-name . "thunderbird_esr"))) @@ -1586,7 +1586,7 @@ standards of the IceCat project.") ;; in the Thunderbird release tarball. We don't use the release ;; tarball because it duplicates the Icecat sources and only adds the ;; "comm" directory, which is provided by this repository. - ,(let ((changeset "14a9afcfb6cc0c466e0d0b8222e85de5b2d8078d")) + ,(let ((changeset "1717d8d5fbd359aab7a4a0a15f4d15c72a7e6afc")) (origin (method hg-fetch) (uri (hg-reference @@ -1595,7 +1595,7 @@ standards of the IceCat project.") (file-name (string-append "thunderbird-" version "-checkout")) (sha256 (base32 - "18658r4b1f5p8jcz68l31z29ny73lic0br7gc827m72nfc85wqz3"))))) + "10l042dd7b8rvla0cbiks5kjrz2b28yy7hr8sr169wlx202hxa01"))))) ("autoconf" ,autoconf-2.13) ("cargo" ,rust-1.41 "cargo") ("clang" ,clang) -- cgit 1.4.1 From 23ab8d417e238e735338c6bf378906ca7953f3de Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Fri, 4 Jun 2021 21:58:07 +1000 Subject: gnu: gparted: Update to 1.3.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/disk.scm (gparted): Update to 1.3.0. Signed-off-by: Ludovic Courtès --- gnu/packages/disk.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm index 84996f9bc4..c31afee627 100644 --- a/gnu/packages/disk.scm +++ b/gnu/packages/disk.scm @@ -552,14 +552,14 @@ and can dramatically shorten the lifespan of the drive if left unchecked.") (define-public gparted (package (name "gparted") - (version "1.2.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/gparted/gparted/gparted-" version "/gparted-" version ".tar.gz")) (sha256 - (base32 "06f72hqx5jf2irzsmi7lgpxxj38ncixh0acb4307wyjd4mfp343c")))) + (base32 "0amx3hb4rc504nl9i73rgyz0hzhq5x8nkg7lwbk4bsnrblj81hcd")))) (build-system glib-or-gtk-build-system) (arguments ;; Tests require access to paths outside the build container, such -- cgit 1.4.1 From 404f6145eeaf572ce824568a470eab98c124e554 Mon Sep 17 00:00:00 2001 From: Dion Mendel Date: Tue, 1 Jun 2021 13:25:53 +0800 Subject: gnu: Add lxcfs. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/virtualization.scm (lxcfs): New Variable. Signed-off-by: Ludovic Courtès --- gnu/packages/virtualization.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index f12f862304..5e7dd8a10a 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -19,6 +19,7 @@ ;;; Copyright © 2020 Brett Gilio ;;; Copyright © 2021 Leo Famulari ;;; Copyright © 2021 Pierre Langlois +;;; Copyright © 2021 Dion Mendel ;;; ;;; This file is part of GNU Guix. ;;; @@ -1065,6 +1066,35 @@ Through a powerful API and simple tools, it lets Linux users easily create and manage system or application containers.") (license license:lgpl2.1+))) +(define-public lxcfs + (package + (name "lxcfs") + (version "4.0.8") + (home-page "https://github.com/lxc/lxcfs") + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) + (commit (string-append "lxcfs-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1f74wy88si2ia035pcvciq5821kc8jcb75w1f8vhbp0cd29rqdpi")))) + (arguments + '(#:configure-flags '("--localstatedir=/var"))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (inputs + `(("fuse" ,fuse))) + (build-system gnu-build-system) + (synopsis "FUSE based filesystem for LXC") + (description "LXCFS is a small FUSE filesystem written with the intention +of making Linux containers feel more like a virtual machine. +It started as a side-project of LXC but is useable by any runtime.") + (license license:lgpl2.1+))) + (define-public libvirt (package (name "libvirt") -- cgit 1.4.1 From 08b55f14435fa04e7c21c066ed35d9494deccaa9 Mon Sep 17 00:00:00 2001 From: Dion Mendel Date: Tue, 1 Jun 2021 14:03:23 +0800 Subject: gnu: Add libdqlite. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/cluster.scm (libdqlite): New Variable. Signed-off-by: Ludovic Courtès --- gnu/packages/cluster.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cluster.scm b/gnu/packages/cluster.scm index 18f2707469..e643cc58f9 100644 --- a/gnu/packages/cluster.scm +++ b/gnu/packages/cluster.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2019 Andrew Miloradovsky ;;; Copyright © 2020 Marius Bakke +;;; Copyright © 2021 Dion Mendel ;;; ;;; This file is part of GNU Guix. ;;; @@ -33,6 +34,7 @@ #:use-module (gnu packages linux) #:use-module (gnu packages pkg-config) #:use-module (gnu packages sphinx) + #:use-module (gnu packages sqlite) #:use-module (gnu packages texinfo) #:use-module (gnu packages tls)) @@ -220,3 +222,42 @@ that, a pluggable interface defines the I/O implementation for networking (send/receive RPC messages) and disk persistence (store log entries and snapshots).") (license license:asl2.0))) + +(define-public libdqlite + (package + (name "libdqlite") + (version "1.7.0") + (home-page "https://github.com/canonical/dqlite") + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "15cg8yl3n7lcg0qyg0byciz8v6y200ghmzzkwpdzggy3m6c168wl")))) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-failing-tests + (lambda _ + (substitute* "Makefile.am" + ;; Test client/query sometimes fails. + ;; The actual tested asserts succeed, but there appears to be a + ;; race condition when tearing down the test server. + ((".*test_client.c.*") ""))))))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (inputs + `(("libraft" ,libraft) + ("libuv" ,libuv))) + (propagated-inputs + `(("sqlite" ,sqlite))) ; dqlite.h includes sqlite3.h + (build-system gnu-build-system) + (synopsis "Distributed SQLite") + (description "dqlite is a C library that implements an embeddable and replicated +SQL database engine with high-availability and automatic failover.") + (license license:lgpl3))) -- cgit 1.4.1 From 524c64152a8458915f42eb4a74b764eb2ab93966 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Sat, 5 Jun 2021 23:05:02 +0200 Subject: gnu: Add soapysdr. * gnu/packages/radio.scm (soapysdr): New variable. --- gnu/packages/radio.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 5fbddc102b..a3cbe99380 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -258,6 +258,35 @@ To install the airspyhf udev rules, you must extend @code{udev-service-type} with this package. E.g.: @code{(udev-rules-service 'airspyhf airspyhf)}") (license license:bsd-3))) +(define-public soapysdr + (package + (name "soapysdr") + (version "0.8.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pothosware/SoapySDR") + (commit (string-append "soapy-sdr-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1dy25zxk7wmg7ik82dx7h3bbbynvalbz1dxsl7kgm3374yxhnixv")))) + (build-system cmake-build-system) + (native-inputs + `(("python" ,python) + ("swig" ,swig))) + (native-search-paths + (list (search-path-specification + (variable "SOAPY_SDR_PLUGIN_PATH") + (files (list (string-append "lib/SoapySDR/modules" + (version-major+minor version))))))) + (home-page "https://github.com/pothosware/SoapySDR/wiki") + (synopsis "Vendor and platform neutral SDR support library") + (description + "SoapySDR is a library designed to support several kinds of software +defined radio hardware devices with a common API.") + (license license:boost1.0))) + (define-public chirp (package (name "chirp") -- cgit 1.4.1 From 59ce8276182891919baad2c306c1d632fff3e7e6 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Sat, 5 Jun 2021 23:14:31 +0200 Subject: gnu: Add soapyhackrf. * gnu/packages/radio.scm (soapyhackrf): New variable. --- gnu/packages/radio.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index a3cbe99380..18545bae79 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -287,6 +287,31 @@ with this package. E.g.: @code{(udev-rules-service 'airspyhf airspyhf)}") defined radio hardware devices with a common API.") (license license:boost1.0))) +(define-public soapyhackrf + (package + (name "soapyhackrf") + (version "0.3.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pothosware/SoapyHackRF") + (commit (string-append "soapy-hackrf-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1awn89z462500gb3fjb7x61b1znkjri9n1d39bqfip1qk4s11pxc")))) + (build-system cmake-build-system) + (inputs + `(("hackrf" ,hackrf) + ("soapysdr" ,soapysdr))) + (arguments + `(#:tests? #f)) ; No test suite + (home-page "https://github.com/pothosware/SoapyHackRF/wiki") + (synopsis "SoapySDR HackRF module") + (description + "This package provides HackRF devices support to the SoapySDR library.") + (license license:expat))) + (define-public chirp (package (name "chirp") -- cgit 1.4.1 From ee586c9437b59093603804e88410f1365c12d3b7 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Sat, 5 Jun 2021 23:19:04 +0200 Subject: gnu: Add soapyrtlsdr. * gnu/packages/radio.scm (soapyrtlsdr): New variable. --- gnu/packages/radio.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 18545bae79..0bc335df95 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -312,6 +312,31 @@ defined radio hardware devices with a common API.") "This package provides HackRF devices support to the SoapySDR library.") (license license:expat))) +(define-public soapyrtlsdr + (package + (name "soapyrtlsdr") + (version "0.3.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pothosware/SoapyRTLSDR") + (commit (string-append "soapy-rtl-sdr-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1dlnryj6k20pk7w7v4v13y099r7ikhvlzbgzgphmi5cxkdv0shrd")))) + (build-system cmake-build-system) + (inputs + `(("rtl-sdr" ,rtl-sdr) + ("soapysdr" ,soapysdr))) + (arguments + `(#:tests? #f)) ; No test suite + (home-page "https://github.com/pothosware/SoapyRTLSDR/wiki") + (synopsis "SoapySDR RTL-SDR module") + (description + "This package provides RTL-SDR devices support to the SoapySDR library.") + (license license:expat))) + (define-public chirp (package (name "chirp") -- cgit 1.4.1 From 0855fd3de526c4b8e5c3fd523ee51279be8d391b Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Sat, 5 Jun 2021 23:25:22 +0200 Subject: gnu: Add soapyairspyhf. * gnu/packages/radio.scm (soapyairspyhf): New variable. --- gnu/packages/radio.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 0bc335df95..60c0a2eee8 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -287,6 +287,31 @@ with this package. E.g.: @code{(udev-rules-service 'airspyhf airspyhf)}") defined radio hardware devices with a common API.") (license license:boost1.0))) +(define-public soapyairspyhf + (package + (name "soapyairspyhf") + (version "0.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pothosware/SoapyAirspyHF") + (commit (string-append "soapy-airspyhf-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "04krqinglgkjvx7klqik6yn8rb4mlpwzb6zvnmvm7szqci2agggz")))) + (build-system cmake-build-system) + (inputs + `(("airspyhf" ,airspyhf) + ("soapysdr" ,soapysdr))) + (arguments + `(#:tests? #f)) ; No test suite + (home-page "https://github.com/pothosware/SoapyAirspyHF/wiki") + (synopsis "SoapySDR Airspy HF+ module") + (description "This package provides Airspy HF+ devices support to the +SoapySDR library.") + (license license:expat))) + (define-public soapyhackrf (package (name "soapyhackrf") -- cgit 1.4.1 From 7a5d3976a2f4755f409e74eb1ddc92c32985ac9f Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Sat, 5 Jun 2021 23:36:22 +0200 Subject: gnu: welle-io: Add SoapySDR support. * gnu/packages/radio.scm (welle-io)[inputs]: Add soapysdr. [arguments]: Update 'configure-flags'. --- gnu/packages/radio.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 60c0a2eee8..1d7f9aa139 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -1704,9 +1704,11 @@ receiver.") ("qtdeclarative" ,qtdeclarative) ("qtgraphicaleffects" ,qtgraphicaleffects) ("qtmultimedia" ,qtmultimedia) - ("qtquickcontrols2" ,qtquickcontrols2))) + ("qtquickcontrols2" ,qtquickcontrols2) + ("soapysdr" ,soapysdr))) (arguments - `(#:configure-flags '("-DRTLSDR=ON") + `(#:configure-flags '("-DRTLSDR=ON" + "-DSOAPYSDR=ON") #:tests? #f)) (home-page "https://www.welle.io/") (synopsis "DAB and DAB+ software radio") -- cgit 1.4.1 From 60cd50af435093f0bd01b8eccf6a3ac80ebde4fa Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Sat, 5 Jun 2021 23:46:28 +0200 Subject: gnu: rtl-433: Add SoapySDR support. * gnu/packages/radio.scm (rtl-433)[inputs]: Add soapysdr. --- gnu/packages/radio.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 1d7f9aa139..67b03e9d96 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -1297,7 +1297,8 @@ their position, altitude, speed, etc.") (inputs `(("libusb" ,libusb) ("openssl" ,openssl) - ("rtl-sdr" ,rtl-sdr))) + ("rtl-sdr" ,rtl-sdr) + ("soapysdr" ,soapysdr))) (synopsis "Decoder for radio transmissions in ISM bands") (description "This is a generic data receiver, mainly for decoding radio transmissions -- cgit 1.4.1 From 9caf7112ee50af26fbc4c1bd3c337f1f86b710af Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Sun, 6 Jun 2021 00:14:21 +0200 Subject: gnu: gr-osmosdr: Add SoapySDR support. * gnu/packages/radio.scm (gr-osmosdr)[inputs]: Add soapysdr. --- gnu/packages/radio.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 67b03e9d96..a7e9de3707 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -653,6 +653,7 @@ environment.") ("python-numpy" ,python-numpy) ("python-pyqt" ,python-pyqt) ("rtl-sdr" ,rtl-sdr) + ("soapysdr" ,soapysdr) ("volk" ,volk))) (arguments `(#:modules ((guix build cmake-build-system) -- cgit 1.4.1 From 78469645fd26036c0742abf56d59768b49dc65c4 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Sun, 6 Jun 2021 02:06:49 +0200 Subject: gnu: Add python-sparse. * gnu/packages/python-xyz.scm(python-sparse): New variable. --- gnu/packages/python-xyz.scm | 47 ++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 46 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b63c2852d5..a4fe31a01f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -67,7 +67,7 @@ ;;; Copyright © 2019, 2020 Giacomo Leidi ;;; Copyright © 2019 Wiktor Żelazny ;;; Copyright © 2019, 2020 Tanguy Le Carrour -;;; Copyright © 2019 Mădălin Ionel Patrașcu +;;; Copyright © 2019, 2021 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Riku Viitanen ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2020 sirgazil @@ -5147,6 +5147,51 @@ objects.") (define-public python2-colormath (package-with-python2 python-colormath)) +(define-public python-sparse + (package + (name "python-sparse") + (version "0.12.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "sparse" version)) + (sha256 + (base32 + "05lmzckv69cvxavhdr36k803bgr5dl04cppglid1l880xswc759c")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "pytest" "-v"))))))) + (propagated-inputs + `(("python-numba" ,python-numba) + ("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy))) + (native-inputs + `(("python-dask" ,python-dask) + ("python-pytest" ,python-pytest) + ("python-pytest-black" ,python-pytest-black) + ("python-pytest-cov" ,python-pytest-cov))) + (home-page "https://github.com/pydata/sparse/") + (synopsis "Library for multi-dimensional sparse arrays") + (description + "This package implements sparse arrays of arbitrary dimension on top of +@code{numpy} and @code{scipy.sparse}. Sparse array is a matrix in which most +of the elements are zero. @code{python-sparse} generalizes the +@code{scipy.sparse.coo_matrix} and @code{scipy.sparse.dok_matrix} layouts, but +extends beyond just rows and columns to an arbitrary number of dimensions. +Additionally, this project maintains compatibility with the +@code{numpy.ndarray} interface rather than the @code{numpy.matrix} interface +used in @code{scipy.sparse}. These differences make this project useful in +certain situations where @code{scipy.sparse} matrices are not well suited, but +it should not be considered a full replacement. It lacks layouts that are not +easily generalized like @dfn{compressed sparse row/column}(CSR/CSC) and +depends on @code{scipy.sparse} for some computations.") + (license license:bsd-3))) + (define-public python-spectra (package (name "python-spectra") -- cgit 1.4.1 From d1e7b50dbf58c59c100f1bf5a7ea735daa3a203f Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Sun, 6 Jun 2021 02:06:51 +0200 Subject: gnu: python-cooler: Update to 0.8.11. * gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.11. [arguments]: Add build phase "patch-tests"; replace "check" phase. [native-inputs]: Add python-codecov, python-pytest-cov, and python-pytest-flake8. [propagated-inputs]: Add python-six and python-sparse. --- gnu/packages/bioinformatics.scm | 42 +++++++++++++++++++++++++++++++++++------ 1 file changed, 36 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dab097381a..2de8a59d3c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11717,15 +11717,39 @@ fasta subsequences.") (define-public python-cooler (package (name "python-cooler") - (version "0.8.7") + (version "0.8.11") (source (origin (method url-fetch) (uri (pypi-uri "cooler" version)) (sha256 (base32 - "01g6gqix9ba27sappz6nfyiwabzrlf8i5fn8kwcz8ra356cq9crp")))) + "1i96fmpsimj4wrx51rxn8lw2gqxf5a2pvrj5rwdd6ivnm3pmhyrn")))) (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-tests + (lambda _ + (substitute* "tests/test_create.py" + (("def test_roundtrip") + (string-append "@pytest.mark.skip(reason=\"requires network " + "access to genome.ucsc.edu\")\n" + "def test_roundtrip"))) + (substitute* "tests/test_util.py" + (("def test_fetch_chromsizes") + (string-append "@pytest.mark.skip(reason=\"requires network " + "access to genome.ucsc.edu\")\n" + "def test_fetch_chromsizes"))) + ;; This test depends on ipytree, which contains a lot of minified + ;; JavaScript. + (substitute* "tests/test_fileops.py" + (("def test_print_trees") + "def _test_print_trees")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "pytest" "-v"))))))) (propagated-inputs `(("python-asciitree" ,python-asciitree) ("python-biopython" ,python-biopython) @@ -11741,11 +11765,17 @@ fasta subsequences.") ("python-pysam" ,python-pysam) ("python-pyyaml" ,python-pyyaml) ("python-scipy" ,python-scipy) - ("python-simplejson" ,python-simplejson))) + ("python-simplejson" ,python-simplejson) + ("python-six" ,python-six) + ("python-sparse" ,python-sparse))) (native-inputs - `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest))) - (home-page "https://github.com/mirnylab/cooler") + `(("python-codecov" ,python-codecov) + ("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-flake8" ,python-pytest-flake8))) + ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella + (home-page "https://github.com/open2c/cooler") (synopsis "Sparse binary format for genomic interaction matrices") (description "Cooler is a support library for a sparse, compressed, binary persistent -- cgit 1.4.1 From 3a9923d4b84c6330bf54defb4eb25cc13c2c2df7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Wed, 2 Jun 2021 16:19:39 -0400 Subject: gnu: rust-v-frame-0.2: Update to 0.2.1. * gnu/packages/crates-io.scm (rust-v-frame-0.2): Update to 0.2.1. [synopsis]: Fix capitalization lint warning. [description]: Re-indent. --- gnu/packages/crates-io.scm | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index cc5dbc4252..81c564f2d8 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -48085,14 +48085,14 @@ first byte.") (define-public rust-v-frame-0.2 (package (name "rust-v-frame") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (crate-uri "v_frame" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0xqf7dynsc6fm94jz3hknwi2n4ch1j7wrs0dd333r1ldniw49rf3")))) + (base32 "0ia1j0j1v5zp9bp91imbnbxnv937x3xfpc06nyj96yjfk8zbmxhp")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t @@ -48104,10 +48104,9 @@ first byte.") ("rust-serde" ,rust-serde-1) ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2)))) (home-page "https://github.com/xiph/rav1e") - (synopsis "@code{Video Frame} data structures, part of rav1e") - (description - "This package provides @code{Video Frame} data structures, as a part of -rav1e.") + (synopsis "Video Frame data structures, part of rav1e") + (description "This package provides @code{Video Frame} data structures, as +a part of rav1e.") (license license:bsd-2))) (define-public rust-value-bag-1 -- cgit 1.4.1 From be59ed491a78021fb1e7fdab32033c9b547a3b77 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 14:10:05 -0400 Subject: gnu: Add rust-rustfix-0.5. * gnu/packages/crates-io.scm (rust-rustfix-0.5): New variable. (rust-rustfix-0.4): Inherit from the above. --- gnu/packages/crates-io.scm | 31 ++++++++++++++++++++++++++----- 1 file changed, 26 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 81c564f2d8..d706c9b9cd 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -16,6 +16,7 @@ ;;; Copyright © 2021 Zheng Junjie <873216071@qq.com> ;;; Copyright © 2021 Alexandru-Sergiu Marton ;;; Copyright © 2021 Antero Mejr +;;; Copyright © 2021 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -64,7 +65,8 @@ #:use-module (gnu packages version-control) #:use-module (gnu packages web) #:use-module (gnu packages xml) - #:use-module (gnu packages xorg)) + #:use-module (gnu packages xorg) + #:use-module (srfi srfi-1)) ;;; ;;; Please: Try to add new module packages in alphabetic order. @@ -35445,10 +35447,10 @@ rustc compiler.") "This package provides a tool to manipulate rustdoc comments.") (license license:asl2.0))) -(define-public rust-rustfix-0.4 +(define-public rust-rustfix-0.5 (package (name "rust-rustfix") - (version "0.4.6") + (version "0.5.1") (source (origin (method url-fetch) @@ -35457,12 +35459,12 @@ rustc compiler.") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "01zn0ysnass3mmrhxk90584y713vjfq1x97mi4saac99g9vsql3i")))) + "0kkhfab60747zpmn8jwfdwl9a2s4rqiq7yjjfs7yppfwp9s0pigj")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t #:cargo-inputs - (("rust-failure" ,rust-failure-0.1) + (("rust-anyhow" ,rust-anyhow-1) ("rust-log" ,rust-log-0.4) ("rust-serde" ,rust-serde-1) ("rust-serde-json" ,rust-serde-json-1)) @@ -35479,6 +35481,25 @@ rustc compiler.") "Automatically apply the suggestions made by rustc.") (license (list license:expat license:asl2.0)))) +(define-public rust-rustfix-0.4 + (package/inherit rust-rustfix-0.5 + (name "rust-rustfix") + (version "0.4.6") + (source + (origin + (method url-fetch) + (uri (crate-uri "rustfix" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "01zn0ysnass3mmrhxk90584y713vjfq1x97mi4saac99g9vsql3i")))) + (arguments + (substitute-keyword-arguments (package-arguments rust-rustfix-0.5) + ((#:cargo-inputs cargo-inputs) + `(("rust-failure" ,rust-failure-0.1) + ,@(alist-delete "rust-anyhow" cargo-inputs))))))) + (define-public rust-rustls-0.19 (package (name "rust-rustls") -- cgit 1.4.1 From 7ea0a2ec970e7cad88f42b7060025dc50eb19dfd Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 14:29:23 -0400 Subject: gnu: Add rust-serde-ignored-0.1. * gnu/packages/crates-io.scm (rust-serde-ignored-0.1): New variable. --- gnu/packages/crates-io.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index d706c9b9cd..4ba032cae6 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -37761,6 +37761,33 @@ TOML/JSON/MessagePack strings and serializable values.") ("rust-serde-codegen-internals" ,rust-serde-codegen-internals-0.14) ("rust-syn" ,rust-syn-0.11)))))) +(define-public rust-serde-ignored-0.1 + (package + (name "rust-serde-ignored") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "serde_ignored" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0bzz3546g3p01hgwh6jh0gyqdwc28xcp3pir4al2wbsgs4wpsb0w")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-serde" ,rust-serde-1)) + #:cargo-development-inputs + (("rust-serde-derive" ,rust-serde-derive-1) + ("rust-serde-json" ,rust-serde-json-1)))) + (home-page "https://github.com/dtolnay/serde-ignored") + (synopsis "Find ignored keys when deserializing data") + (description "Find out about keys that are ignored when deserializing +data. This crate provides a wrapper that works with any existing Serde +@code{Deserializer} and invokes a callback on every ignored field.") + (license (list license:expat license:asl2.0)))) + (define-public rust-serde-json-1 (package (name "rust-serde-json") -- cgit 1.4.1 From 1c47e771a5dc9a2b1ce274ea442e317b5018bc1e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 14:37:22 -0400 Subject: gnu: Add rust-rustc-workspace-hack-1. * gnu/packages/crates-io.scm (rust-rustc-workspace-hack-1): New variable. --- gnu/packages/crates-io.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 4ba032cae6..31852669d3 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -50950,6 +50950,26 @@ configuration file and/or environment variables.") "High performance inflection transformation library for changing properties of words like the case.") (license license:expat))) +(define-public rust-rustc-workspace-hack-1 + (package + (name "rust-rustc-workspace-hack") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "rustc-workspace-hack" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1yx8l58n2vb2ldpi3z1jn4dmi5hnxvikbhpd5lilpdvkl7xd4wgw")))) + (build-system cargo-build-system) + (home-page "https://crates.io/crates/rustc-workspace-hack") + (synopsis "Hack for the compiler's own build system") + (description "Hack for the compiler's own build system. It is used by +@code{cargo}.") + (license (list license:expat license:asl2.0)))) + (define-public skim (package (name "skim") -- cgit 1.4.1 From 41e6f47071b61887f927ce83a00332be5e82bf6a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 14:39:30 -0400 Subject: gnu: Add rust-opener-0.4. * gnu/packages/crates-io.scm (rust-opener-0.4): New variable. --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 31852669d3..d5ce804cd2 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -27328,6 +27328,29 @@ contents.") the system.") (license license:expat))) +(define-public rust-opener-0.4 + (package + (name "rust-opener") + (version "0.4.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "opener" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1bpknqvhqkalhmq8n2m97apc0r3y194ppybl1qxay34xr83p848k")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-winapi" ,rust-winapi-0.3)))) + (home-page "https://github.com/Seeker14491/opener") + (synopsis "Open a file or link using the system default program") + (description "This crate provides the ability to open a file or link with +the default program configured on the system.") + (license (list license:expat license:asl2.0)))) + (define-public rust-openssl-0.10 (package (name "rust-openssl") -- cgit 1.4.1 From e6c5d0847996c170638008ba1dd42f20654245d1 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 16:21:57 -0400 Subject: gnu: Add rust-derive-arbitrary-1. * gnu/packages/crates-io.scm (rust-derive-arbitrary-1): New variable. (rust-derive-arbitrary-0.4): Inherit from the above. --- gnu/packages/crates-io.scm | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index d5ce804cd2..83353f311c 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -11282,17 +11282,17 @@ algorithm which serves to quantify the difference between two colors.") Rust.") (license (list license:expat license:asl2.0)))) -(define-public rust-derive-arbitrary-0.4 +(define-public rust-derive-arbitrary-1 (package (name "rust-derive-arbitrary") - (version "0.4.7") + (version "1.0.1") (source (origin (method url-fetch) (uri (crate-uri "derive_arbitrary" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1rp0z4k0j5ip0bx6dssg97l4q6bakhf6lm5h1lpr3p3kwjsi585i")))) + (base32 "0nig0iydva7a9h9i9qyi6an9w5qjafmn3qlzvdqqiw0x2kp824jz")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t @@ -11307,6 +11307,18 @@ Rust.") Instead, enable the @code{derive} feature of the @code{arbitrary} crate.") (license (list license:expat license:asl2.0)))) +(define-public rust-derive-arbitrary-0.4 + (package/inherit rust-derive-arbitrary-1 + (name "rust-derive-arbitrary") + (version "0.4.7") + (source + (origin + (method url-fetch) + (uri (crate-uri "derive_arbitrary" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1rp0z4k0j5ip0bx6dssg97l4q6bakhf6lm5h1lpr3p3kwjsi585i")))))) + (define-public rust-derive-builder-0.9 (package (name "rust-derive-builder") -- cgit 1.4.1 From 6661e83a2344920a028119fc5bde1720ed1a7ae6 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 16:23:42 -0400 Subject: gnu: Add rust-arbitrary-1. * gnu/packages/crates-io.scm (rust-arbitrary-1): New variable. (rust-arbitrary-0.4): Inherit from rust-arbitrary-1. --- gnu/packages/crates-io.scm | 26 +++++++++++++++++++++----- 1 file changed, 21 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 83353f311c..d0f09c697b 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -1932,23 +1932,23 @@ on every platform.") "153awzwywmb61xg857b80l63b1x6hifx2pha7lxf6fck9qxwraq8")))) (arguments '()))) -(define-public rust-arbitrary-0.4 +(define-public rust-arbitrary-1 (package (name "rust-arbitrary") - (version "0.4.7") + (version "1.0.1") (source (origin (method url-fetch) (uri (crate-uri "arbitrary" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0sa55cynafwzvlhyhfpm3vmi2fydj3ipdj5yfbaif7l56cixfmfv")))) + (base32 "14a6r7q9b1kf1m7810p8bcl51q11mrwc5z7fjkz0lx6kdvyk0x13")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t #:cargo-inputs - (("rust-derive-arbitrary" ,rust-derive-arbitrary-0.4)))) - (home-page "https://github.com/nagisa/rust_arbitrary") + (("rust-derive-arbitrary" ,rust-derive-arbitrary-1)))) + (home-page "https://github.com/rust-fuzz/arbitrary") (synopsis "Trait for generating structured data from unstructured data") (description "The @code{Arbitrary} crate lets you construct arbitrary instance of @@ -1961,6 +1961,22 @@ values. This allows you to combine structure-aware test case generation with coverage-guided, mutation-based fuzzers.") (license (list license:expat license:asl2.0)))) +(define-public rust-arbitrary-0.4 + (package/inherit rust-arbitrary-1 + (name "rust-arbitrary") + (version "0.4.7") + (source + (origin + (method url-fetch) + (uri (crate-uri "arbitrary" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0sa55cynafwzvlhyhfpm3vmi2fydj3ipdj5yfbaif7l56cixfmfv")))) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-derive-arbitrary" ,rust-derive-arbitrary-0.4)))))) + (define-public rust-arbitrary-0.2 (package (inherit rust-arbitrary-0.4) -- cgit 1.4.1 From 014d0ee878d050cd5734853b05bb5cfa175ea95c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 16:24:44 -0400 Subject: gnu: rust-jobserver-0.1: Update to 0.1.22. * gnu/packages/crates-io.scm (rust-jobserver-0.1): Update to 0.1.22. --- gnu/packages/crates-io.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index d0f09c697b..cb2e1f5215 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -20932,7 +20932,7 @@ the jni-bindgen code generator for binding to JVM APIs from Rust.") (define-public rust-jobserver-0.1 (package (name "rust-jobserver") - (version "0.1.19") + (version "0.1.22") (source (origin (method url-fetch) @@ -20941,7 +20941,7 @@ the jni-bindgen code generator for binding to JVM APIs from Rust.") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1q2w80v8p2pbfm8ayhjs6zi11a1hp4535z4ck8kg872z8ldnrc37")))) + "1zg7p4khibisbvd8b1lqvvni6lr00g49d4bq2zj6m76bs7jmlbwp")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs -- cgit 1.4.1 From b36299c7f426d8337770bb8d833e33f6016eaa50 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 16:24:52 -0400 Subject: gnu: Add rust-array-ops-0.1. * gnu/packages/crates-io.scm (rust-array-ops-0.1): New variable. --- gnu/packages/crates-io.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index cb2e1f5215..1922c40419 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -2136,6 +2136,31 @@ coverage-guided, mutation-based fuzzers.") that runs on Argon2.") (license license:expat))) +(define-public rust-array-ops-0.1 + (package + (name "rust-array-ops") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "array-ops" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1jn7l9gppp6kr9kgsy22sw5p9cn1jazmqxy296gjwiwz5d11i4fc")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-rand-core" ,rust-rand-core-0.5) + ("rust-rand-xoshiro" ,rust-rand-xoshiro-0.4)))) + (home-page "https://github.com/bodil/array-ops") + (synopsis "Automatic method implementations for array data types") + (description "This package provides a number of traits with default +implementations for most of the standard library's methods on array like data +structures.") + (license license:mpl2.0))) + (define-public rust-arrayref-0.3 (package (name "rust-arrayref") -- cgit 1.4.1 From 94b41147c22d3a1ec41f3629c2c3ca6a3a66942b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 16:33:19 -0400 Subject: gnu: Add rust-bitmaps-2. * gnu/packages/crates-io.scm (rust-bitmaps-2): New variable. --- gnu/packages/crates-io.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 1922c40419..cdf3b1ef92 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -4864,6 +4864,32 @@ behave like a set of bitflags.") (build-system cargo-build-system) (arguments `(#:skip-build? #t)))) +(define-public rust-bitmaps-2 + (package + (name "rust-bitmaps") + (version "2.1.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "bitmaps" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "18k4mcwxl96yvii5kcljkpb8pg5j4jj1zbsdn26nsx4r83846403")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-typenum" ,rust-typenum-1)) + #:cargo-development-inputs + (("rust-proptest", rust-proptest-0.9) + ("rust-proptest-derive", rust-proptest-derive-0.1)))) + (home-page "https://github.com/bodil/bitmaps") + (synopsis "Fixed size compact boolean array in Rust") + (description "This crate provides a convenient and efficient way of +declaring and working with fixed size bitmaps in Rust.") + (license license:mpl2.0))) + (define-public rust-bitstream-io-1 (package (name "rust-bitstream-io") -- cgit 1.4.1 From 269e63865c222aeac941325fe8ab55a6fbc1436f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 16:38:39 -0400 Subject: gnu: Add rust-refpool-0.4. * gnu/packages/crates-io.scm (rust-refpool-0.4): New variable. --- gnu/packages/crates-io.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index cdf3b1ef92..e5839cf870 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -33155,6 +33155,30 @@ functionality.") (base32 "0av43xxjlinfqklb67rpj217cmaxfjsf8151gs0hbs4hnr5664ck")))))) +(define-public rust-refpool-0.4 + (package + (name "rust-refpool") + (version "0.4.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "refpool" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0n6b1qpq0fcyzm3nrmiw0z9x4nawy9dklqfr3mb8rp571yw8d7in")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-development-inputs + (("rust-criterion" ,rust-criterion-0.3)))) + (home-page "https://github.com/bodil/refpool") + (synopsis "Efficient memory pool with reference counting") + (description "@code{refpool} is a re-implementation of Rust's +@code{std::boxed::Box} and @code{std::rc::Rc} which uses a pool of reusable +memory to speed up reallocation.") + (license license:mpl2.0))) + (define-public rust-regex-1 (package (name "rust-regex") -- cgit 1.4.1 From 2394bd78facb8fc66ebcf99fd5af072a636c31c0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 16:46:24 -0400 Subject: gnu: Add rust-sized-chunks-0.6. * gnu/packages/crates-io.scm (rust-sized-chunks-0.6): New variable. --- gnu/packages/crates-io.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index e5839cf870..5ba7c5257d 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -57,6 +57,7 @@ #:use-module (gnu packages pcre) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages rust) #:use-module (gnu packages rust-apps) #:use-module (gnu packages serialization) #:use-module (gnu packages sqlite) @@ -39478,6 +39479,34 @@ variants in pure Rust.") (description "This package allows for easier formatting of sizes.") (license (list license:expat license:asl2.0)))) +(define-public rust-sized-chunks-0.6 + (package + (name "rust-sized-chunks") + (version "0.6.5") + (source + (origin + (method url-fetch) + (uri (crate-uri "sized-chunks" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "07ix5fsdnpf2xsb0k5rbiwlmsicm2237fcx7blirp9p7pljr5mhn")))) + (build-system cargo-build-system) + (arguments + `(#:rust ,rust-1.52 ;requires the "if in const fn" feature + #:cargo-inputs + (("rust-arbitrary" ,rust-arbitrary-1) + ("rust-array-ops" ,rust-array-ops-0.1) + ("rust-bitmaps" ,rust-bitmaps-2) + ("rust-refpool" ,rust-refpool-0.4) + ("rust-typenum" ,rust-typenum-1)))) + (home-page "https://github.com/bodil/sized-chunks") + (synopsis "Efficient sized chunk datatypes") + (description "This package provides various fixed length array data types, +designed for @code{immutable.rs}.") + (license license:mpl2.0))) + (define-public rust-skeptic-0.9 (package (name "rust-skeptic") -- cgit 1.4.1 From 3de4953eacafe88286bdcc87db8ccd8f97904a07 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 4 Jun 2021 23:40:12 -0400 Subject: gnu: rust-digest-0.8: Fix the version of its rust-generic-array input. * gnu/packages/crates-io.scm (rust-digest-0.8) [cargo-inputs]: Adjust the version of the rust-generic-array to 0.12. --- gnu/packages/crates-io.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 5ba7c5257d..24a220ab4e 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -11965,7 +11965,7 @@ diff.") `(#:skip-build? #t #:cargo-inputs (("rust-blobby" ,rust-blobby-0.1) - ("rust-generic-array" ,rust-generic-array-0.13)))))) + ("rust-generic-array" ,rust-generic-array-0.12)))))) (define-public rust-digest-0.7 (package -- cgit 1.4.1 From 3cc41bcadea2450e6fd4cc2d7fa3a7f8bdad7e64 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 4 Jun 2021 23:41:33 -0400 Subject: gnu: Add rust-twox-hash-1. * gnu/packages/crates-io.scm (rust-twox-hash-1): New variable. --- gnu/packages/crates-io.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 24a220ab4e..69036c5b7d 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -23983,6 +23983,36 @@ based on Rustls and Ring.") (("rust-sema" ,rust-sema-0.1) ("rust-winit" ,rust-winit-0.19)))))) ; 0.17? +(define-public rust-twox-hash-1 + (package + (name "rust-twox-hash") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "twox-hash" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0ndb4pil758kn0av83jjgq8kkfkwc5lhi5ii7fk5yw96h1wapy04")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cfg-if" ,rust-cfg-if-0.1) + ("rust-digest" ,rust-digest-0.8) + ("rust-digest" ,rust-digest-0.9) + ("rust-rand" ,rust-rand-0.7) + ("rust-serde" ,rust-serde-1) + ("rust-static-assertions" ,rust-static-assertions-1)) + #:cargo-development-inputs + (("rust-serde-json" ,rust-serde-json-1)))) + (home-page "https://github.com/shepmaster/twox-hash") + (synopsis "Rust implementation of the XXHash and XXH3 algorithms") + (description "This package provides a Rust implementation of the XXHash +and XXH3 algorithms.") + (license license:expat))) + (define-public rust-meval-0.2 (package (name "rust-meval") -- cgit 1.4.1 From a38cb9c70ef13dfc2a616805bb5b8dc6196b8e8b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 4 Jun 2021 23:43:40 -0400 Subject: gnu: Add rust-metrohash-1. * gnu/packages/crates-io.scm (rust-metrohash-1): New variable. --- gnu/packages/crates-io.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 69036c5b7d..92f8c25bfb 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -24013,6 +24013,31 @@ based on Rustls and Ring.") and XXH3 algorithms.") (license license:expat))) +(define-public rust-metrohash-1 + (package + (name "rust-metrohash") + (version "1.0.6") + (source + (origin + (method url-fetch) + (uri (crate-uri "metrohash" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0v2hn33ypx79naimfcz58pz46qhj2prawvx1p9abrb72375m799v")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-development-inputs + (("rust-fnv" ,rust-fnv-1) + ("rust-twox-hash" ,rust-twox-hash-1)))) + (home-page + "https://github.com/arthurprs/metrohash-rs") + (synopsis "Rust implementation of the MetroHash hash algorithm") + (description "This library is a Rust implementation of MetroHash, a high +quality, high performance hash algorithm.") + (license license:expat))) + (define-public rust-meval-0.2 (package (name "rust-meval") -- cgit 1.4.1 From 93f2fde4c5ba3339435981446f04d921add99c78 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 16:54:13 -0400 Subject: gnu: Add rust-im-rc-15. * gnu/packages/crates-io.scm (rust-im-rc-15): New variable. --- gnu/packages/crates-io.scm | 46 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 92f8c25bfb..b21c3383d0 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -51139,6 +51139,52 @@ configuration file and/or environment variables.") (description "This package provides a Rust XML XPath library.") (license (list license:expat license:asl2.0)))) +(define-public rust-im-rc-15 + (package + (name "rust-im-rc") + (version "15.0.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "im-rc" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0gsgcs1nn38r40973l6zr1v4d85f4s9qyl32n5f20jphf5z9ba1w")))) + (build-system cargo-build-system) + (arguments + `(#:rust ,rust-1.52 ;for rust-sized-chunks + #:cargo-inputs + (("rust-arbitrary" ,rust-arbitrary-0.4) + ("rust-bitmaps" ,rust-bitmaps-2) + ("rust-proptest" ,rust-proptest-0.9) + ("rust-quickcheck" ,rust-quickcheck-0.9) + ("rust-rand-core" ,rust-rand-core-0.5) + ("rust-rand-xoshiro" ,rust-rand-xoshiro-0.4) + ("rust-rayon" ,rust-rayon-1) + ("rust-refpool" ,rust-refpool-0.4) + ("rust-serde" ,rust-serde-1) + ("rust-sized-chunks" ,rust-sized-chunks-0.6) + ("rust-typenum" ,rust-typenum-1) + ("rust-version-check" ,rust-version-check-0.9)) + #:cargo-development-inputs + (("rust-metrohash" ,rust-metrohash-1) + ("rust-pretty-assertions" ,rust-pretty-assertions-0.6) + ("rust-proptest" ,rust-proptest-0.9) + ("rust-proptest-derive" ,rust-proptest-derive-0.1) + ("rust-rand" ,rust-rand-0.7) + ("rust-rayon" ,rust-rayon-1) + ("rust-serde" ,rust-serde-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-version-check" ,rust-version-check-0.9)))) + (home-page "https://docs.rs/crate/im") + (synopsis "Fast immutable collection datatypes for Rust") + (description "@code{im-rc} provides immutable collection datatypes for +Rust that are very fast but not thread-safe. A thread-safe (and slower) +variant of this library is available separately as @code{im}.") + (license license:mpl2.0))) + (define-public rust-inflections-1 (package (name "rust-inflections") -- cgit 1.4.1 From b96fd1a4a2382544c1e8d9646021a024bb1c161d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 16:59:14 -0400 Subject: gnu: Add rust-home-0.5. * gnu/packages/crates-io.scm (rust-home-0.5): New variable. --- gnu/packages/crates-io.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index b21c3383d0..a90c6b6a58 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -17665,6 +17665,30 @@ of gzip files based on the gzip header implementation in the @code{flate2} crate IEEE 754-2008 binary16 type.") (license (list license:expat license:asl2.0)))) +(define-public rust-home-0.5 + (package + (name "rust-home") + (version "0.5.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "home" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0m3nfcksrj784liji1c5j47dymxw2l7hqy5fj90piadnwvrawmi4")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-winapi" ,rust-winapi-0.3)))) + (home-page "https://github.com/brson/home") + (synopsis "Shared definitions of home directories") + (description "This packages provides the definition of @code{home_dir} +used by @command{cargo} and @command{rustup}, as well as functions to find the +correct value of @samp{CARGO_HOME} and @samp{RUSTUP_HOME}.") + (license (list license:expat license:asl2.0)))) + (define-public rust-bat-0.17 (package (name "rust-bat") -- cgit 1.4.1 From bb162c120a231fed9a282a85d30280faf54112cc Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 17:12:22 -0400 Subject: gnu: Add rust-git2-curl-0.14. * gnu/packages/crates-io.scm (rust-git2-curl-0.14): New variable. --- gnu/packages/crates-io.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index a90c6b6a58..f22c842991 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -16983,6 +16983,33 @@ reading and writing git repositories.") ("rust-thread-id" ,rust-thread-id-3) ("rust-time" ,rust-time-0.1)))))) +(define-public rust-git2-curl-0.14 + (package + (name "rust-git2-curl") + (version "0.14.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "git2-curl" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0l1sckmpvhd498c9ji04gkpfkfrpx7c8rabihczsnjx91v5kjdc8")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t ;need rust-civet and others + #:cargo-inputs + (("rust-curl" ,rust-curl-0.4) + ("rust-git2" ,rust-git2-0.13) + ("rust-log" ,rust-log-0.4) + ("rust-url" ,rust-url-2)))) + (home-page "https://github.com/rust-lang/git2-rs") + (synopsis "Libgit2 HTTP transport backend powered by @code{libcurl}") + (description "Backend for an HTTP transport in @code{libgit2}, powered by +libcurl, which is intended to be used with the @code{git2} crate.") + (license (list license:expat license:asl2.0)))) + (define-public rust-gjson-0.7 (package (name "rust-gjson") -- cgit 1.4.1 From b0c53f5c28690fa9596e431ddb688fa62e6d6467 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 17:17:24 -0400 Subject: gnu: rust-libgit2-sys-0.12: Update to 0.12.21+1.1.0. * gnu/packages/crates-io.scm (rust-libgit2-sys-0.12): Update to 0.12.21+1.1.0. --- gnu/packages/crates-io.scm | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index f22c842991..fe6635882a 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -21845,17 +21845,16 @@ algorithm and related formats (ZLIB, GZIP).") (define-public rust-libgit2-sys-0.12 (package (name "rust-libgit2-sys") - (version "0.12.17+1.1.0") + (version "0.12.21+1.1.0") (source (origin (method url-fetch) (uri (crate-uri "libgit2-sys" version)) - (file-name (string-append name "-" version ".tar.gz")) + (file-name + (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0hc89v7kp2b3rbc64cxq024shd85m8vqcs14i3gjclblr9jxzszl")) - (modules '((guix build utils))) - (snippet - '(begin (delete-file-recursively "libgit2") #t)))) + (base32 + "09b85x3gpvq0d7v1mhg4f3w1b3skzlpbikrx9j2rwarbsyn1n9w6")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs -- cgit 1.4.1 From 8550b417449c12589121c532b9ad88d5f646d186 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 4 Jun 2021 07:56:20 -0400 Subject: gnu: rust-libgit2-sys-0.7: Remove unused package. * gnu/packages/crates-io.scm (rust-libgit2-sys-0.7): Delete variable. --- gnu/packages/crates-io.scm | 26 -------------------------- 1 file changed, 26 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index fe6635882a..ae20743e9f 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -21920,32 +21920,6 @@ library.") (snippet '(begin (delete-file-recursively "libgit2") #t)))))) -(define-public rust-libgit2-sys-0.7 - (package - (inherit rust-libgit2-sys-0.8) - (name "rust-libgit2-sys") - (version "0.7.11") - (source - (origin - (method url-fetch) - (uri (crate-uri "libgit2-sys" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1wcvg2qqra2aviasvqcscl8gb2rnjnd6h998wy5dlmf2bnriqi28")) - (modules '((guix build utils))) - (snippet - '(begin (delete-file-recursively "libgit2") #t)))) - (arguments - `(#:cargo-inputs - (("rust-curl-sys" ,rust-curl-sys-0.4) - ("rust-libc" ,rust-libc-0.2) - ("rust-libssh2-sys" ,rust-libssh2-sys-0.2) - ("rust-libz-sys" ,rust-libz-sys-1) - ("rust-openssl-sys" ,rust-openssl-sys-0.9) - ("rust-cc" ,rust-cc-1) - ("rust-pkg-config" ,rust-pkg-config-0.3)))))) - (define-public rust-libloading-0.6 (package (name "rust-libloading") -- cgit 1.4.1 From 0fbaf75b1a39fbbf1dd9b3733376ebb310cde177 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 17:21:40 -0400 Subject: gnu: rust-git2-0.13: Update to 0.13.20. * gnu/packages/crates-io.scm (rust-git2-0.13): Update to 0.13.20. [cargo-development-inputs]{rust-paste}: Update to version 1. --- gnu/packages/crates-io.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index ae20743e9f..dfca6de341 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -16885,14 +16885,16 @@ dirty state into your program.") (define-public rust-git2-0.13 (package (name "rust-git2") - (version "0.13.15") + (version "0.13.20") (source (origin (method url-fetch) (uri (crate-uri "git2" version)) - (file-name (string-append name "-" version ".tar.gz")) + (file-name + (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0na3vsa44nn1sr6pzscn93w69wbmdih277mm2p3f6kcavb4ngwj4")))) + (base32 + "1fkc2gzcnl4ci3rja9mc5jl2ygl3fkc1fgym3rcwby216ac1x0yr")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs @@ -16904,7 +16906,7 @@ dirty state into your program.") ("rust-openssl-sys" ,rust-openssl-sys-0.9) ("rust-url" ,rust-url-2)) #:cargo-development-inputs - (("rust-paste" ,rust-paste-0.1) + (("rust-paste" ,rust-paste-1) ("rust-structopt" ,rust-structopt-0.3) ("rust-time" ,rust-time-0.1)))) (native-inputs -- cgit 1.4.1 From 4acd1213a360fe2a8b012245f18c0ad886e4d97e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 17:30:29 -0400 Subject: gnu: Add rust-fwdansi-1. * gnu/packages/crates-io.scm (rust-fwdansi-1): New variable. --- gnu/packages/crates-io.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index dfca6de341..e6f01e8b93 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -16156,6 +16156,32 @@ futures-rs library.") (description "This package provides a fuzzy matching library in Rust.") (license license:expat))) +(define-public rust-fwdansi-1 + (package + (name "rust-fwdansi") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "fwdansi" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "027jz2x5fbi6rskic8sd6xx0mn03a7dnhwkpyz8hamg8gxwgbh88")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-memchr" ,rust-memchr-2) + ("rust-termcolor" ,rust-termcolor-1)) + #:cargo-development-inputs + (("rust-proptest" ,rust-proptest-0.9)))) + (home-page "https://github.com/kennytm/fwdansi") + (synopsis "ANSI escape codes to termcolor terminal library") + (description "This library can be used to forward a byte string with ANSI +escape codes to a termcolor terminal.") + (license license:expat))) + (define-public rust-fxhash-0.2 (package (name "rust-fxhash") -- cgit 1.4.1 From 2e79f847fdd771067493c25e1d9154df221a28b8 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 17:33:36 -0400 Subject: gnu: rust-filetime-0.2: Update to 0.2.14. * gnu/packages/crates-io.scm (rust-filetime-0.2): Update to 0.2.14. [cargo-inputs]{rust-cargo-if}: Update to version 1. {rust-redox-syscall}: Update to version 0.2. --- gnu/packages/crates-io.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index e6f01e8b93..da8a657fd2 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -14348,7 +14348,7 @@ sparse files.") (define-public rust-filetime-0.2 (package (name "rust-filetime") - (version "0.2.8") + (version "0.2.14") (source (origin (method url-fetch) @@ -14356,14 +14356,14 @@ sparse files.") (file-name (string-append name "-" version ".crate")) (sha256 (base32 - "0zfc90802dbw11bx6kmm8zw6r88k7glm4q6l8riqw35an3dd9xhz")))) + "1s71cb7hzkk4ahc5j53w8933gnxv2giyj7v0za5hbbk37ahwyd0x")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t #:cargo-inputs - (("rust-cfg-if" ,rust-cfg-if-0.1) + (("rust-cfg-if" ,rust-cfg-if-1) ("rust-libc" ,rust-libc-0.2) - ("rust-redox-syscall" ,rust-redox-syscall-0.1) + ("rust-redox-syscall" ,rust-redox-syscall-0.2) ("rust-winapi" ,rust-winapi-0.3)) #:cargo-development-inputs (("rust-tempfile" ,rust-tempfile-3)))) -- cgit 1.4.1 From bc11792923bc42053800a442661def8ed91223da Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 17:43:24 -0400 Subject: gnu: Add rust-crypto-hash-0.3. * gnu/packages/crates-io.scm (rust-crypto-hash-0.3): New variable. --- gnu/packages/crates-io.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index da8a657fd2..d72c2d4d8a 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -10108,6 +10108,34 @@ Code (MAC) algorithms.") algorithms.") (license (list license:expat license:asl2.0)))) +(define-public rust-crypto-hash-0.3 + (package + (name "rust-crypto-hash") + (version "0.3.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "crypto-hash" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1jnxgpk0j29hzcv42viq5dckyfjnxdjsar55366j95zx80i1cxwa")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-commoncrypto" ,rust-commoncrypto-0.2) + ("rust-hex" ,rust-hex-0.3) + ("rust-openssl" ,rust-openssl-0.10) + ("rust-winapi" ,rust-winapi-0.3)))) + (inputs + `(("openssl" ,openssl))) + (home-page "https://github.com/malept/crypto-hash") + (synopsis "Wrapper for OS-level cryptographic hash functions") + (description "This package provides a wrapper for OS-level cryptographic +hash functions.") + (license license:expat))) + (define-public rust-cryptovec-0.4 (package (name "rust-cryptovec") -- cgit 1.4.1 From b5a68bde6a9db8549ebbd6b78acdf49f789ce1d7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 17:43:32 -0400 Subject: gnu: Add rust-crates-io-0.33. * gnu/packages/crates-io.scm (rust-crates-io-0.33): New variable. --- gnu/packages/crates-io.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index d72c2d4d8a..835c89d09c 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -9146,6 +9146,39 @@ to @code{is_x86_feature_detected}.") "Library for retrieving and interacting with the crates.io index.") (license license:asl2.0))) +(define-public rust-crates-io-0.33 + (package + (name "rust-crates-io") + (version "0.33.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "crates-io" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "147mggf85fz77vsrzsvsxxwid4f4fg30zwfyirx7sl1k7y33hw91")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-anyhow" ,rust-anyhow-1) + ("rust-curl" ,rust-curl-0.4) + ("rust-percent-encoding" ,rust-percent-encoding-2) + ("rust-serde" ,rust-serde-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-url" ,rust-url-2)))) + (native-inputs + `(("curl" ,curl) + ("openssl" ,openssl) + ("pkg-config" ,pkg-config) + ("zlib" ,zlib))) + (home-page "https://github.com/rust-lang/cargo") + (synopsis "Helpers for interacting with @url{crates.io}") + (description "This package provides helpers for interacting with +@url{crates.io}.") + (license (list license:expat license:asl2.0)))) + (define-public rust-crc-1 (package (name "rust-crc") -- cgit 1.4.1 From c5f0ce224460ba8dc5e3c53af5795efce4f993d5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 17:46:38 -0400 Subject: gnu: Add rust-cargo-platform-0.1. * gnu/packages/crates-io.scm (rust-cargo-platform-0.1): New variable. --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 835c89d09c..91acf23752 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -6762,6 +6762,29 @@ metadata}.") (;("rust-docopt" ,rust-docopt-0.8) ("rust-clap" ,rust-clap-2)))))) +(define-public rust-cargo-platform-0.1 + (package + (name "rust-cargo-platform") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "cargo-platform" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1mzi60pf0z83qkzqp7jwd61xnqz2b5ydsj7rnnikbgyicd5989h2")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-serde" ,rust-serde-1)))) + (home-page "https://github.com/rust-lang/cargo") + (synopsis "Target platform abstraction for Cargo") + (description "This package provides abstractions for the target platforms +supported by Cargo.") + (license (list license:expat license:asl2.0)))) + (define-public rust-cargon-0.0 (package (name "rust-cargon") -- cgit 1.4.1 From 25c4ad2771f27d65db817fb1feb599b391af0097 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 21:23:12 -0400 Subject: gnu: Add rust-bytesize-1. * gnu/packages/crates-io.scm (rust-bytesize-1): New variable. --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 91acf23752..cb91d76ba1 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -6253,6 +6253,29 @@ little-endian.") exposed as Reader/Writer streams.") (license (list license:expat license:asl2.0)))) +(define-public rust-bytesize-1 + (package + (name "rust-bytesize") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "bytesize" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1nl2j2bi9nk3q564jhyb77947wdv5ch54r14gjv4c59s563qd8c1")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-serde" ,rust-serde-1)))) + (home-page "https://github.com/hyunsik/bytesize/") + (synopsis "Human-readable byte count representation library for Rust") + (description "ByteSize is an utility for human-readable byte count +representation, with support for both SI and binary units.") + (license license:asl2.0))) + (define-public rust-bzip2-0.3 (package (inherit rust-bzip2-0.4) -- cgit 1.4.1 From aacc47eb4cc2814f24087e796b70f0b865cb2f81 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 21:23:42 -0400 Subject: gnu: Add rust-commoncrypto-sys-0.2. * gnu/packages/crates-io.scm (rust-commoncrypto-sys-0.2): New variable. --- gnu/packages/crates-io.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index cb91d76ba1..b6d4ac207b 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -8074,6 +8074,32 @@ combinator.") and 1.0.") (license (list license:expat license:asl2.0)))) +(define-public rust-commoncrypto-sys-0.2 + (package + (name "rust-commoncrypto-sys") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "commoncrypto-sys" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1ql381ziqh594a7z6m9bvs583lkrhbynk02pmbgp7aj7czs39v8z")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t ;requires the Mac OS library + #:cargo-inputs + (("rust-clippy" ,rust-clippy-0.0) + ("rust-libc" ,rust-libc-0.2)))) + (home-page "https://github.com/malept/rust-commoncrypto") + (synopsis "FFI bindings to Mac OS X's CommonCrypto library") + (description "This package is a component of the @code{commoncrypto} +library which provides Rust FFI bindings and idiomatic wrappers for Mac OS X's +CommonCrypto library.") + (license license:expat))) + (define-public rust-common-path-1 (package (name "rust-common-path") -- cgit 1.4.1 From 0ededfaaad3a0114528f92f8b64aab706fdceccf Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 21:28:49 -0400 Subject: gnu: Add rust-commoncrypto-0.2. * gnu/packages/crates-io.scm (rust-commoncrypto-0.2): New variable. --- gnu/packages/crates-io.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index b6d4ac207b..a6c6ea84cf 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -8100,6 +8100,31 @@ library which provides Rust FFI bindings and idiomatic wrappers for Mac OS X's CommonCrypto library.") (license license:expat))) +(define-public rust-commoncrypto-0.2 + (package + (name "rust-commoncrypto") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "commoncrypto" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "01whnqcziclsj1gwavvqhrw2r5cmwh00j2fbc56iwnm2ddcahmnh")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-clippy" ,rust-clippy-0.0) + ("rust-commoncrypto-sys" ,rust-commoncrypto-sys-0.2)))) + (home-page "https://github.com/malept/rust-commoncrypto") + (synopsis "Idiomatic Rust wrappers for Mac OS X's CommonCrypto library") + (description "The @{commoncrypto} library provides Rust FFI bindings and +idiomatic wrappers for Mac OS X's CommonCrypto library.") + (license license:expat))) + (define-public rust-common-path-1 (package (name "rust-common-path") -- cgit 1.4.1 From 9fed4419bc692eecd1b7ca0fe312c6588e152cca Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 22:55:21 -0400 Subject: gnu: Add rust-cargo-0.53. * gnu/packages/crates-io.scm (rust-cargo-0.53): New variable. --- gnu/packages/crates-io.scm | 90 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 90 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index a6c6ea84cf..06ed61af81 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -6727,6 +6727,96 @@ remote procedure call protocol") capabilities") (license (list license:expat license:asl2.0)))) +(define-public rust-cargo-0.53 + (package + (name "rust-cargo") + (version "0.53.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "cargo" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "12ns9v4dd8vnvsaqgd897h2zc19w00i5ii3slda653zbhfzm6zna")))) + (build-system cargo-build-system) + (arguments + `(;; The test suite is disabled as the internal 'cargo-test-macro' and + ;; 'cargo-test-support' crates are not included in the release. + #:tests? #f + #:rust ,rust-1.52 ;transitively inherited from rust-sized-chunks + #:cargo-inputs + (("rust-anyhow" ,rust-anyhow-1) + ("rust-atty" ,rust-atty-0.2) + ("rust-bytesize" ,rust-bytesize-1) + ("rust-cargo-platform" ,rust-cargo-platform-0.1) + ("rust-clap" ,rust-clap-2) + ("rust-core-foundation" ,rust-core-foundation-0.9) + ("rust-crates-io" ,rust-crates-io-0.33) + ("rust-crossbeam-utils" ,rust-crossbeam-utils-0.8) + ("rust-crypto-hash" ,rust-crypto-hash-0.3) + ("rust-curl" ,rust-curl-0.4) + ("rust-curl-sys" ,rust-curl-sys-0.4) + ("rust-env-logger" ,rust-env-logger-0.8) + ("rust-filetime" ,rust-filetime-0.2) + ("rust-flate2" ,rust-flate2-1) + ("rust-flate2" ,rust-flate2-1) + ("rust-fwdansi" ,rust-fwdansi-1) + ("rust-git2" ,rust-git2-0.13) + ("rust-git2-curl" ,rust-git2-curl-0.14) + ("rust-glob" ,rust-glob-0.3) + ("rust-hex" ,rust-hex-0.4) + ("rust-home" ,rust-home-0.5) + ("rust-humantime" ,rust-humantime-2) + ("rust-ignore" ,rust-ignore-0.4) + ("rust-im-rc" ,rust-im-rc-15) + ("rust-jobserver" ,rust-jobserver-0.1) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-lazycell" ,rust-lazycell-1) + ("rust-libc" ,rust-libc-0.2) + ("rust-libgit2-sys" ,rust-libgit2-sys-0.12) + ("rust-log" ,rust-log-0.4) + ("rust-memchr" ,rust-memchr-2) + ("rust-miow" ,rust-miow-0.3) + ("rust-num-cpus" ,rust-num-cpus-1) + ("rust-opener" ,rust-opener-0.4) + ("rust-openssl" ,rust-openssl-0.10) + ("rust-percent-encoding" ,rust-percent-encoding-2) + ("rust-pretty-env-logger" ,rust-pretty-env-logger-0.4) + ("rust-rand" ,rust-rand-0.8) + ("rust-rustc-workspace-hack" ,rust-rustc-workspace-hack-1) + ("rust-rustfix" ,rust-rustfix-0.5) + ("rust-same-file" ,rust-same-file-1) + ("rust-semver" ,rust-semver-0.10) + ("rust-serde" ,rust-serde-1) + ("rust-serde-ignored" ,rust-serde-ignored-0.1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-shell-escape" ,rust-shell-escape-0.1) + ("rust-strip-ansi-escapes" ,rust-strip-ansi-escapes-0.1) + ("rust-tar" ,rust-tar-0.4) + ("rust-tar" ,rust-tar-0.4) + ("rust-tempfile" ,rust-tempfile-3) + ("rust-termcolor" ,rust-termcolor-1) + ("rust-toml" ,rust-toml-0.5) + ("rust-unicode-width" ,rust-unicode-width-0.1) + ("rust-unicode-xid" ,rust-unicode-xid-0.2) + ("rust-url" ,rust-url-2) + ("rust-walkdir" ,rust-walkdir-2) + ("rust-winapi" ,rust-winapi-0.3)))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("curl" ,curl) + ("libssh2" ,libssh2) + ("openssl" ,openssl) + ("zlib" ,zlib))) + (home-page "https://crates.io") + (synopsis "Package manager for Rust") + (description "Cargo, a package manager for Rust. This package provides +the library crate of Cargo.") + (license (list license:expat license:asl2.0)))) + (define-public rust-cargo-metadata-0.9 (package (name "rust-cargo-metadata") -- cgit 1.4.1 From b95e43b4fd3e0ef794b22776409d241f0e1fb5a1 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 23:18:24 -0400 Subject: gnu: rust-serde-json-1: Update to 1.0.64. * gnu/packages/crates-io.scm (rust-serde-json-1): Update to 1.0.64. --- gnu/packages/crates-io.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 06ed61af81..5762a0da0c 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -38273,14 +38273,14 @@ data. This crate provides a wrapper that works with any existing Serde (define-public rust-serde-json-1 (package (name "rust-serde-json") - (version "1.0.61") + (version "1.0.64") (source (origin (method url-fetch) (uri (crate-uri "serde_json" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0nijvxvgcncvd1wbn73zx7q14bdxah0gf2789qd8kdjpa1cv5kjg")))) + (base32 "0y9gk3yikncrc0zajmwc0pidr7zfwafawb4gidf6mqyskzf9g7kr")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs -- cgit 1.4.1 From 62b1c4718c55835812cae45da568776d8202e0fe Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 3 Jun 2021 12:57:06 -0400 Subject: gnu: rust-cargo-c: Update to 0.8.1+cargo-0.53. * gnu/packages/rust-apps.scm (rust-cargo-c): Update to 0.8.1+cargo-0.53. [cargo-inputs]{rust-cbindgen}: Update to 0.19. {rust-semver}: Update to 0.10. {rust-serde-json}: Update to 1. {rust-cargo, rust-anyhow}: New inputs. [native-inputs]: New field. [inputs]: New field. --- gnu/packages/rust-apps.scm | 24 ++++++++++++++++++++---- 1 file changed, 20 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm index 0219c4053d..a530c750d9 100644 --- a/gnu/packages/rust-apps.scm +++ b/gnu/packages/rust-apps.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2021 Sharlatan Hellseher ;;; Copyright © 2021 Zheng Junjie <873216071@qq.com> ;;; Copyright © 2021 Alexandru-Sergiu Marton +;;; Copyright © 2021 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -35,13 +36,16 @@ #:use-module (gnu packages compression) #:use-module (gnu packages crates-io) #:use-module (gnu packages crates-graphics) + #:use-module (gnu packages curl) #:use-module (gnu packages documentation) #:use-module (gnu packages fontutils) #:use-module (gnu packages gtk) #:use-module (gnu packages jemalloc) + #:use-module (gnu packages ssh) #:use-module (gnu packages pcre) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages rust) #:use-module (gnu packages tls) #:use-module (gnu packages version-control)) @@ -773,7 +777,7 @@ the details of how it was triggered. (define-public rust-cargo-c (package (name "rust-cargo-c") - (version "0.5.3") + (version "0.8.1+cargo-0.53") (source (origin (method url-fetch) @@ -782,19 +786,31 @@ the details of how it was triggered. (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0hsag5g4qngm8alfil2dyvl5sagpqi5nb40c7bhwng2z8mv9r41k")))) + "0fwdxhdj2963xr6xfqr56i7hikhsdv562vgxq2dj3h2mi3dil1k6")))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs - (("rust-cbindgen" ,rust-cbindgen) + `(#:rust ,rust-1.52 ;inherited from rust-cargo + #:cargo-inputs + (("rust-cbindgen" ,rust-cbindgen-0.19) + ("rust-cargo" ,rust-cargo-0.53) ; + ("rust-anyhow" ,rust-anyhow-1) ("rust-pretty-env-logger" ,rust-pretty-env-logger-0.4) ("rust-structopt" ,rust-structopt-0.3) ("rust-log" ,rust-log-0.4) ("rust-toml" ,rust-toml-0.5) ("rust-cargo-metadata" ,rust-cargo-metadata-0.9) + ("rust-semver" ,rust-semver-0.10) ("rust-serde" ,rust-serde-1) ("rust-serde-derive" ,rust-serde-derive-1) + ("rust-serde-json" ,rust-serde-json-1) ("rust-regex" ,rust-regex-1)))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("curl" ,curl) + ("libssh2" ,libssh2) + ("openssl" ,openssl) + ("zlib" ,zlib))) (home-page "https://github.com/lu-zero/cargo-c") (synopsis "Build and install C-compatible libraries") (description -- cgit 1.4.1 From 636e478bacd01ddc1050e416430f1a6219ecfa6c Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Wed, 2 Jun 2021 22:30:19 -0400 Subject: gnu: rav1e: Update to 0.4.1. * gnu/packages/video.scm (rav1e): Update to 0.4.1. [source]: Fix indentation. [cargo-inputs]{rust-arbitrary}: Update to 0.4. {rust-av-metrics}: New input. {rust-bitstream-io}: Update to 1. {rust-cfg-if}: Update to 1. {rust-console}: Update to 0.14. {rust-crossbeam}: New input. {rust-itertools}: Update to 0.10. {rust-libfuzzer-sys}: New input. {rust-noop-proc-macro}: Update to 0.3. {rust-paste}: Update to 1. {rust-rand}: Update to 0.8. {rust-rand-chacha}: Update to 0.3. {rust-regex}: New input. {rust-rustc-version}: Update to 0.3. {rust-signal-hook}: Update to 0.3. {rust-v-frame, rust-wasm-bindgen}: New inputs. {rust-cc: Move to... [cargo-development-inputs]: ... here. {rust-rand}: Update to 0.8. {rust-rand-chacha}: Update to 0.3. {rust-semver}: Update to 0.11. [inputs]{nasm}: Move to... [native-inputs]: ... here. This was spotted by 'guix lint'. [synopsis]: Focus on facts, toning down marketing. [description]: Expound. --- gnu/packages/video.scm | 69 +++++++++++++++++++++++++++----------------------- 1 file changed, 38 insertions(+), 31 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index d85a4045f1..f40736f51a 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -50,6 +50,7 @@ ;;; Copyright © 2021 Alexey Abramov ;;; Copyright © 2021 Andrew Tropin ;;; Copyright © 2021 David Wilson +;;; Copyright © 2021 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -4864,64 +4865,70 @@ result in several formats: (define-public rav1e (package (name "rav1e") - (version "0.3.5") + (version "0.4.1") (source - (origin - (method url-fetch) - (uri (crate-uri "rav1e" version)) - (file-name - (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "0c40gq4qid2apmlgzx98f6826jmn2n61prk0rn7sjxaw7yimw854")))) + (origin + (method url-fetch) + (uri (crate-uri "rav1e" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "00rjil6qbrwfxhhlq9yvidxm0gp9qdbywhf5zvkj85lykbhyff09")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs (("rust-aom-sys" ,rust-aom-sys-0.2) - ("rust-arbitrary" ,rust-arbitrary-0.2) + ("rust-arbitrary" ,rust-arbitrary-0.4) ("rust-arg-enum-proc-macro" ,rust-arg-enum-proc-macro-0.3) ("rust-arrayvec" ,rust-arrayvec-0.5) + ("rust-av-metrics" ,rust-av-metrics-0.6) ("rust-backtrace" ,rust-backtrace-0.3) - ("rust-bitstream-io" ,rust-bitstream-io-0.8) + ("rust-bitstream-io" ,rust-bitstream-io-1) ("rust-byteorder" ,rust-byteorder-1) - ("rust-cc" ,rust-cc-1) - ("rust-cfg-if" ,rust-cfg-if-0.1) + ("rust-cfg-if" ,rust-cfg-if-1) ("rust-clap" ,rust-clap-2) - ("rust-console" ,rust-console-0.11) + ("rust-console" ,rust-console-0.14) + ("rust-crossbeam" ,rust-crossbeam-0.8) ("rust-dav1d-sys" ,rust-dav1d-sys-0.3) ("rust-fern" ,rust-fern-0.6) ("rust-image" ,rust-image-0.23) ("rust-interpolate-name" ,rust-interpolate-name-0.2) - ("rust-itertools" ,rust-itertools-0.9) + ("rust-itertools" ,rust-itertools-0.10) ("rust-ivf" ,rust-ivf-0.1) ("rust-libc" ,rust-libc-0.2) + ("rust-libfuzzer-sys" ,rust-libfuzzer-sys-0.3) ("rust-log" ,rust-log-0.4) ("rust-nasm-rs" ,rust-nasm-rs-0.2) - ("rust-noop-proc-macro" ,rust-noop-proc-macro-0.2) + ("rust-noop-proc-macro" ,rust-noop-proc-macro-0.3) ("rust-num-derive" ,rust-num-derive-0.3) ("rust-num-traits" ,rust-num-traits-0.2) - ("rust-paste" ,rust-paste-0.1) - ("rust-rand" ,rust-rand-0.7) - ("rust-rand-chacha" ,rust-rand-chacha-0.2) + ("rust-paste" ,rust-paste-1) + ("rust-rand" ,rust-rand-0.8) + ("rust-rand-chacha" ,rust-rand-chacha-0.3) ("rust-rayon" ,rust-rayon-1) + ("rust-regex" ,rust-regex-1) ("rust-rust-hawktracer" ,rust-rust-hawktracer-0.7) - ("rust-rustc-version" ,rust-rustc-version-0.2) + ("rust-rustc-version" ,rust-rustc-version-0.3) ("rust-scan-fmt" ,rust-scan-fmt-0.2) ("rust-serde" ,rust-serde-1) - ("rust-signal-hook" ,rust-signal-hook-0.1) + ("rust-signal-hook" ,rust-signal-hook-0.3) ("rust-simd-helpers" ,rust-simd-helpers-0.1) ("rust-thiserror" ,rust-thiserror-1) ("rust-toml" ,rust-toml-0.5) + ("rust-v-frame" ,rust-v-frame-0.2) ("rust-vergen" ,rust-vergen-3) - ("rust-y4m" ,rust-y4m-0.5)) + ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2) + ("rust-y4m" ,rust-y4m-0.7)) #:cargo-development-inputs (("rust-assert-cmd" ,rust-assert-cmd-1) + ("rust-cc" ,rust-cc-1) ("rust-criterion" ,rust-criterion-0.3) ("rust-interpolate-name" ,rust-interpolate-name-0.2) ("rust-pretty-assertions" ,rust-pretty-assertions-0.6) - ("rust-rand" ,rust-rand-0.7) - ("rust-rand-chacha" ,rust-rand-chacha-0.2) - ("rust-semver" ,rust-semver-0.9)) + ("rust-rand" ,rust-rand-0.8) + ("rust-rand-chacha" ,rust-rand-chacha-0.3) + ("rust-semver" ,rust-semver-0.11)) #:phases (modify-phases %standard-phases (replace 'build @@ -4930,13 +4937,13 @@ result in several formats: (invoke "cargo" "cinstall" "--release" (string-append "--prefix=" out)))))))) (native-inputs - `(("cargo-c" ,rust-cargo-c))) - (inputs - `(("nasm" ,nasm))) + `(("cargo-c" ,rust-cargo-c) + ("nasm" ,nasm))) (home-page "https://github.com/xiph/rav1e/") - (synopsis "The fastest and safest AV1 encoder") - (description - "The fastest and safest AV1 encoder.") + (synopsis "Fast and safe AV1 encoder") + (description "@code{rav1e} is an AV1 video encoder. It is designed to +eventually cover all use cases, though in its current form it is most suitable +for cases where libaom (the reference encoder) is too slow.") (license license:bsd-2))) (define-public peek -- cgit 1.4.1 From 916bbf53a9a44eb8922f4cdd7dfdc4d7006f99a0 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 4 Jun 2021 21:24:44 -0400 Subject: gnu: Add rust-fallible-collections-0.4. * gnu/packages/crates-io.scm (rust-fallible-collections-0.4): New variable. --- gnu/packages/crates-io.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 5762a0da0c..8b51018963 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -14281,6 +14281,34 @@ traits but without the boilerplate.") "Crate for mimicking simd crate on stable Rust.") (license (list license:asl2.0 license:expat)))) +(define-public rust-fallible-collections-0.4 + (package + (name "rust-fallible-collections") + (version "0.4.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "fallible_collections" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1sk6ckixvf0pax47qgs8lfd2zi2gmyg1xgk1k7z2qgalhaaidnaa")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-hashbrown" ,rust-hashbrown-0.9)))) + (home-page "https://github.com/vcombey/fallible_collections") + (synopsis "Fallible collections implementation in Rust") + (description "This library extends the Rust standard collections to return +a result when an allocation error occurs, ala +@url{https://github.com/rust-lang/rfcs/blob/master/text/2116-alloc-me-maybe.md,RFC +2116}. The API currently proposes a fallible interface for @code{Vec}, +@code{Box}, @code{Arc}, @code{Btree} and @code{Rc}, as well as a +@code{TryClone} trait wich is implemented for primitive Rust traits and a +fallible format macro.") + (license (list license:expat license:asl2.0)))) + (define-public rust-failure-0.1 (package (name "rust-failure") -- cgit 1.4.1 From 93baaf55cc12aa2a358c44c7db4ff3094ba97b5b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 4 Jun 2021 21:30:49 -0400 Subject: gnu: Add rust-bitreader-0.3. * gnu/packages/crates-io.scm (rust-bitreader-0.3): New variable. --- gnu/packages/crates-io.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 8b51018963..a27b68369e 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -4891,6 +4891,31 @@ behave like a set of bitflags.") declaring and working with fixed size bitmaps in Rust.") (license license:mpl2.0))) +(define-public rust-bitreader-0.3 + (package + (name "rust-bitreader") + (version "0.3.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "bitreader" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "06wlzf8ra7k8ya0m71dq0kxbaalaan48dymairn9q8s4gld1hy4i")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-cfg-if" ,rust-cfg-if-1)))) + (home-page "https://github.com/irauta/bitreader") + (synopsis "Individual bits reader from a slice of bytes") + (description "BitReader helps reading individual bits from a slice of +bytes. You can read an arbitrary numbers of bits from the byte slice, for +example 13 bits at once. The reader internally keeps track of position within +the buffer.") + (license (list license:expat license:asl2.0)))) + (define-public rust-bitstream-io-1 (package (name "rust-bitstream-io") -- cgit 1.4.1 From ba047d8bc2d5a65e21447b769cd55ec76b2261f1 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 4 Jun 2021 21:35:52 -0400 Subject: gnu: Add rust-avif-parse-0.13. * gnu/packages/crates-graphics.scm (rust-avif-parse-0.13): New variable. --- gnu/packages/crates-graphics.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/crates-graphics.scm b/gnu/packages/crates-graphics.scm index e5719f97e4..5ea5473c3b 100644 --- a/gnu/packages/crates-graphics.scm +++ b/gnu/packages/crates-graphics.scm @@ -10,6 +10,7 @@ ;;; Copyright © 2020 Leo Famulari ;;; Copyright © 2020, 2021 Nicolas Goaziou ;;; Copyright © 2020 Antoine Côté +;;; Copyright © 2021 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -269,6 +270,38 @@ the term library to handle the ANSI nonsense and hence it works on Windows, Mac, and Unix.") (license (list license:asl2.0 license:expat)))) +(define-public rust-avif-parse-0.13 + (package + (name "rust-avif-parse") + (version "0.13.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "avif-parse" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1vylrjq77mpl6flmd85j5f2qimh6vjn03syvq8agb62x56khm0xj")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-bitreader" ,rust-bitreader-0.3) + ("rust-byteorder" ,rust-byteorder-1) + ("rust-fallible-collections" ,rust-fallible-collections-0.4) + ("rust-log" ,rust-log-0.4) + ("rust-static-assertions" ,rust-static-assertions-1)) + #:cargo-development-inputs + (("rust-env-logger" ,rust-env-logger-0.8) + ("rust-walkdir" ,rust-walkdir-2)))) + (home-page "https://github.com/kornelski/avif-parse") + (synopsis "Parser for AVIF image files") + (description "This AVIF parser allows extracting the AV1 payload and alpha +channel metadata out of AVIF image files. The parser is a fork of Mozilla's +MP4 parser used in Firefox, so it's designed to be robust and safely handle +untrusted data.") + (license license:mpl2.0))) + (define-public rust-avif-serialize-0.6 (package (name "rust-avif-serialize") -- cgit 1.4.1 From 1c5781bc0d5b3132d90ed57ca198a9b9fa401ca5 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 4 Jun 2021 22:33:27 -0400 Subject: gnu: rust-ravif: Use rav1e instead of rust-rav1e. With the rav1e package having been brought up to par with rust-rav1e, rust-ravif can use rav1e directly. * gnu/packages/crates-graphics.scm (rust-ravif) [cargo-inputs]{rust-rav1e}: Replace with... {rav1e}: ... this. [cargo-development-inputs]: New argument. [native-inputs]: New field. --- gnu/packages/crates-graphics.scm | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-graphics.scm b/gnu/packages/crates-graphics.scm index 5ea5473c3b..ac54dd40ff 100644 --- a/gnu/packages/crates-graphics.scm +++ b/gnu/packages/crates-graphics.scm @@ -33,6 +33,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (gnu packages) + #:use-module (gnu packages assembly) #:use-module (gnu packages crates-io) #:use-module (gnu packages freedesktop) #:use-module (gnu packages llvm) @@ -2030,20 +2031,22 @@ where libaom (the reference encoder) is too slow.") (base32 "1gyc7w1fz3qdk95cdpkj185dm6lskxfp329xm69waxc565fcz9rx")))) (build-system cargo-build-system) (arguments - `(#:skip-build? #t - #:cargo-inputs + `(#:cargo-inputs (("rust-avif-serialize" ,rust-avif-serialize-0.6) ("rust-imgref" ,rust-imgref-1) ("rust-loop9" ,rust-loop9-0.1) ("rust-num-cpus" ,rust-num-cpus-1) - ("rust-rav1e" ,rust-rav1e-0.4) + ("rav1e" ,rav1e) ("rust-rayon" ,rust-rayon-1) - ("rust-rgb" ,rust-rgb-0.8)))) + ("rust-rgb" ,rust-rgb-0.8)) + #:cargo-development-inputs + (("rust-avif-parse" ,rust-avif-parse-0.13)))) + (native-inputs + `(("nasm" ,nasm))) ;for building rav1e (home-page "https://lib.rs/ravif") (synopsis "Library for encoding images in AVIF format") - (description - "This package is a rav1e-based pure Rust library for encoding images in -AVIF format.") + (description "This package is a rav1e-based pure Rust library for encoding +images in AVIF format.") (license license:bsd-3))) (define-public rust-raw-window-handle-0.3 -- cgit 1.4.1 From d8c06d8789226354a7ca21b9fc2f20353a68ce5b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 4 Jun 2021 22:40:31 -0400 Subject: gnu: Remove rust-rav1e. This package is superseded by rav1e. Note: I tried defining an alias like so: (define-public rust-rav1e (deprecated-package "rust-rav1e" rav1e)) But it caused a problem where the 'rav1e' variable would appear unbound. * gnu/packages/crates-graphics.scm (rust-rav1e-0.4): Remove. --- gnu/packages/crates-graphics.scm | 69 ---------------------------------------- 1 file changed, 69 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crates-graphics.scm b/gnu/packages/crates-graphics.scm index ac54dd40ff..bc47bf1287 100644 --- a/gnu/packages/crates-graphics.scm +++ b/gnu/packages/crates-graphics.scm @@ -1949,75 +1949,6 @@ interactive applications.") ("rust-glob" ,rust-glob-0.2) ("rust-term" ,rust-term-0.4)))))) -(define-public rust-rav1e-0.4 - (package - (name "rust-rav1e") - (version "0.4.0") - (source - (origin - (method url-fetch) - (uri (crate-uri "rav1e" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 "02cpgzycfgnflnv8sck6ajasa7abfgdzn6b4jv01sf6r21yfipbq")))) - (build-system cargo-build-system) - (arguments - `(#:skip-build? #t - #:cargo-inputs - (("rust-aom-sys" ,rust-aom-sys-0.2) - ("rust-arbitrary" ,rust-arbitrary-0.4) - ("rust-arg-enum-proc-macro" ,rust-arg-enum-proc-macro-0.3) - ("rust-arrayvec" ,rust-arrayvec-0.5) - ("rust-assert-cmd" ,rust-assert-cmd-1) - ("rust-av-metrics" ,rust-av-metrics-0.6) - ("rust-backtrace" ,rust-backtrace-0.3) - ("rust-bitstream-io" ,rust-bitstream-io-1) - ("rust-byteorder" ,rust-byteorder-1) - ("rust-cc" ,rust-cc-1) - ("rust-cfg-if" ,rust-cfg-if-1) - ("rust-clap" ,rust-clap-2) - ("rust-console" ,rust-console-0.14) - ("rust-criterion" ,rust-criterion-0.3) - ("rust-crossbeam" ,rust-crossbeam-0.8) - ("rust-dav1d-sys" ,rust-dav1d-sys-0.3) - ("rust-fern" ,rust-fern-0.6) - ("rust-image" ,rust-image-0.23) - ("rust-interpolate-name" ,rust-interpolate-name-0.2) - ("rust-itertools" ,rust-itertools-0.10) - ("rust-ivf" ,rust-ivf-0.1) - ("rust-libc" ,rust-libc-0.2) - ("rust-libfuzzer-sys" ,rust-libfuzzer-sys-0.3) - ("rust-log" ,rust-log-0.4) - ("rust-nasm-rs" ,rust-nasm-rs-0.2) - ("rust-noop-proc-macro" ,rust-noop-proc-macro-0.3) - ("rust-num-derive" ,rust-num-derive-0.3) - ("rust-num-traits" ,rust-num-traits-0.2) - ("rust-paste" ,rust-paste-1) - ("rust-pretty-assertions" ,rust-pretty-assertions-0.6) - ("rust-rand" ,rust-rand-0.8) - ("rust-rand-chacha" ,rust-rand-chacha-0.3) - ("rust-rayon" ,rust-rayon-1) - ("rust-regex" ,rust-regex-1) - ("rust-rust-hawktracer" ,rust-rust-hawktracer-0.7) - ("rust-rustc-version" ,rust-rustc-version-0.3) - ("rust-scan-fmt" ,rust-scan-fmt-0.2) - ("rust-serde" ,rust-serde-1) - ("rust-signal-hook" ,rust-signal-hook-0.3) - ("rust-simd-helpers" ,rust-simd-helpers-0.1) - ("rust-thiserror" ,rust-thiserror-1) - ("rust-toml" ,rust-toml-0.5) - ("rust-v-frame" ,rust-v-frame-0.2) - ("rust-vergen" ,rust-vergen-3) - ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2) - ("rust-y4m" ,rust-y4m-0.7)))) - (home-page "https://github.com/xiph/rav1e") - (synopsis "Fast and safe AV1 encoder") - (description - "@code{rav1e} is an AV1 video encoder. It is designed to eventually -cover all use cases, though in its current form it is most suitable for cases -where libaom (the reference encoder) is too slow.") - (license license:bsd-2))) - (define-public rust-ravif-0.6 (package (name "rust-ravif") -- cgit 1.4.1 From f02b9d6d2ce336fe0cd746bb60199085cd18834b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Wed, 2 Jun 2021 15:03:23 -0400 Subject: gnu: ffmpeg: Update to 4.4. * gnu/packages/video.scm (ffmpeg): Update to 4.4. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index f40736f51a..7140052e89 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1422,14 +1422,14 @@ operate properly.") (define-public ffmpeg (package (name "ffmpeg") - (version "4.3.2") + (version "4.4") (source (origin (method url-fetch) (uri (string-append "https://ffmpeg.org/releases/ffmpeg-" version ".tar.xz")) (sha256 (base32 - "1nyd9jlcy0pqnwzi29a7sg50hq37vb0g3f9l16y3q8yh3m7ydr26")))) + "02fr8mvf2agwmyb9q2bmh9p09gpz3xxmpcbbbj8iydz57hc0mc86")))) (build-system gnu-build-system) (inputs `(("dav1d" ,dav1d) -- cgit 1.4.1 From 4d0030eec5fbd6b4a2cf42c172c2db91ecc172ab Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sat, 5 Jun 2021 15:15:41 -0400 Subject: gnu: diffoscope: Update to 177. This resolves a problem with ffmpeg 4.4. * gnu/packages/diffoscope.scm (diffoscope): Update to 177. --- gnu/packages/diffoscope.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm index 21c78ae6f0..35e4783b2a 100644 --- a/gnu/packages/diffoscope.scm +++ b/gnu/packages/diffoscope.scm @@ -72,7 +72,7 @@ (define-public diffoscope (package (name "diffoscope") - (version "175") + (version "177") (source (origin (method git-fetch) (uri (git-reference @@ -81,7 +81,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "1qzdi9110mdm5af4nq1nwx9b1hrin9a1v3vhnxwrkyb7j0mvcg7v")))) + "02np9dq7jnq48lcmz4k1hvwc6xiqgjhrwr1vsbsfw8rxnp9vs0a5")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases -- cgit 1.4.1 From 30eccefa398ee05fa372efb5ae16db1cc7c0fc59 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sat, 5 Jun 2021 17:23:57 -0400 Subject: gnu: Add ffmpeg-4.3. * gnu/packages/video.scm (ffmpeg-4.3): New variable. --- gnu/packages/video.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 7140052e89..f3a0436786 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1613,6 +1613,17 @@ convert and stream audio and video. It includes the libavcodec audio/video codec library.") (license license:gpl2+))) +(define-public ffmpeg-4.3 + (package/inherit ffmpeg + (version "4.3.2") + (source (origin + (method url-fetch) + (uri (string-append "https://ffmpeg.org/releases/ffmpeg-" + version ".tar.xz")) + (sha256 + (base32 + "1nyd9jlcy0pqnwzi29a7sg50hq37vb0g3f9l16y3q8yh3m7ydr26")))))) + (define-public ffmpeg-3.4 (package (inherit ffmpeg) -- cgit 1.4.1 From 6a0d0c3c473d51d113d0c4efd7ed85d542f45c09 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sat, 5 Jun 2021 17:24:10 -0400 Subject: gnu: libopenshot: Use ffmpeg-4.3. * gnu/packages/video.scm (libopenshot) [propagated-inputs]{ffmpeg}: Downgrade to ffmpeg 4.3 to fix build. --- gnu/packages/video.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index f3a0436786..e01594fb28 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -4494,7 +4494,9 @@ create smoother and stable videos.") ("unittest++" ,unittest-cpp))) (propagated-inputs ;all referenced in installed headers `(("cppzmq" ,cppzmq) - ("ffmpeg" ,ffmpeg) + ;; libopenshot doesn't yet build with ffmpeg 4.4 (see: + ;; https://github.com/OpenShot/libopenshot/issues/676). + ("ffmpeg" ,ffmpeg-4.3) ("imagemagick" ,imagemagick) ("jsoncpp" ,jsoncpp) ("libopenshot-audio" ,libopenshot-audio) -- cgit 1.4.1 From a18079288f8b26b32e1388350f5d55240b1a6381 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sat, 5 Jun 2021 23:16:07 -0400 Subject: gnu: ppsspp: Update to 1.11.3-1.69fa207. This fixes the build with ffmpeg 4.4. * gnu/packages/patches/ppsspp-disable-upgrade-and-gold.patch: Rebase patch. * gnu/packages/emulators.scm (ppsspp): Update to 1.11.3-1.69fa207. [source]: Adjust origin snippet to unbundle the newly added zstd library. --- gnu/packages/emulators.scm | 396 +++++++++++---------- .../patches/ppsspp-disable-upgrade-and-gold.patch | 148 ++++---- 2 files changed, 289 insertions(+), 255 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index 716d1174ad..c25a45b785 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -15,6 +15,7 @@ ;;; Copyright © 2020 Christopher Howard ;;; Copyright © 2021 Felipe Balbi ;;; Copyright © 2021 Felix Gruber +;;; Copyright © 2021 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -2134,200 +2135,211 @@ framework based on QEMU.") (license license:gpl2+)))) (define-public ppsspp - (package - (name "ppsspp") - (version "1.11.3") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/hrydgard/ppsspp") - (commit (string-append "v" version)))) - (sha256 - (base32 "1dpxnwvl6jq7z67lbjws4lqc1bxc31xi6ddlmg5n3aig008yi2fp")) - (file-name (git-file-name name version)) - (patches - (search-patches "ppsspp-disable-upgrade-and-gold.patch")) - (modules '((guix build utils))) - (snippet - `(begin - ;; The following is quite a heavy-handed way of unbundling PPSSPP. - ;; There are still a number of external sources, that we don't - ;; remove here. Some may be packaged, others are not. - ;; First, we patch existing sources to include the right headers. - (substitute* (append (find-files "Common" ".*\\.(h|cpp)") - (find-files "Core" ".*\\.(h|cpp)") - (find-files "GPU" ".*\\.(h|cpp)") - (find-files "SDL" ".*\\.(h|cpp)") - (find-files "UI" ".*\\.(h|cpp)")) - ;; These headers are all hard-coded in the original source. - (("ext/cityhash/") "") - (("ext/glslang/glslang/") "glslang/") - (("ext/glslang/") "glslang/") - (("ext/miniupnp/") "") - (("ext/SPIRV-Cross/") "spirv_cross/") - (("ext/vulkan/") "vulkan/") - (("ext/xxhash.h") "xxhash.h") - ;; These definitions do not actually exist in the Vulkan headers, - ;; but PPSSPP defines them in ext/vulkan. - (("VK_FORMAT_BEGIN_RANGE") "VK_FORMAT_UNDEFINED") - (("VK_FORMAT_END_RANGE") "VK_FORMAT_ASTC_12x12_SRGB_BLOCK")) - ;; Next, we patch CMakeLists. - (substitute* "CMakeLists.txt" - ;; Drop unnecessary includes and targets. - (("include_directories\\(ext/glslang\\)") "") - (("include_directories\\(ext/xxhash\\)") "") - (("include_directories\\(ext/cityhash\\)") "") - (("set_target_properties\\(cityhash .*\\)") "") - ;; Fix linking to GLEW. - (("TARGET Ext::GLEW") "true") - (("target_link_libraries\\(native Ext::GLEW\\)") - "find_package(GLEW)\ntarget_link_libraries(native GLEW::GLEW)") - (("Ext::Snappy") "snappy") - ;; Don't search for cityhash/xxhash, we already have them. - (("add_library\\((city|xx)hash STATIC") "if()\nendif(") - (("ext/xxhash\\.[ch]") "") - (("ext/cityhash/.*\\.(cpp|h)") "") - (("if\\(USE_MINIUPNPC\\)" all) - (string-append all " + ;; Use a recent commit as fixes for ffmpeg 4.4 haven't been released as of + ;; 1.11.3. + (let ((commit "69fa20744958aef8da9ca052ba7675fdc1636e46") + (revision "1")) + (package + (name "ppsspp") + (version (git-version "1.11.3" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hrydgard/ppsspp") + (commit commit))) + (sha256 + (base32 "0r8w4hllhn6zsfxlajxw3sn3f8vsri45srr4mdwsffzcb4hvl0cr")) + (file-name (git-file-name name version)) + (patches + (search-patches "ppsspp-disable-upgrade-and-gold.patch")) + (modules '((guix build utils))) + (snippet + `(begin + ;; The following is quite a heavy-handed way of unbundling PPSSPP. + ;; There are still a number of external sources, that we don't + ;; remove here. Some may be packaged, others are not. + ;; First, we patch existing sources to include the right headers. + (substitute* (append (find-files "Common" ".*\\.(h|cpp)") + (find-files "Core" ".*\\.(h|cpp)") + (find-files "GPU" ".*\\.(h|cpp)") + (find-files "SDL" ".*\\.(h|cpp)") + (find-files "UI" ".*\\.(h|cpp)")) + ;; These headers are all hard-coded in the original source. + (("ext/cityhash/") "") + (("ext/glslang/glslang/") "glslang/") + (("ext/glslang/") "glslang/") + (("ext/miniupnp/") "") + (("ext/SPIRV-Cross/") "spirv_cross/") + (("ext/vulkan/") "vulkan/") + (("ext/xxhash.h") "xxhash.h") + ;; These definitions do not actually exist in the Vulkan headers, + ;; but PPSSPP defines them in ext/vulkan. + (("VK_FORMAT_BEGIN_RANGE") "VK_FORMAT_UNDEFINED") + (("VK_FORMAT_END_RANGE") "VK_FORMAT_ASTC_12x12_SRGB_BLOCK")) + ;; Next, we patch CMakeLists. + (substitute* "CMakeLists.txt" + ;; Drop unnecessary includes and targets. + (("include_directories\\(ext/glslang\\)") "") + (("include_directories\\(ext/xxhash\\)") "") + (("include_directories\\(ext/cityhash\\)") "") + (("include_directories\\(ext/zstd.*") "") + (("libzstd_static") "zstd") + (("set_target_properties\\(cityhash .*\\)") "") + ;; Fix linking to GLEW. + (("TARGET Ext::GLEW") "true") + (("target_link_libraries\\(native Ext::GLEW\\)") + "find_package(GLEW)\ntarget_link_libraries(native GLEW::GLEW)") + (("Ext::Snappy") "snappy") + ;; Don't search for cityhash/xxhash, we already have them. + (("add_library\\((city|xx)hash STATIC") "if()\nendif(") + (("ext/xxhash\\.[ch]") "") + (("ext/cityhash/.*\\.(cpp|h)") "") + (("if\\(USE_MINIUPNPC\\)" all) + (string-append all " find_package(miniupnpc) target_link_libraries(${CoreLibName} miniupnpc ${LDLIBS}) elseif(FALSE)")) - ;; Link all of spirv-cross. - (("spirv-cross-glsl" all) - (string-append all - " spirv-cross-core spirv-cross-cpp" - " spirv-cross-reflect spirv-cross-util"))) - (substitute* "ext/CMakeLists.txt" - (("add_subdirectory\\(glew\\)") "") - (("add_subdirectory\\(glslang( [A-Z_]*)*\\)") "") - (("add_subdirectory\\(snappy\\)") "") - (("add_subdirectory\\(SPIRV-Cross-build\\)") "")) - ;; Finally, we can delete the bundled sources. - (for-each delete-file-recursively - '("MoltenVK" - "ext/cmake" - "ext/glew" - "ext/glslang" "ext/glslang-build" - "ext/miniupnp" "ext/miniupnp-build" - "ext/native" - "ext/snappy" - "ext/SPIRV-Cross" "ext/SPIRV-Cross-build" - "ext/vulkan" - "ext/xxhash.c" - "ext/xxhash.h" - "ext/zlib")) - ;; Since we are not including git as an input, PPSSPP is confused - ;; about its version. Let's fix that here. - (substitute* "git-version.cmake" - (("unknown") ,version)))))) - (build-system cmake-build-system) - (native-inputs - `(("pkg-config" ,pkg-config) - ("python" ,python))) - (inputs - `(("cityhash" ,cityhash) - ("ffmpeg" ,ffmpeg) - ("glew" ,glew) - ("glslang" ,glslang) - ("libpng" ,libpng) - ("libzip" ,libzip) - ("mesa" ,mesa) - ("miniupnpc" ,miniupnpc) - ("sdl2" ,sdl2) - ("snappy" ,snappy) - ("spirv-cross" ,spirv-cross) - ("vulkan-headers" ,vulkan-headers) - ("vulkan-loader" ,vulkan-loader) - ("xxhash" ,xxhash) - ("zlib" ,zlib) - ;; TODO: unbundle armips. - ("armips-source" ,(package-source armips)) - ("lang" - ,(let ((commit "6bd5b4bc983917ea8402f73c726b46e36f3de0b4")) - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/hrydgard/ppsspp-lang") - (commit commit))) - (sha256 - (base32 "08npr3a4xskf85gnlxidl4ksc3rhc7m5rgnj7vsbjvhvw5ap02qx")) - (file-name (git-file-name "ppsspp-lang" commit))))) - ("tests" - ,(let ((commit "1047400eaec6bcbdb2a64d326375ef6a6617c4ac")) - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/hrydgard/pspautotests") - (commit commit))) - (sha256 - (base32 "0nxv1lskcr8zbg6nrfai21mxsw0n5vaqhbsa41c3cxfyx5c4w2pg")) - (file-name (git-file-name "pspautotests" commit))))))) - (arguments - `(#:out-of-source? #f - #:configure-flags (list "-DUSE_DISCORD=OFF" - "-DUSE_SYSTEM_FFMPEG=ON" - "-DUSE_SYSTEM_LIBZIP=ON" - ;; for testing - "-DUNITTEST=ON" "-DHEADLESS=ON") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'add-external-sources - (lambda* (#:key inputs #:allow-other-keys) - ;; TODO: unbundle armips. - (copy-recursively (assoc-ref inputs "armips-source") - "ext/armips") - ;; Some tests are externalised, so we add them here. - (copy-recursively (assoc-ref inputs "tests") - "pspautotests") - ;; i18n is externalised, so we add it here. - (copy-recursively (assoc-ref inputs "lang") - "assets/lang") - #t)) - (add-after 'unpack 'fix-unittest-build - (lambda _ - (substitute* "CMakeLists.txt" - (("unittest/TestVertexJit.cpp" all) - (string-append all " unittest/TestShaderGenerators.cpp"))) - (substitute* "unittest/TestVertexJit.cpp" - (("#include \"unittest/UnitTest.h\"" all) - (string-append all "\n#include "))) - #t)) - (replace 'check - (lambda _ - (for-each - (lambda (t) (invoke "./unitTest" t)) - '("Arm64Emitter" "ArmEmitter" "X64Emitter" "VertexJit" "Asin" - "SinCos" #|"VFPUSinCos" SIGSEGV|# "MathUtil" "Parsers" "Jit" - "MatrixTranspose" "ParseLBN" "QuickTexHash" "CLZ" - #|"ShaderGenerators"|#)) - (invoke "python3" "test.py" "-g") - #t)) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin/ppsspp (string-append out "/bin/ppsspp")) - (share (string-append out "/share/ppsspp"))) - (copy-recursively "icons/hicolor" - (string-append out "/share/icons/hicolor")) - (install-file "PPSSPPSDL" share) - (copy-recursively "assets" (string-append share "/assets")) + ;; Link all of spirv-cross. + (("spirv-cross-glsl" all) + (string-append all + " spirv-cross-core spirv-cross-cpp" + " spirv-cross-reflect spirv-cross-util"))) + (substitute* "ext/CMakeLists.txt" + (("add_subdirectory\\(glew.*") "") + (("add_subdirectory\\(glslang.*") "") + (("add_subdirectory\\(snappy.*") "") + (("add_subdirectory\\(SPIRV-Cross-build.*") "") + (("add_subdirectory\\(zstd.*") "")) + ;; Finally, we can delete the bundled sources. + (for-each delete-file-recursively + '("MoltenVK" + "ext/cmake" + "ext/glew" + "ext/glslang" "ext/glslang-build" + "ext/miniupnp" "ext/miniupnp-build" + "ext/native" + "ext/snappy" + "ext/SPIRV-Cross" "ext/SPIRV-Cross-build" + "ext/vulkan" + "ext/xxhash.c" + "ext/xxhash.h" + "ext/zlib" + "ext/zstd")) + ;; Since we are not including git as an input, PPSSPP is confused + ;; about its version. Let's fix that here. + (substitute* "git-version.cmake" + (("unknown") ,version)))))) + (build-system cmake-build-system) + (native-inputs + `(("pkg-config" ,pkg-config) + ("python" ,python))) + (inputs + `(("cityhash" ,cityhash) + ;; ppsspp doesn't yet build with ffmpeg 4.4 (see: + ("ffmpeg" ,ffmpeg) + ("glew" ,glew) + ("glslang" ,glslang) + ("libpng" ,libpng) + ("libzip" ,libzip) + ("mesa" ,mesa) + ("miniupnpc" ,miniupnpc) + ("sdl2" ,sdl2) + ("snappy" ,snappy) + ("spirv-cross" ,spirv-cross) + ("vulkan-headers" ,vulkan-headers) + ("vulkan-loader" ,vulkan-loader) + ("xxhash" ,xxhash) + ("zlib" ,zlib) + ("zstd" ,zstd "lib") +; ("zstd" ,zstd "static") + ;; TODO: unbundle armips. + ("armips-source" ,(package-source armips)) + ("lang" + ,(let ((commit "6bd5b4bc983917ea8402f73c726b46e36f3de0b4")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hrydgard/ppsspp-lang") + (commit commit))) + (sha256 + (base32 "08npr3a4xskf85gnlxidl4ksc3rhc7m5rgnj7vsbjvhvw5ap02qx")) + (file-name (git-file-name "ppsspp-lang" commit))))) + ("tests" + ,(let ((commit "1047400eaec6bcbdb2a64d326375ef6a6617c4ac")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hrydgard/pspautotests") + (commit commit))) + (sha256 + (base32 "0nxv1lskcr8zbg6nrfai21mxsw0n5vaqhbsa41c3cxfyx5c4w2pg")) + (file-name (git-file-name "pspautotests" commit))))))) + (arguments + `(#:out-of-source? #f + #:configure-flags (list "-DUSE_DISCORD=OFF" + "-DUSE_SYSTEM_FFMPEG=ON" + "-DUSE_SYSTEM_LIBZIP=ON" + ;; for testing + "-DUNITTEST=ON" "-DHEADLESS=ON") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'add-external-sources + (lambda* (#:key inputs #:allow-other-keys) + ;; TODO: unbundle armips. + (copy-recursively (assoc-ref inputs "armips-source") + "ext/armips") + ;; Some tests are externalised, so we add them here. + (copy-recursively (assoc-ref inputs "tests") + "pspautotests") + ;; i18n is externalised, so we add it here. + (copy-recursively (assoc-ref inputs "lang") + "assets/lang") + #t)) + (add-after 'unpack 'fix-unittest-build + (lambda _ + (substitute* "CMakeLists.txt" + (("unittest/TestVertexJit.cpp" all) + (string-append all " unittest/TestShaderGenerators.cpp"))) + (substitute* "unittest/TestVertexJit.cpp" + (("#include \"unittest/UnitTest.h\"" all) + (string-append all "\n#include "))) + #t)) + (replace 'check + (lambda _ + (for-each + (lambda (t) (invoke "./unitTest" t)) + '("Arm64Emitter" "ArmEmitter" "X64Emitter" "VertexJit" "Asin" + "SinCos" #|"VFPUSinCos" SIGSEGV|# "MathUtil" "Parsers" "Jit" + "MatrixTranspose" "ParseLBN" "QuickTexHash" "CLZ" + #|"ShaderGenerators"|#)) + (invoke "python3" "test.py" "-g") + #t)) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin/ppsspp (string-append out "/bin/ppsspp")) + (share (string-append out "/share/ppsspp"))) + (copy-recursively "icons/hicolor" + (string-append out "/share/icons/hicolor")) + (install-file "PPSSPPSDL" share) + (copy-recursively "assets" (string-append share "/assets")) - (make-desktop-entry-file - (string-append out "/share/applications/ppsspp.desktop") - #:name "PPSSPP" - #:exec (string-append share "/PPSSPPSDL") - #:icon "ppsspp") - (mkdir-p (string-append out "/bin")) - (with-output-to-file bin/ppsspp - (lambda () - (format #t "#!~a~%exec ~a/PPSSPPSDL \"$@\"" - (which "sh") share))) - (chmod bin/ppsspp #o755) - #t)))))) - (home-page "https://www.ppsspp.org/") - (synopsis "PSP emulator") - (description - "PPSSPP is a ``high-level'' emulator simulating the PSP operating + (make-desktop-entry-file + (string-append out "/share/applications/ppsspp.desktop") + #:name "PPSSPP" + #:exec (string-append share "/PPSSPPSDL") + #:icon "ppsspp") + (mkdir-p (string-append out "/bin")) + (with-output-to-file bin/ppsspp + (lambda () + (format #t "#!~a~%exec ~a/PPSSPPSDL \"$@\"" + (which "sh") share))) + (chmod bin/ppsspp #o755) + #t)))))) + (home-page "https://www.ppsspp.org/") + (synopsis "PSP emulator") + (description + "PPSSPP is a ``high-level'' emulator simulating the PSP operating system.") - (license license:gpl2+))) + (license license:gpl2+)))) diff --git a/gnu/packages/patches/ppsspp-disable-upgrade-and-gold.patch b/gnu/packages/patches/ppsspp-disable-upgrade-and-gold.patch index 760ab97568..155ba35efd 100644 --- a/gnu/packages/patches/ppsspp-disable-upgrade-and-gold.patch +++ b/gnu/packages/patches/ppsspp-disable-upgrade-and-gold.patch @@ -1,28 +1,32 @@ -From 0c57874ebb5982154da127ae338f9190b1581804 Mon Sep 17 00:00:00 2001 +From 942730ce7148cd54a30d4a606ce71a2654c8a2e0 Mon Sep 17 00:00:00 2001 From: Leo Prikler -Date: Fri, 26 Jun 2020 18:20:04 +0200 -Subject: [PATCH] ppsspp: disable upgrade and gold +Date: Sat, 5 Jun 2021 22:47:00 -0400 +Subject: [PATCH] ppsspp: Remove upgrade code and gold support. +Original patch from Leo Prikler. +Rebased on master (commit 69fa20744958aef8da9ca052ba7675fdc1636e46) by +Maxim Cournoyer. --- Core/Config.cpp | 11 ------ Core/Config.h | 2 -- Qt/QtMain.cpp | 6 ---- SDL/SDLMain.cpp | 6 ---- UI/DevScreens.cpp | 3 -- - UI/GameSettingsScreen.cpp | 1 - + UI/GameSettingsScreen.cpp | 2 -- UI/MainScreen.cpp | 70 +------------------------------------ UI/MiscScreens.cpp | 31 ++-------------- UWP/PPSSPP_UWPMain.cpp | 6 ---- Windows/MainWindowMenu.cpp | 2 +- Windows/main.cpp | 6 ---- android/jni/app-android.cpp | 6 ---- - 12 files changed, 5 insertions(+), 145 deletions(-) + ios/main.mm | 6 ---- + 13 files changed, 5 insertions(+), 152 deletions(-) diff --git a/Core/Config.cpp b/Core/Config.cpp -index 1c53e8e57..2fa74a6b8 100644 +index 74be99d75..b14aa22c7 100644 --- a/Core/Config.cpp +++ b/Core/Config.cpp -@@ -439,7 +439,6 @@ static ConfigSetting generalSettings[] = { +@@ -467,7 +467,6 @@ static ConfigSetting generalSettings[] = { ConfigSetting("IgnoreBadMemAccess", &g_Config.bIgnoreBadMemAccess, true, true), ConfigSetting("CurrentDirectory", &g_Config.currentDirectory, ""), ConfigSetting("ShowDebuggerOnLoad", &g_Config.bShowDebuggerOnLoad, false), @@ -30,7 +34,7 @@ index 1c53e8e57..2fa74a6b8 100644 ConfigSetting("Language", &g_Config.sLanguageIni, &DefaultLangRegion), ConfigSetting("ForceLagSync2", &g_Config.bForceLagSync, false, true, true), ConfigSetting("DiscordPresence", &g_Config.bDiscordPresence, true, true, false), // Or maybe it makes sense to have it per-game? Race conditions abound... -@@ -1293,16 +1292,6 @@ void Config::Load(const char *iniFileName, const char *controllerIniFilename) { +@@ -1323,16 +1322,6 @@ void Config::Load(const char *iniFileName, const char *controllerIniFilename) { upgradeMessage = ""; } @@ -40,7 +44,7 @@ index 1c53e8e57..2fa74a6b8 100644 - // upgrade number in the ini. - if (iRunCount % 10 == 0 && bCheckForNewVersion) { - std::shared_ptr dl = g_DownloadManager.StartDownloadWithCallback( -- "http://www.ppsspp.org/version.json", "", &DownloadCompletedCallback); +- "http://www.ppsspp.org/version.json", Path(), &DownloadCompletedCallback); - dl->SetHidden(true); - } - @@ -48,10 +52,10 @@ index 1c53e8e57..2fa74a6b8 100644 bSaveSettings = true; diff --git a/Core/Config.h b/Core/Config.h -index 13bce8a36..70d6c8aaf 100644 +index 79323eefc..d47bec0c7 100644 --- a/Core/Config.h +++ b/Core/Config.h -@@ -101,7 +101,6 @@ struct Config { +@@ -103,7 +103,6 @@ struct Config { bool bFastMemory; int iCpuCore; @@ -59,16 +63,16 @@ index 13bce8a36..70d6c8aaf 100644 bool bForceLagSync; bool bFuncReplacements; bool bHideSlowWarnings; -@@ -540,4 +539,3 @@ std::string CreateRandMAC(); +@@ -542,4 +541,3 @@ std::string CreateRandMAC(); // TODO: Find a better place for this. extern http::Downloader g_DownloadManager; extern Config g_Config; - diff --git a/Qt/QtMain.cpp b/Qt/QtMain.cpp -index 5be0cefa0..b11cb1c64 100644 +index b642f7442..a880d7c94 100644 --- a/Qt/QtMain.cpp +++ b/Qt/QtMain.cpp -@@ -218,12 +218,6 @@ bool System_GetPropertyBool(SystemProperty prop) { +@@ -219,12 +219,6 @@ bool System_GetPropertyBool(SystemProperty prop) { case SYSPROP_HAS_FILE_BROWSER: case SYSPROP_HAS_FOLDER_BROWSER: return true; @@ -78,14 +82,14 @@ index 5be0cefa0..b11cb1c64 100644 -#else - return false; -#endif + case SYSPROP_CAN_JIT: + return true; default: - return false; - } diff --git a/SDL/SDLMain.cpp b/SDL/SDLMain.cpp -index 98b56fe91..6af0fcb1a 100644 +index f0f74f979..f963f36e9 100644 --- a/SDL/SDLMain.cpp +++ b/SDL/SDLMain.cpp -@@ -380,12 +380,6 @@ bool System_GetPropertyBool(SystemProperty prop) { +@@ -381,12 +381,6 @@ bool System_GetPropertyBool(SystemProperty prop) { switch (prop) { case SYSPROP_HAS_BACK_BUTTON: return true; @@ -95,14 +99,14 @@ index 98b56fe91..6af0fcb1a 100644 -#else - return false; -#endif + case SYSPROP_CAN_JIT: + return true; default: - return false; - } diff --git a/UI/DevScreens.cpp b/UI/DevScreens.cpp -index 8daac5bc8..c0c09ce79 100644 +index 29baf2f2e..926692363 100644 --- a/UI/DevScreens.cpp +++ b/UI/DevScreens.cpp -@@ -605,9 +605,6 @@ void SystemInfoScreen::CreateViews() { +@@ -635,9 +635,6 @@ void SystemInfoScreen::CreateViews() { #ifdef _M_SSE buildConfig->Add(new InfoItem("_M_SSE", StringFromFormat("0x%x", _M_SSE))); #endif @@ -113,35 +117,36 @@ index 8daac5bc8..c0c09ce79 100644 ViewGroup *cpuExtensionsScroll = new ScrollView(ORIENT_VERTICAL, new LinearLayoutParams(FILL_PARENT, FILL_PARENT)); cpuExtensionsScroll->SetTag("DevSystemInfoCPUExt"); diff --git a/UI/GameSettingsScreen.cpp b/UI/GameSettingsScreen.cpp -index 2f1e157ee..38c586b06 100644 +index 393e33cd9..d07d00d45 100644 --- a/UI/GameSettingsScreen.cpp +++ b/UI/GameSettingsScreen.cpp -@@ -914,7 +914,6 @@ void GameSettingsScreen::CreateViews() { +@@ -922,8 +922,6 @@ void GameSettingsScreen::CreateViews() { } } #endif - systemSettings->Add(new CheckBox(&g_Config.bCheckForNewVersion, sy->T("VersionCheck", "Check for new versions of PPSSPP"))); - const std::string bgPng = GetSysDirectory(DIRECTORY_SYSTEM) + "background.png"; - const std::string bgJpg = GetSysDirectory(DIRECTORY_SYSTEM) + "background.jpg"; - if (File::Exists(bgPng) || File::Exists(bgJpg)) { +- + systemSettings->Add(new Choice(sy->T("Restore Default Settings")))->OnClick.Handle(this, &GameSettingsScreen::OnRestoreDefaultSettings); + systemSettings->Add(new CheckBox(&g_Config.bEnableStateUndo, sy->T("Savestate slot backups"))); + static const char *autoLoadSaveStateChoices[] = { "Off", "Oldest Save", "Newest Save", "Slot 1", "Slot 2", "Slot 3", "Slot 4", "Slot 5" }; diff --git a/UI/MainScreen.cpp b/UI/MainScreen.cpp -index ca870ab8f..84cde88ac 100644 +index f88509276..51b21b640 100644 --- a/UI/MainScreen.cpp +++ b/UI/MainScreen.cpp -@@ -1064,11 +1064,7 @@ void MainScreen::CreateViews() { +@@ -1080,11 +1080,7 @@ void MainScreen::CreateViews() { sprintf(versionString, "%s", PPSSPP_GIT_VERSION); rightColumnItems->SetSpacing(0.0f); AnchorLayout *logos = new AnchorLayout(new AnchorLayoutParams(FILL_PARENT, 60.0f, false)); - if (System_GetPropertyBool(SYSPROP_APP_GOLD)) { -- logos->Add(new ImageView(ImageID("I_ICONGOLD"), IS_DEFAULT, new AnchorLayoutParams(64, 64, 0, 0, NONE, NONE, false))); +- logos->Add(new ImageView(ImageID("I_ICONGOLD"), "", IS_DEFAULT, new AnchorLayoutParams(64, 64, 0, 0, NONE, NONE, false))); - } else { -- logos->Add(new ImageView(ImageID("I_ICON"), IS_DEFAULT, new AnchorLayoutParams(64, 64, 0, 0, NONE, NONE, false))); +- logos->Add(new ImageView(ImageID("I_ICON"), "", IS_DEFAULT, new AnchorLayoutParams(64, 64, 0, 0, NONE, NONE, false))); - } -+ logos->Add(new ImageView(ImageID("I_ICON"), IS_DEFAULT, new AnchorLayoutParams(64, 64, 0, 0, NONE, NONE, false))); - logos->Add(new ImageView(ImageID("I_LOGO"), IS_DEFAULT, new AnchorLayoutParams(180, 64, 64, -5.0f, NONE, NONE, false))); ++ logos->Add(new ImageView(ImageID("I_ICON"), "", IS_DEFAULT, new AnchorLayoutParams(64, 64, 0, 0, NONE, NONE, false))); + logos->Add(new ImageView(ImageID("I_LOGO"), "PPSSPP", IS_DEFAULT, new AnchorLayoutParams(180, 64, 64, -5.0f, NONE, NONE, false))); #if !defined(MOBILE_DEVICE) -@@ -1089,11 +1085,6 @@ void MainScreen::CreateViews() { +@@ -1107,11 +1103,6 @@ void MainScreen::CreateViews() { rightColumnItems->Add(new Choice(mm->T("Game Settings", "Settings")))->OnClick.Handle(this, &MainScreen::OnGameSettings); rightColumnItems->Add(new Choice(mm->T("Credits")))->OnClick.Handle(this, &MainScreen::OnCredits); rightColumnItems->Add(new Choice(mm->T("www.ppsspp.org")))->OnClick.Handle(this, &MainScreen::OnPPSSPPOrg); @@ -153,7 +158,7 @@ index ca870ab8f..84cde88ac 100644 #if !PPSSPP_PLATFORM(UWP) // Having an exit button is against UWP guidelines. -@@ -1118,32 +1109,6 @@ void MainScreen::CreateViews() { +@@ -1136,32 +1127,6 @@ void MainScreen::CreateViews() { } else if (tabHolder_->GetVisibility() != V_GONE) { root_->SetDefaultFocusView(tabHolder_); } @@ -186,7 +191,7 @@ index ca870ab8f..84cde88ac 100644 } UI::EventReturn MainScreen::OnAllowStorage(UI::EventParams &e) { -@@ -1151,30 +1116,6 @@ UI::EventReturn MainScreen::OnAllowStorage(UI::EventParams &e) { +@@ -1169,30 +1134,6 @@ UI::EventReturn MainScreen::OnAllowStorage(UI::EventParams &e) { return UI::EVENT_DONE; } @@ -217,7 +222,7 @@ index ca870ab8f..84cde88ac 100644 void MainScreen::sendMessage(const char *message, const char *value) { // Always call the base class method first to handle the most common messages. UIScreenWithBackground::sendMessage(message, value); -@@ -1390,15 +1331,6 @@ UI::EventReturn MainScreen::OnCredits(UI::EventParams &e) { +@@ -1396,15 +1337,6 @@ UI::EventReturn MainScreen::OnCredits(UI::EventParams &e) { return UI::EVENT_DONE; } @@ -234,10 +239,10 @@ index ca870ab8f..84cde88ac 100644 LaunchBrowser("https://www.ppsspp.org"); return UI::EVENT_DONE; diff --git a/UI/MiscScreens.cpp b/UI/MiscScreens.cpp -index a7284654b..2413d6c89 100644 +index 901a5fb09..9d067aee6 100644 --- a/UI/MiscScreens.cpp +++ b/UI/MiscScreens.cpp -@@ -539,11 +539,7 @@ void LogoScreen::render() { +@@ -661,11 +661,7 @@ void LogoScreen::render() { char temp[256]; // Manually formatting UTF-8 is fun. \xXX doesn't work everywhere. snprintf(temp, sizeof(temp), "%s Henrik Rydg%c%crd", cr->T("created", "Created by"), 0xC3, 0xA5); @@ -248,9 +253,9 @@ index a7284654b..2413d6c89 100644 - } + dc.Draw()->DrawImage(ImageID("I_ICON"), bounds.centerX() - 120, bounds.centerY() - 30, 1.2f, textColor, ALIGN_CENTER); dc.Draw()->DrawImage(ImageID("I_LOGO"), bounds.centerX() + 40, bounds.centerY() - 30, 1.5f, textColor, ALIGN_CENTER); - //dc.Draw()->DrawTextShadow(UBUNTU48, "PPSSPP", xres / 2, yres / 2 - 30, textColor, ALIGN_CENTER); + //dc.Draw()->DrawTextShadow(UBUNTU48, "PPSSPP", bounds.w / 2, bounds.h / 2 - 30, textColor, ALIGN_CENTER); dc.SetFontScale(1.0f, 1.0f); -@@ -579,10 +575,6 @@ void CreditsScreen::CreateViews() { +@@ -701,10 +697,6 @@ void CreditsScreen::CreateViews() { // Really need to redo this whole layout with some linear layouts... int rightYOffset = 0; @@ -261,14 +266,14 @@ index a7284654b..2413d6c89 100644 root_->Add(new Button(cr->T("PPSSPP Forums"), new AnchorLayoutParams(260, 64, 10, NONE, NONE, 158, false)))->OnClick.Handle(this, &CreditsScreen::OnForums); root_->Add(new Button(cr->T("Discord"), new AnchorLayoutParams(260, 64, 10, NONE, NONE, 232, false)))->OnClick.Handle(this, &CreditsScreen::OnDiscord); root_->Add(new Button("www.ppsspp.org", new AnchorLayoutParams(260, 64, 10, NONE, NONE, 10, false)))->OnClick.Handle(this, &CreditsScreen::OnPPSSPPOrg); -@@ -591,20 +583,7 @@ void CreditsScreen::CreateViews() { +@@ -713,20 +705,7 @@ void CreditsScreen::CreateViews() { #if PPSSPP_PLATFORM(ANDROID) || PPSSPP_PLATFORM(IOS) root_->Add(new Button(cr->T("Share PPSSPP"), new AnchorLayoutParams(260, 64, NONE, NONE, 10, rightYOffset + 158, false)))->OnClick.Handle(this, &CreditsScreen::OnShare); #endif - if (System_GetPropertyBool(SYSPROP_APP_GOLD)) { -- root_->Add(new ImageView(ImageID("I_ICONGOLD"), IS_DEFAULT, new AnchorLayoutParams(100, 64, 10, 10, NONE, NONE, false))); +- root_->Add(new ImageView(ImageID("I_ICONGOLD"), "", IS_DEFAULT, new AnchorLayoutParams(100, 64, 10, 10, NONE, NONE, false))); - } else { -- root_->Add(new ImageView(ImageID("I_ICON"), IS_DEFAULT, new AnchorLayoutParams(100, 64, 10, 10, NONE, NONE, false))); +- root_->Add(new ImageView(ImageID("I_ICON"), "", IS_DEFAULT, new AnchorLayoutParams(100, 64, 10, 10, NONE, NONE, false))); - } -} - @@ -279,11 +284,11 @@ index a7284654b..2413d6c89 100644 - LaunchBrowser("https://central.ppsspp.org/buygold"); -#endif - return UI::EVENT_DONE; -+ root_->Add(new ImageView(ImageID("I_ICON"), IS_DEFAULT, new AnchorLayoutParams(100, 64, 10, 10, NONE, NONE, false))); ++ root_->Add(new ImageView(ImageID("I_ICON"), "", IS_DEFAULT, new AnchorLayoutParams(100, 64, 10, 10, NONE, NONE, false))); } UI::EventReturn CreditsScreen::OnTwitter(UI::EventParams &e) { -@@ -794,11 +773,7 @@ void CreditsScreen::render() { +@@ -916,11 +895,7 @@ void CreditsScreen::render() { // TODO: This is kinda ugly, done on every frame... char temp[256]; @@ -297,10 +302,10 @@ index a7284654b..2413d6c89 100644 UIContext &dc = *screenManager()->getUIContext(); diff --git a/UWP/PPSSPP_UWPMain.cpp b/UWP/PPSSPP_UWPMain.cpp -index 0ba7fac4b..d1b687c47 100644 +index 29afda806..b7028fc0c 100644 --- a/UWP/PPSSPP_UWPMain.cpp +++ b/UWP/PPSSPP_UWPMain.cpp -@@ -433,12 +433,6 @@ bool System_GetPropertyBool(SystemProperty prop) { +@@ -426,12 +426,6 @@ bool System_GetPropertyBool(SystemProperty prop) { return false; case SYSPROP_HAS_BACK_BUTTON: return true; @@ -310,14 +315,14 @@ index 0ba7fac4b..d1b687c47 100644 -#else - return false; -#endif + case SYSPROP_CAN_JIT: + return true; default: - return false; - } diff --git a/Windows/MainWindowMenu.cpp b/Windows/MainWindowMenu.cpp -index 979a60ecb..a57927544 100644 +index c0d790e06..e8de4f956 100644 --- a/Windows/MainWindowMenu.cpp +++ b/Windows/MainWindowMenu.cpp -@@ -1393,7 +1393,7 @@ namespace MainWindow { +@@ -1395,7 +1395,7 @@ namespace MainWindow { { W32Util::CenterWindow(hDlg); HWND versionBox = GetDlgItem(hDlg, IDC_VERSION); @@ -327,10 +332,10 @@ index 979a60ecb..a57927544 100644 SetWindowText(versionBox, ConvertUTF8ToWString(windowText).c_str()); } diff --git a/Windows/main.cpp b/Windows/main.cpp -index 4d948cfe5..e609cc1e0 100644 +index ecfe18fa4..3261151d2 100644 --- a/Windows/main.cpp +++ b/Windows/main.cpp -@@ -301,12 +301,6 @@ bool System_GetPropertyBool(SystemProperty prop) { +@@ -304,12 +304,6 @@ bool System_GetPropertyBool(SystemProperty prop) { return true; case SYSPROP_HAS_BACK_BUTTON: return true; @@ -340,26 +345,43 @@ index 4d948cfe5..e609cc1e0 100644 -#else - return false; -#endif + case SYSPROP_CAN_JIT: + return true; default: - return false; - } diff --git a/android/jni/app-android.cpp b/android/jni/app-android.cpp -index 10fdf97e5..736b1fa66 100644 +index 2fad16224..8ed6dd9cd 100644 --- a/android/jni/app-android.cpp +++ b/android/jni/app-android.cpp -@@ -437,12 +437,6 @@ bool System_GetPropertyBool(SystemProperty prop) { +@@ -490,12 +490,6 @@ bool System_GetPropertyBool(SystemProperty prop) { case SYSPROP_HAS_FOLDER_BROWSER: // Uses OPEN_DOCUMENT_TREE to let you select a folder. - return androidVersion >= 21; + return androidVersion >= 21; // when ACTION_OPEN_DOCUMENT_TREE was added - case SYSPROP_APP_GOLD: -#ifdef GOLD - return true; -#else - return false; -#endif - default: - return false; - } + case SYSPROP_CAN_JIT: + return true; + case SYSPROP_ANDROID_SCOPED_STORAGE: +diff --git a/ios/main.mm b/ios/main.mm +index e53b7c7ab..fe69647ed 100644 +--- a/ios/main.mm ++++ b/ios/main.mm +@@ -148,12 +148,6 @@ bool System_GetPropertyBool(SystemProperty prop) { + switch (prop) { + case SYSPROP_HAS_BACK_BUTTON: + return false; +- case SYSPROP_APP_GOLD: +-#ifdef GOLD +- return true; +-#else +- return false; +-#endif + case SYSPROP_CAN_JIT: + return g_jitAvailable; + -- -2.30.1 +2.31.1 -- cgit 1.4.1 From 544a980f3acecefcf8d88a9f1f4b8537e275b35b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sat, 5 Jun 2021 20:40:23 -0400 Subject: gnu: czmq: Re-enable previously failing tests, fixed in 4.2.1. * gnu/packages/networking.scm (czmq)[phases]: Delete argument. --- gnu/packages/networking.scm | 15 +-------------- 1 file changed, 1 insertion(+), 14 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index ff28ad7233..d0bf86c0b8 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1058,20 +1058,7 @@ more.") "0fdclvd7fcwixp0k57ccv7d159v3slasyhvndxfn8n1a9hh0lwjx")))) (build-system gnu-build-system) (arguments - '(#:configure-flags '("--enable-drafts") - #:phases (modify-phases %standard-phases - (add-before 'check 'patch-tests - (lambda _ - (substitute* "src/czmq_selftest.c" - ;; Disable the zproc test, which fails on some hardware - ;; (see: https://github.com/zeromq/czmq/issues/2007). - (("\\{ \"zproc\", zproc_test.*") - "") - ;; Also disable the zarmour test, which fails as well - ;; (see: https://github.com/zeromq/czmq/issues/2125). - (("\\{ \"zarmour\", zarmour_test.*") - "")) - #t))))) + '(#:configure-flags '("--enable-drafts"))) (inputs `(("zeromq" ,zeromq))) (home-page "https://zeromq.org") -- cgit 1.4.1 From 876f4071ab4379875d4490c83d4c0ca19a4eb366 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 6 Jun 2021 01:12:55 -0400 Subject: gnu: libvpx: Update to 1.10.0. * gnu/packages/video.scm (libvpx): Update to 1.10.0. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index e01594fb28..7d072dd7ec 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2148,7 +2148,7 @@ To load this plugin, specify the following option when starting mpv: (define-public libvpx (package (name "libvpx") - (version "1.9.0") + (version "1.10.0") (source (origin (method git-fetch) (uri (git-reference @@ -2157,7 +2157,7 @@ To load this plugin, specify the following option when starting mpv: (file-name (git-file-name name version)) (sha256 (base32 - "16xv6ambc82g14h1y0q1vyy57wp6j9fbp0nk0wd5csnrw407rhry")) + "1p4v6j1505n3gnvx3iksciyi818ymxpazj9fmdrchzbl9pfzg4qi")) (patches (search-patches "libvpx-CVE-2016-2818.patch")))) (build-system gnu-build-system) (arguments -- cgit 1.4.1 From 7fd2c9a00e8f915d214a2831045c06f51995f62e Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 6 Jun 2021 02:19:51 -0400 Subject: gnu: msgpack: Update to 3.3.0. * gnu/packages/serialization.scm (msgpack): Update to 3.3.0. --- gnu/packages/serialization.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index 4ef74c2a7f..56847a5ddf 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -141,7 +141,7 @@ such as compact binary encodings, XML, or JSON.") (define-public msgpack (package (name "msgpack") - (version "3.2.1") + (version "3.3.0") (source (origin (method url-fetch) @@ -156,7 +156,7 @@ such as compact binary encodings, XML, or JSON.") (close-output-port p) #t)) (sha256 - (base32 "1ljqmgscdb0f8w8kx2lnswnisyxchcmijbjbmswkv0g187bvqg23")))) + (base32 "0yzhq50ijvwrfkr97knhvn54lj3f4hr3zy39yq8wpf6xll94s4bf")))) (build-system cmake-build-system) (native-inputs `(("googletest" ,googletest-1.8) -- cgit 1.4.1 From 36fd42ded23eb2c066a8b25b0f1567c2286b61c1 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sun, 6 Jun 2021 09:03:24 +0200 Subject: gnu: emacs-elfeed-score: Update to 0.7.9. * gnu/packages/emacs-xyz.scm (emacs-elfeed-score): Update to 0.7.9. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 773e484953..b85bf5f0d5 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -9862,7 +9862,7 @@ with Elfeed.") (define-public emacs-elfeed-score (package (name "emacs-elfeed-score") - (version "0.7.8") + (version "0.7.9") (source (origin (method git-fetch) @@ -9872,7 +9872,7 @@ with Elfeed.") (file-name (git-file-name name version)) (sha256 (base32 - "0lcpj2vp947kbfk6fq7xz7j71mcpjs9086pqh690w4mzv1253gra")))) + "17hf6b5db4d0cm1996z4sl00y4c8gl3rga97xxp2bmwbhdr7kaxw")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-elfeed" ,emacs-elfeed))) -- cgit 1.4.1 From 04beee1632a55963a05f227a6481e0912c390600 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sun, 6 Jun 2021 09:06:40 +0200 Subject: gnu: emacs-company-irony: Update to 1.1.1. * gnu/packages/emacs-xyz.scm (emacs-company-irony): Update to 1.1.1. [inputs]: Re-order alphabetically. [descrption]: Properly capitalize. --- gnu/packages/emacs-xyz.scm | 29 +++++++++++++++-------------- 1 file changed, 15 insertions(+), 14 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index b85bf5f0d5..1d954ec5bd 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6024,22 +6024,23 @@ described on the homepage.") (define-public emacs-company-irony (package (name "emacs-company-irony") - (version "1.1.0") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/Sarcasm/company-irony") - (commit (string-append "v" version)))) - (sha256 (base32 - "1qgyam2vyjw90kpxns5cd6bq3qiqjhzpwrlvmi18vyb69qcgqd8a")) - (file-name (git-file-name name version)))) + (version "1.1.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Sarcasm/company-irony") + (commit (string-append "v" version)))) + (sha256 + (base32 "1d3jw0d4zymznri86a5iixyxnw16jzkkrbhrh657ys73189c1c73")) + (file-name (git-file-name name version)))) (build-system emacs-build-system) (inputs - `(("emacs-irony-mode" ,emacs-irony-mode) - ("emacs-company" ,emacs-company))) - (synopsis "C++ completion backend for Company using irony-mode") - (description "This backend for company-mode allows for C++ code completion -with irony-mode using clang-tooling.") + `(("emacs-company" ,emacs-company) + ("emacs-irony-mode" ,emacs-irony-mode))) + (synopsis "C++ completion backend for Company using Irony mode") + (description "This backend for Company allows for C++ code completion +with Irony mode using Clang tooling.") (home-page "https://github.com/Sarcasm/company-irony") (license license:gpl3+))) -- cgit 1.4.1 From da28abcfb04d9a4911264d2921512b0ad5acf8e6 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Sun, 6 Jun 2021 09:43:59 +0200 Subject: gnu: sdrangel: Add SoapySDR support. * gnu/packages/radio.scm (sdrangel)[inputs]: Add soapysdr. [arguments]: Update 'configure-flags'. --- gnu/packages/radio.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index a7e9de3707..b3a6aceaff 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -1947,6 +1947,7 @@ voice formats.") ("qtwebsockets" ,qtwebsockets) ("rtl-sdr" ,rtl-sdr) ("serialdv" ,serialdv) + ("soapysdr" ,soapysdr) ("sgp4" ,sgp4) ("zlib" ,zlib))) (arguments @@ -1963,7 +1964,9 @@ voice formats.") (string-append "-DSERIALDV_DIR=" (assoc-ref %build-inputs "serialdv")) (string-append "-DSGP4_DIR=" - (assoc-ref %build-inputs "sgp4"))))) + (assoc-ref %build-inputs "sgp4")) + (string-append "-DSOAPYSDR_DIR=" + (assoc-ref %build-inputs "soapysdr"))))) (home-page "https://github.com/f4exb/sdrangel/wiki") (synopsis "Software defined radio") (description -- cgit 1.4.1 From 1fd8819fac313d99c06f07477076be2d66e06a92 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 6 Jun 2021 10:53:46 +0300 Subject: gnu: poke: Update to 1.3. * gnu/packages/engineering.scm (poke): Update to 1.3. --- gnu/packages/engineering.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index 5a97d25b27..981dd9e5e3 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -2745,14 +2745,14 @@ GUI.") (define-public poke (package (name "poke") - (version "1.2") + (version "1.3") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/poke/poke-" version ".tar.gz")) (sha256 (base32 - "0qnz7lc681nxa16rw9n9q4spy9fas6m2adrpb49imh34bgdgh77n")))) + "06qgry1pal2vampmbmc1lzlhf1qnjkd8py781r5h020v981n6y5s")))) (build-system gnu-build-system) ;; The GUI, which we elide, requires tcl and tk. (native-inputs `(;; Requires bison 3.6+ but we currently only have 3.5. -- cgit 1.4.1 From b65c02e2d35af6fbe1d1810d6c69cfab194e13e2 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 6 Jun 2021 12:07:01 +0300 Subject: gnu: freebayes: Update to 1.3.5. * gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.5. [source]: Remove patch. [arguments]: Adjust custom 'patch-source phase for changes in source. [inputs]: Remove zlib. * gnu/packages/patches/freebayes-devendor-deps.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 16 +-- gnu/packages/patches/freebayes-devendor-deps.patch | 152 --------------------- 3 files changed, 7 insertions(+), 162 deletions(-) delete mode 100644 gnu/packages/patches/freebayes-devendor-deps.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 1c692e0ce4..153f6ee8d7 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1019,7 +1019,6 @@ dist_patch_DATA = \ %D%/packages/patches/fpc-reproducibility.patch \ %D%/packages/patches/fplll-std-fenv.patch \ %D%/packages/patches/freedink-engine-fix-sdl-hints.patch \ - %D%/packages/patches/freebayes-devendor-deps.patch \ %D%/packages/patches/freeimage-unbundle.patch \ %D%/packages/patches/fuse-overlapping-headers.patch \ %D%/packages/patches/gajim-honour-GAJIM_PLUGIN_PATH.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2de8a59d3c..1e38c6e0e7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13572,7 +13572,7 @@ manipulations on VCF files.") (define-public freebayes (package (name "freebayes") - (version "1.3.3") + (version "1.3.5") (source (origin (method git-fetch) (uri (git-reference @@ -13580,8 +13580,7 @@ manipulations on VCF files.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0myz3giad7jqp6ricdfnig9ymlcps2h67mlivadvx97ngagm85z8")) - (patches (search-patches "freebayes-devendor-deps.patch")) + (base32 "1l0z88gq57kva677a6xri5g9k2d9h9lk5yk1q2xmq64wqhv7dvc3")) (modules '((guix build utils))) (snippet '(begin @@ -13593,8 +13592,7 @@ manipulations on VCF files.") ("htslib" ,htslib) ("smithwaterman" ,smithwaterman) ("tabixpp" ,tabixpp) - ("vcflib" ,vcflib) - ("zlib" ,zlib))) + ("vcflib" ,vcflib))) (native-inputs `(("bash-tap" ,bash-tap) ("bc" ,bc) @@ -13627,13 +13625,13 @@ manipulations on VCF files.") (string-append bash-tap "/bin/bash-tap-bootstrap")) (("source.*bash-tap-bootstrap") (string-append "source " bash-tap "/bin/bash-tap-bootstrap"))) - (substitute* "meson.build" - ;; Some inputs aren't actually needed. - ((".*bamtools/src.*") "") - ((".*multichoose.*") "")) (substitute* '("src/BedReader.cpp" "src/BedReader.h") (("../intervaltree/IntervalTree.h") "IntervalTree.h")) + (substitute* "meson.build" + ;; Our pkg-config file is vcflib.pc + (("libvcflib") "vcflib") + (("vcflib_inc,") "")) #t))) (add-after 'unpack 'unpack-submodule-sources (lambda* (#:key inputs #:allow-other-keys) diff --git a/gnu/packages/patches/freebayes-devendor-deps.patch b/gnu/packages/patches/freebayes-devendor-deps.patch deleted file mode 100644 index 9886de11fb..0000000000 --- a/gnu/packages/patches/freebayes-devendor-deps.patch +++ /dev/null @@ -1,152 +0,0 @@ -This patch is original to Guix, ongoing work to upstream bits as possible. - -From 9acc56db5e7469f5976be38b52ba4993de98ee38 Mon Sep 17 00:00:00 2001 -From: Efraim Flashner -Date: Sun, 17 Jan 2021 13:27:17 +0200 -Subject: [PATCH] devendor-dependants - ---- - meson.build | 84 +++++++++++++++++++++++++++++++++++++++++------------ - 1 file changed, 66 insertions(+), 18 deletions(-) - -diff --git a/meson.build b/meson.build -index f6bf242..bded4af 100644 ---- a/meson.build -+++ b/meson.build -@@ -9,8 +9,13 @@ project('freebayes', ['cpp', 'c'], - - zlib_dep = dependency('zlib') - lzma_dep = dependency('liblzma') -+simde_dep = dependency('simde') - bzip2_dep = dependency('bz2lib', required: false) - htslib_dep = dependency('htslib', required : false) -+tabixpp_dep = dependency('tabixpp', required : false) -+fastahack_dep = dependency('fastahack', required : false) -+smithwaterman_dep = dependency('smithwaterman', required : false) -+vcflib_dep = dependency('vcflib', required: false) - thread_dep = dependency('threads') - - if htslib_dep.found() -@@ -59,6 +64,56 @@ else - ] - endif - -+if tabixpp_dep.found() -+ tabixpp_includes = '' -+ tabixpp_src = [] -+else -+ tabixpp_includes = [ -+ 'vcflib/tabixpp', -+ ] -+ tabixpp_src = [ -+ 'vcflib/tabixpp/tabix.cpp', -+ ] -+endif -+ -+if vcflib_dep.found() -+ vcflib_includes = '' -+ vcflib_src = [] -+else -+ vcflib_includes = [ -+ 'vcflib/src', -+ 'vcflib/multichoose', -+ 'vcflib/filevercmp', -+ ] -+ vcflib_src = [ -+ 'vcflib/src/Variant.cpp', -+ ] -+endif -+ -+if fastahack_dep.found() -+ fastahack_src = [] -+else -+ fastahack_src = [ -+ 'vcflib/fastahack/Fasta.cpp', -+ 'vcflib/src/split.cpp', -+ ] -+endif -+ -+if smithwaterman_dep.found() -+ smithwaterman_includes = '' -+ smithwaterman_src = [] -+else -+ smithwaterman_includes = [ -+ 'vcflib/smithwaterman', -+ ] -+ smithwaterman_src = [ -+ 'vcflib/smithwaterman/SmithWatermanGotoh.cpp', -+ 'vcflib/smithwaterman/disorder.cpp', -+ 'vcflib/smithwaterman/Repeats.cpp', -+ 'vcflib/smithwaterman/LeftAlign.cpp', -+ 'vcflib/smithwaterman/IndelAllele.cpp', -+ ] -+endif - - - # -@@ -105,23 +160,18 @@ seqlib_src = [ - ] - - vcflib_src = [ -- 'vcflib/tabixpp/tabix.cpp', -- 'vcflib/src/Variant.cpp', -- 'vcflib/smithwaterman/SmithWatermanGotoh.cpp', -- 'vcflib/smithwaterman/disorder.cpp', -- 'vcflib/smithwaterman/Repeats.cpp', -- 'vcflib/smithwaterman/LeftAlign.cpp', -- 'vcflib/smithwaterman/IndelAllele.cpp', -+ vcflib_src, -+ tabixpp_src, -+ smithwaterman_src, - ] - - bamleftalign_src = [ - 'src/bamleftalign.cpp', - 'src/IndelAllele.cpp', - 'contrib/SeqLib/src/BamWriter.cpp', -- 'vcflib/fastahack/Fasta.cpp', -- 'vcflib/smithwaterman/LeftAlign.cpp', -- 'vcflib/smithwaterman/IndelAllele.cpp', -- 'vcflib/src/split.cpp', -+ fastahack_src, -+ smithwaterman_src, -+ vcflib_src, - 'src/LeftAlign.cpp', - ] - -@@ -134,11 +184,9 @@ incdir = include_directories( - 'ttmath', - 'contrib', - 'contrib/SeqLib', -- 'vcflib/src', -- 'vcflib/tabixpp', -- 'vcflib/smithwaterman', -- 'vcflib/multichoose', -- 'vcflib/filevercmp') -+ tabixpp_includes, -+ smithwaterman_includes, -+ vcflib_includes) - - c_args = ['-fpermissive','-w'] - cpp_args = ['-fpermissive','-w','-Wc++14-compat'] -@@ -152,7 +200,7 @@ executable('freebayes', - include_directories : incdir, - cpp_args : cpp_args, - c_args : c_args, -- dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep], -+ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, smithwaterman_dep, vcflib_dep, thread_dep], - install: true - ) - -@@ -165,7 +213,7 @@ executable('bamleftalign', - include_directories : incdir, - cpp_args : cpp_args, - c_args : c_args, -- dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep], -+ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, fastahack_dep, smithwaterman_dep, vcflib_dep, thread_dep], - install: true - ) - --- -2.30.0 - -- cgit 1.4.1 From db8ea15ba0bea3ec48d733baf8b430aa5d655535 Mon Sep 17 00:00:00 2001 From: Jonathan Brielmaier Date: Sun, 6 Jun 2021 11:13:35 +0200 Subject: gnu: icedove-wayland: Refactor as a wrapper around icedove. This saves us a full build of icedove-wayland analogue to chromium-wayland. * gnu/packages/gnuzilla.scm (icedove-wayland)[inputs]: Add bash and icedove. [arguments]: Copy the binary over and wrap it for Wayland. As well as the desktop-file and the license file. --- gnu/packages/gnuzilla.scm | 49 +++++++++++++++++++++++++++++++---------------- 1 file changed, 32 insertions(+), 17 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index ab4c9ac193..c63809c20c 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -1618,25 +1618,40 @@ Thunderbird. It supports email, news feeds, chat, calendar and contacts.") (license license:mpl2.0))) (define-public icedove/wayland - (package/inherit icedove + (package + (inherit icedove) (name "icedove-wayland") + (native-inputs '()) + (inputs + `(("bash" ,bash-minimal) + ("icedove" ,icedove))) + (build-system trivial-build-system) (arguments - (substitute-keyword-arguments (package-arguments icedove) - ((#:phases phases) - `(modify-phases ,phases - (replace 'wrap-program - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (lib (string-append out "/lib")) - (gtk (assoc-ref inputs "gtk+")) - (gtk-share (string-append gtk "/share")) - (pulseaudio (assoc-ref inputs "pulseaudio")) - (pulseaudio-lib (string-append pulseaudio "/lib"))) - (wrap-program (car (find-files lib "^icedove$")) - `("MOZ_ENABLE_WAYLAND" = ("1")) - `("XDG_DATA_DIRS" prefix (,gtk-share)) - `("LD_LIBRARY_PATH" prefix (,pulseaudio-lib))) - #t))))))))) + '(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((bash (assoc-ref %build-inputs "bash")) + (icedove (assoc-ref %build-inputs "icedove")) + (out (assoc-ref %outputs "out")) + (exe (string-append out "/bin/icedove"))) + (mkdir-p (dirname exe)) + + (call-with-output-file exe + (lambda (port) + (format port "#!~a + MOZ_ENABLE_WAYLAND=1 exec ~a $@" + (string-append bash "/bin/bash") + (string-append icedove "/bin/icedove")))) + (chmod exe #o555) + + ;; Provide the manual and .desktop file. + (copy-recursively (string-append icedove "/share") + (string-append out "/share")) + (substitute* (string-append + out "/share/applications/icedove.desktop") + ((icedove) out)) + #t)))))) (define-public firefox-decrypt (package -- cgit 1.4.1 From ed057e33a559b4d3f89c88c6b6d60cd811579069 Mon Sep 17 00:00:00 2001 From: Solene Rapenne Date: Sun, 6 Jun 2021 00:00:23 +0200 Subject: gnu: tig: Update to 2.5.4. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/version-control.scm (tig): Update to 2.5.4. Signed-off-by: 宋文武 --- gnu/packages/version-control.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index cd262402c1..4156c97cea 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -2280,7 +2280,7 @@ from Subversion to any supported Distributed Version Control System (DVCS).") (define-public tig (package (name "tig") - (version "2.5.3") + (version "2.5.4") (source (origin (method url-fetch) (uri (string-append @@ -2288,7 +2288,7 @@ from Subversion to any supported Distributed Version Control System (DVCS).") version "/tig-" version ".tar.gz")) (sha256 (base32 - "1p1575yh4daxjifywxkd0hgyfwciylqcm2qakawvwn6mk620ca75")))) + "19va4jn46s0vjv9f337g3ad6hy1f285ynl27i9gkd9l70b9q90n4")))) (build-system gnu-build-system) (native-inputs `(("asciidoc" ,asciidoc) -- cgit 1.4.1 From 77056478a2de22db6613d24ed37f7496afba42db Mon Sep 17 00:00:00 2001 From: Domagoj Stolfa Date: Mon, 24 May 2021 21:11:55 +0100 Subject: gnu: strongswan: Configure more sensible defaults. * gnu/packages/networking.scm (strongswan)[arguments]<#:configure-flags>: Enable aesni, attr-sql, chapoly, curl, dhcp, eap-aka, eap-aka-3gpp, eap-dynamic, eap-identity, eap-md5, eap-mschapv2, eap-peap, eap-radius, eap-sim, eap-sim-file, eap-simaka-pseudonym, eap-simaka-reauth, eap-simaka-sql, eap-tls, eap-tnc, eap-ttls, ext-auth, farp, ha, led, md4, mediation, openssl, soup, sql, sqlite, xauth-eap, xauth-noauth, and xauth-pam support. Disable ldap, mysql, and systemd support. Use libcap by default. [inputs]: Add libcap, libsoup, and linux-pam. [native-inputs]: Add pkg-config. Signed-off-by: Tobias Geerinckx-Rice --- gnu/packages/networking.scm | 53 +++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 51 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index d0bf86c0b8..82c7a0161a 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2881,16 +2881,65 @@ displays the results in real time.") #t))) #:configure-flags (list - ;; Disable bsd-4 licensed plugins. + "--disable-ldap" + "--disable-mysql" + "--disable-systemd" + + ;; Disable BSD-4 licensed plugins. + "--disable-blowfish" "--disable-des" - "--disable-blowfish"))) + + ;; Make it usable. The default configuration is far too minimal to be + ;; used with most common VPN set-ups. + ;; See . + "--enable-aesni" + "--enable-attr-sql" + "--enable-chapoly" + "--enable-curl" + "--enable-dhcp" + "--enable-eap-aka" + "--enable-eap-aka-3gpp" + "--enable-eap-dynamic" + "--enable-eap-identity" + "--enable-eap-md5" + "--enable-eap-mschapv2" + "--enable-eap-peap" + "--enable-eap-radius" + "--enable-eap-sim" + "--enable-eap-sim-file" + "--enable-eap-simaka-pseudonym" + "--enable-eap-simaka-reauth" + "--enable-eap-simaka-sql" + "--enable-eap-tls" + "--enable-eap-tnc" + "--enable-eap-ttls" + "--enable-ext-auth" + "--enable-farp" + "--enable-ha" + "--enable-led" + "--enable-md4" + "--enable-mediation" + "--enable-openssl" + "--enable-soup" + "--enable-sql" + "--enable-sqlite" + "--enable-xauth-eap" + "--enable-xauth-noauth" + "--enable-xauth-pam" + + ;; Use libcap by default. + "--with-capabilities=libcap"))) (inputs `(("curl" ,curl) ("gmp" ,gmp) + ("libcap" ,libcap) ("libgcrypt" ,libgcrypt) + ("libsoup" ,libsoup) + ("linux-pam" ,linux-pam) ("openssl" ,openssl))) (native-inputs `(("coreutils" ,coreutils) + ("pkg-config" ,pkg-config) ("tzdata" ,tzdata-for-tests))) (synopsis "IKEv1/v2 keying daemon") (description "StrongSwan is an IPsec implementation originally based upon -- cgit 1.4.1 From b6affc5c0466e801224db4400bb62ccc26cd5346 Mon Sep 17 00:00:00 2001 From: Matthew James Kraai Date: Sun, 6 Jun 2021 06:47:10 -0700 Subject: gnu: xterm: Update to 367. * gnu/packages/xorg.scm (xterm): Update to 367. Signed-off-by: Tobias Geerinckx-Rice --- gnu/packages/xorg.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 34d7997550..db058c697b 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -27,6 +27,7 @@ ;;; Copyright © 2020 Maxim Cournoyer ;;; Copyright © 2020 Jean-Baptiste Note ;;; Copyright © 2021 Nicolò Balzarotti +;;; Copyright © 2021 Matthew James Kraai ;;; ;;; This file is part of GNU Guix. ;;; @@ -6092,7 +6093,7 @@ to answer a question. Xmessage can also exit after a specified time.") (define-public xterm (package (name "xterm") - (version "366") + (version "367") (source (origin (method url-fetch) @@ -6102,7 +6103,7 @@ to answer a question. Xmessage can also exit after a specified time.") (string-append "ftp://ftp.invisible-island.net/xterm/" "xterm-" version ".tgz"))) (sha256 - (base32 "0vmzffy3hzgcgwx305h07ars5sxsq6nnl1ir4xqpxs9zjs2ji2w5")))) + (base32 "07y51l06n344pjyxdddq6sdvxw25nl10irl4avynkqjnqyqsiw97")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("--enable-wide-chars" "--enable-load-vt-fonts" -- cgit 1.4.1 From db6ff6da1588a84bdc02dfc8eccd59a885b46fde Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 6 Jun 2021 16:15:29 +0200 Subject: gnu: xf86-input-libinput: Fix licence information. * gnu/packages/xorg.scm (xf86-input-libinput)[license]: This package is almost exclusively expat, with a single x11 file that's not installed. --- gnu/packages/xorg.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index db058c697b..8ab77d521d 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -2555,7 +2555,8 @@ including most mice, keyboards, tablets and touchscreens.") "xf86-input-libinput is an input driver for the Xorg X server based on libinput. It is a thin wrapper around libinput, so while it does provide all features that libinput supports it does little beyond.") - (license license:x11))) + (license (list license:x11 ; only install-sh + license:expat)))) ; everything else (define-public xf86-input-joystick (package -- cgit 1.4.1 From b2122b07dc24007263b92247cc479713c2101390 Mon Sep 17 00:00:00 2001 From: Matthew James Kraai Date: Sun, 6 Jun 2021 06:42:49 -0700 Subject: gnu: xf86-input-libinput: Update to 1.0.1. * gnu/packages/xorg.scm (xf86-input-libinput): Update to 1.0.1. Signed-off-by: Tobias Geerinckx-Rice --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 8ab77d521d..9156fb3163 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -2530,7 +2530,7 @@ including most mice, keyboards, tablets and touchscreens.") (define-public xf86-input-libinput (package (name "xf86-input-libinput") - (version "0.30.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (string-append @@ -2538,7 +2538,7 @@ including most mice, keyboards, tablets and touchscreens.") name "-" version ".tar.bz2")) (sha256 (base32 - "1h4np66p87jf0c85ig524w8f5rbhl5gx8fww1qg0c55f87yzkizr")))) + "0nr4r9x8c7y1l0ipivjch5zps093mxmg2nqmfn2934am26fc9ppx")))) (build-system gnu-build-system) (arguments '(#:configure-flags -- cgit 1.4.1 From b477a9f42e52cf07e05add0632bc01e9d268dd55 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:22:44 +0000 Subject: gnu: ocaml-integers: Update to 0.4.0. * gnu/packages/ocaml.scm (ocaml-integers): Update to 0.4.0. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 29 ++++++++++------------------- 1 file changed, 10 insertions(+), 19 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 272f5bf268..b297a5202e 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -17,7 +17,7 @@ ;;; Copyright © 2020 Marius Bakke ;;; Copyright © 2020 Simon Tournier ;;; Copyright © 2020 divoplade -;;; Copyright © 2020 pukkamustard +;;; Copyright © 2020, 2021 pukkamustard ;;; Copyright © 2021 aecepoglu ;;; Copyright © 2021 Sharlatan Hellseher ;;; @@ -3809,29 +3809,20 @@ sensitive completion, colors, and more.") (define-public ocaml-integers (package (name "ocaml-integers") - (version "0.3.0") + (version "0.4.0") (home-page "https://github.com/ocamllabs/ocaml-integers") (source (origin - (method url-fetch) - (uri (string-append home-page - "/releases/download/v0.2.2/integers-" - version ".tbz")) - (file-name (string-append name "-" version ".tbz")) + (method git-fetch) + (uri (git-reference + (url home-page) + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "08b1ljw88ny3l0mdq6xmffjk8anfc77igryva5jz1p6f4f746ywk")))) - (build-system ocaml-build-system) + "0yp3ab0ph7mp5741g7333x4nx8djjvxzpnv3zvsndyzcycspn9dd")))) + (build-system dune-build-system) (arguments - `(#:tests? #f; no tests - #:build-flags (list "build") - #:phases - (modify-phases %standard-phases - (delete 'configure)))) - (native-inputs - `(("ocamlbuild" ,ocamlbuild))) - (inputs - `(("topkg" ,ocaml-topkg) - ("opam" ,opam))) + `(#:tests? #f)) ; no tests (synopsis "Various signed and unsigned integer types for OCaml") (description "The ocaml-integers library provides a number of 8-, 16-, 32- and 64-bit signed and unsigned integer types, together with aliases such as -- cgit 1.4.1 From 0f62ea0774fee735a97b63a1d2dc9397cc21908b Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:22:45 +0000 Subject: gnu: ocaml-ctypes: Update to 0.18.0. * gnu/packages/ocaml.scm (ocaml-ctypes): Update to 0.18.0. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index b297a5202e..cf31c2eae7 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -3832,7 +3832,7 @@ long and size_t whose sizes depend on the host platform.") (define-public ocaml-ctypes (package (name "ocaml-ctypes") - (version "0.14.0") + (version "0.18.0") (home-page "https://github.com/ocamllabs/ocaml-ctypes") (source (origin (method git-fetch) @@ -3842,7 +3842,7 @@ long and size_t whose sizes depend on the host platform.") (file-name (git-file-name name version)) (sha256 (base32 - "1b2q3h63ngf4x9qp65qwapf2dg9q0mcdah6qjm2q0c7v2p5vysv9")))) + "03zrbnl16m67ls0yfhq7a4k4238x6x6b3m456g4dw2yqwc153vks")))) (build-system ocaml-build-system) (arguments `(#:tests? #f; require an old lwt @@ -3861,6 +3861,8 @@ long and size_t whose sizes depend on the host platform.") (delete 'configure)))) (native-inputs `(("pkg-config" ,pkg-config))) + (propagated-inputs + `(("bigarray-compat" ,ocaml-bigarray-compat))) (inputs `(("libffi" ,libffi) ("ounit" ,ocaml-ounit) -- cgit 1.4.1 From 5a4acc53311c7013a2afeb5ce7460e2aa24a4c2b Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:22:46 +0000 Subject: gnu: ocaml-ctypes: Make ocaml-integers a propagated input. * gnu/packages/ocaml.scm (ocaml-ctypes)[propagated-inputs]: Add ocaml-integers. [inputs]: Remove ocaml-integers. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index cf31c2eae7..9e163994d9 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -3862,11 +3862,11 @@ long and size_t whose sizes depend on the host platform.") (native-inputs `(("pkg-config" ,pkg-config))) (propagated-inputs - `(("bigarray-compat" ,ocaml-bigarray-compat))) + `(("bigarray-compat" ,ocaml-bigarray-compat) + ("integers" ,ocaml-integers))) (inputs `(("libffi" ,libffi) ("ounit" ,ocaml-ounit) - ("integers" ,ocaml-integers) ("lwt" ,ocaml-lwt) ("topkg" ,ocaml-topkg) ("opam" ,opam))) -- cgit 1.4.1 From 0f5f8d48f8aadf3778cd967c522c06352f260c21 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:22:47 +0000 Subject: gnu: ocaml-lwt: Make libev a propagated input. * gnu/packages/ocaml.scm (ocaml-lwt) [propagated-inputs]: Add libev. [inputs]: Remove libev. (ocaml-ouint2, ocaml4.07-lambda-term, ocaml-markup) [inputs]: Remove libev. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 9e163994d9..1f47eab52e 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -1341,9 +1341,6 @@ compilers that can directly deal with packages.") (base32 "0gxjw1bhmjcjzri6x6psqrkbbyq678b69bqfl9i1zswp7cj2lryg")))) (build-system dune-build-system) - (inputs - ;; XXX Should libev be a propagated-input of ocaml-lwt? - `(("libev" ,libev))) (propagated-inputs `(("lwt" ,ocaml-lwt) ("ocaml-stdlib-shims" ,ocaml-stdlib-shims))) @@ -2317,13 +2314,13 @@ for mapping files in memory. This function is the same as the ("ocaml-cppo" ,ocaml-cppo) ("pkg-config" ,pkg-config))) (inputs - `(("libev" ,libev) - ("glib" ,glib))) + `(("glib" ,glib))) (propagated-inputs `(("ocaml-mmap" ,ocaml-mmap) ("ocaml-ocplib-endian" ,ocaml-ocplib-endian) ("ocaml-result" ,ocaml-result) - ("ocaml-seq" ,ocaml-seq))) + ("ocaml-seq" ,ocaml-seq) + ("libev" ,libev))) (home-page "https://github.com/ocsigen/lwt") (synopsis "Cooperative threads and I/O in monadic style") (description "Lwt provides typed, composable cooperative threads. These @@ -3760,8 +3757,6 @@ connect an engine to your inputs and rendering functions to get an editor.") ("ocaml-lwt-log" ,(package-with-ocaml4.07 ocaml-lwt-log)) ("ocaml-lwt-react" ,(package-with-ocaml4.07 ocaml-lwt-react)) ("ocaml-zed" ,ocaml4.07-zed))) - (inputs - `(("libev" ,libev))) (home-page "https://github.com/diml/lambda-term") (synopsis "Terminal manipulation library for OCaml") (description "Lambda-Term is a cross-platform library for manipulating the @@ -6010,8 +6005,6 @@ the full Core is not available, such as in Javascript.") (build-system dune-build-system) (arguments `(#:package "markup")) - (inputs - `(("libev" ,libev))) (propagated-inputs `(("ocaml-bisect-ppx" ,ocaml-bisect-ppx) ("ocaml-uchar" ,ocaml-uchar) -- cgit 1.4.1 From b3bc7489c678ad1f86097cce869cc7260c39a09c Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:22:48 +0000 Subject: gnu: ocaml-lwt: Update to 5.4.0. * gnu/packages/ocaml.scm (ocaml-lwt): Update to 5.4.0. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 1f47eab52e..d160c78d1b 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -2296,7 +2296,7 @@ for mapping files in memory. This function is the same as the (define-public ocaml-lwt (package (name "ocaml-lwt") - (version "5.1.1") + (version "5.4.0") (source (origin (method git-fetch) @@ -2305,7 +2305,7 @@ for mapping files in memory. This function is the same as the (commit version))) (file-name (git-file-name name version)) (sha256 (base32 - "1nl7rdnwfdhwcsm5zpay1nr9y5cbapd9x1qzily7zk9ab4v52m8g")))) + "1ay1zgadnw19r9hl2awfjr22n37l7rzxd9v73pjbahavwm2ay65d")))) (build-system dune-build-system) (arguments `(#:package "lwt")) -- cgit 1.4.1 From 99ed037081513909e0317f6e576860d83110ddca Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:22:49 +0000 Subject: gnu: ocaml4.07-gen: Update to 0.5.3. * gnu/packages/ocaml.scm (ocaml4.07-gen): Update to 4.07. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index d160c78d1b..5ebe942d23 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -2510,7 +2510,7 @@ representation of the data.") (define-public ocaml4.07-gen (package (name "ocaml4.07-gen") - (version "0.5.2") + (version "0.5.3") (source (origin (method git-fetch) (uri (git-reference @@ -2519,7 +2519,7 @@ representation of the data.") (file-name (git-file-name name version)) (sha256 (base32 - "1h9g508rnj2j8va5nvhamzscp954vrkh0hdf4pn3d10pcfyslfg2")))) + "1jzrs0nsdk55annkd2zrk5svi61i3b1nk6qyqdc2y26vnzqvzfg8")))) (build-system dune-build-system) (arguments `(#:tests? #f; no tests -- cgit 1.4.1 From 4b6e1fba5a3cb6c22552053dd336f2a76f0aa4d4 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:22:50 +0000 Subject: gnu: Add ocaml-gen. * gnu/packages/ocaml.scm (ocaml-gen): New variable. (ocaml4.07-gen): Remove variable. (ocaml4.07-sedlex): Replace ocaml4.07-gen with ocaml-gen. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 5ebe942d23..23606f1e9d 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -2507,9 +2507,9 @@ format. It can process XML documents without a complete in-memory representation of the data.") (license license:isc))) -(define-public ocaml4.07-gen +(define-public ocaml-gen (package - (name "ocaml4.07-gen") + (name "ocaml-gen") (version "0.5.3") (source (origin (method git-fetch) @@ -2522,16 +2522,13 @@ representation of the data.") "1jzrs0nsdk55annkd2zrk5svi61i3b1nk6qyqdc2y26vnzqvzfg8")))) (build-system dune-build-system) (arguments - `(#:tests? #f; no tests - #:package "gen" - #:ocaml ,ocaml-4.07 - #:findlib ,ocaml4.07-findlib - #:dune ,ocaml4.07-dune)) + `(#:package "gen" + #:test-target ".")) (propagated-inputs - `(("ocaml-odoc" ,(package-with-ocaml4.07 ocaml4.07-odoc)))) + `(("ocaml-odoc" ,ocaml-odoc))) (native-inputs - `(("ocaml-qtest" ,(package-with-ocaml4.07 ocaml-qtest)) - ("ocaml-qcheck" ,(package-with-ocaml4.07 ocaml-qcheck)))) + `(("ocaml-qtest" ,ocaml-qtest) + ("ocaml-qcheck" ,ocaml-qcheck))) (home-page "https://github.com/c-cube/gen/") (synopsis "Iterators for OCaml, both restartable and consumable") (description "Gen implements iterators of OCaml, that are both restartable @@ -2576,7 +2573,7 @@ and consumable.") (native-inputs `(("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild)))) (propagated-inputs - `(("ocaml-gen" ,ocaml4.07-gen) + `(("ocaml-gen" ,(package-with-ocaml4.07 ocaml-gen)) ("ocaml-ppx-tools-versioned" ,(package-with-ocaml4.07 ocaml-ppx-tools-versioned)) ("ocaml-uchar" ,(package-with-ocaml4.07 ocaml-uchar)))) -- cgit 1.4.1 From 8f5aa879de8d9d94c9c590e2ac128f84b53beac8 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:22:51 +0000 Subject: gnu: Add ocaml-stdio. * gnu/packages/ocaml.scm (ocaml-stdio): New variable. (ocaml4.07-stdio): Inherit from ocaml-stdio. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 58 +++++++++++++++++++++++++------------------------- 1 file changed, 29 insertions(+), 29 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 23606f1e9d..dbb34cbe78 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -1977,7 +1977,7 @@ library.") #:dune ,ocaml4.07-dune)) (native-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-stdio" ,ocaml4.07-stdio) + ("ocaml-stdio" ,(package-with-ocaml4.07 ocaml-stdio)) ("pkg-config" ,pkg-config))) (inputs `(("sqlite" ,sqlite))) @@ -4085,7 +4085,7 @@ syntax checking on dedukti files.") ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) ("ocaml-compiler-libs" ,ocaml4.07-compiler-libs) ("ocaml-sexplib0" ,(package-with-ocaml4.07 ocaml-sexplib0)) - ("ocaml-stdio" ,ocaml4.07-stdio) + ("ocaml-stdio" ,(package-with-ocaml4.07 ocaml-stdio)) ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) (properties `((upstream-name . "ppx_inline_test"))) (synopsis "Syntax extension for writing in-line tests in ocaml code") @@ -4428,7 +4428,7 @@ Atom.") `(("gsl" ,gsl))) (propagated-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-stdio" ,ocaml4.07-stdio))) + ("ocaml-stdio" ,(package-with-ocaml4.07 ocaml-stdio)))) (home-page "https://mmottl.github.io/gsl-ocaml") (synopsis "Bindings to the GNU Scientific Library") (description @@ -4713,30 +4713,20 @@ so they don't expose everything at toplevel. For instance, @code{Ast_helper} is now @code{Ocaml_common.Ast_helper}.") (license license:expat))) -(define-public ocaml4.07-stdio +(define-public ocaml-stdio (package - (name "ocaml4.07-stdio") - (version "0.11.0") + (name "ocaml-stdio") + (version "0.14.0") (home-page "https://github.com/janestreet/stdio") (source - (origin - (method git-fetch) - (uri (git-reference - (url (string-append home-page ".git")) - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1facajqhvq34g2wrg368y0ajxd6lrj5b3lyzyj0jhdmraxajjcwn")))) + (janestreet-origin "stdio" version + "1hj5hraprqy2i90a690l11yjszvb99j818q3d684ryx6p2lddk0l")) (build-system dune-build-system) (propagated-inputs - `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-sexplib0" ,(package-with-ocaml4.07 ocaml-sexplib0)))) - (arguments - `(#:tests? #f ;no tests - #:ocaml ,ocaml-4.07 - #:findlib ,ocaml4.07-findlib - #:dune ,ocaml4.07-dune)) + `(("ocaml-base" ,ocaml-base) + ("ocaml-sexplib0" ,ocaml-sexplib0))) + (arguments `(#:tests? #f)) ;no tests + (properties `((ocaml4.07-variant . ,(delay ocaml4.07-stdio)))) (synopsis "Standard IO library for OCaml") (description "Stdio implements simple input/output functionalities for OCaml. It @@ -4744,6 +4734,16 @@ re-exports the input/output functions of the OCaml standard libraries using a more consistent API.") (license license:expat))) +(define-public ocaml4.07-stdio + (package-with-ocaml4.07 + (package + (inherit ocaml-stdio) + (version "0.11.0") + (source + (janestreet-origin "stdio" version + "0pqbp2wy5fgmc38irwvmj9nlcvclb1ix1mp4y7l39bgvvlz303h9")) + (properties '())))) + (define-public ocaml-ppx-derivers (package (name "ocaml-ppx-derivers") @@ -4793,7 +4793,7 @@ as part of the same ocaml-migrate-parsetree driver.") ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) ("ocaml-ppx-derivers" ,(package-with-ocaml4.07 ocaml-ppx-derivers)) - ("ocaml-stdio" ,ocaml4.07-stdio) + ("ocaml-stdio" ,(package-with-ocaml4.07 ocaml-stdio)) ("ocaml-result" ,(package-with-ocaml4.07 ocaml-result)) ("ocaml-sexplib0" ,(package-with-ocaml4.07 ocaml-sexplib0)))) (arguments @@ -5421,7 +5421,7 @@ else expression.") #:dune ,ocaml4.07-dune)) (propagated-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-stdio" ,ocaml4.07-stdio) + ("ocaml-stdio" ,(package-with-ocaml4.07 ocaml-stdio)) ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) (properties `((upstream-name . "ppx_optcomp"))) (home-page "https://github.com/janestreet/ppx_optcomp") @@ -5550,7 +5550,7 @@ useful errors on failure.") ("ocaml-ppx-inline-test" ,ocaml4.07-ppx-inline-test) ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv) ("ocaml-ppx-variants-conv" ,ocaml4.07-ppx-variants-conv) - ("ocaml-stdio" ,ocaml4.07-stdio) + ("ocaml-stdio" ,(package-with-ocaml4.07 ocaml-stdio)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) ("ocaml-ppxlib" ,ocaml4.07-ppxlib) @@ -5826,7 +5826,7 @@ various Jane Street packages.") #:dune ,ocaml4.07-dune)) (propagated-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-stdio" ,ocaml4.07-stdio))) + ("ocaml-stdio" ,(package-with-ocaml4.07 ocaml-stdio)))) (home-page "https://github.com/janestreet/configurator") (synopsis "Helper library for gathering system configuration") (description "Configurator is a small library that helps writing OCaml @@ -5919,7 +5919,7 @@ thousands of times faster than fork. ("ocaml-ppx-jane" ,ocaml4.07-ppx-jane) ("ocaml-sexplib" ,(package-with-ocaml4.07 ocaml-sexplib)) ("ocaml-spawn" ,ocaml4.07-spawn) - ("ocaml-stdio" ,ocaml4.07-stdio) + ("ocaml-stdio" ,(package-with-ocaml4.07 ocaml-stdio)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) @@ -5966,7 +5966,7 @@ standard library that was developed by Jane Street.") ("ocaml-ppx-sexp-message" ,ocaml4.07-ppx-sexp-message) ("ocaml-sexplib" ,(package-with-ocaml4.07 ocaml-sexplib)) ("ocaml-splittable-random" ,ocaml4.07-splittable-random) - ("ocaml-stdio" ,ocaml4.07-stdio) + ("ocaml-stdio" ,(package-with-ocaml4.07 ocaml-stdio)) ("ocaml-typerep" ,ocaml4.07-typerep) ("ocaml-variantslib" ,ocaml4.07-variantslib) ("ocaml-migrate-parsetree" @@ -6250,7 +6250,7 @@ library FFTW.") `(("openblas" ,openblas) ("lapack" ,lapack) ("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-stdio" ,ocaml4.07-stdio))) + ("ocaml-stdio" ,(package-with-ocaml4.07 ocaml-stdio)))) (home-page "https://mmottl.github.io/lacaml/") (synopsis "OCaml-bindings to BLAS and LAPACK") -- cgit 1.4.1 From cfa65d777071675ca66d59b32f34c4f79a6b16e1 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:22:52 +0000 Subject: gnu: Add ocaml-compiler-libs. * gnu/packages/ocaml.scm (ocaml-compiler-libs): New variable. (ocaml4.07-compiler-libs): Inherit from ocaml-compiler-libs. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 42 +++++++++++++++++++++++++++++------------- 1 file changed, 29 insertions(+), 13 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index dbb34cbe78..08b62278d1 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -4083,7 +4083,7 @@ syntax checking on dedukti files.") `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-compiler-libs" ,ocaml4.07-compiler-libs) + ("ocaml-compiler-libs" ,(package-with-ocaml4.07 ocaml-compiler-libs)) ("ocaml-sexplib0" ,(package-with-ocaml4.07 ocaml-sexplib0)) ("ocaml-stdio" ,(package-with-ocaml4.07 ocaml-stdio)) ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) @@ -4685,34 +4685,50 @@ provided by companion libraries such as #:dune ,ocaml4.07-dune)) (properties '())))) -(define-public ocaml4.07-compiler-libs +(define-public ocaml-compiler-libs (package - (name "ocaml4.07-compiler-libs") - (version "0.11.0") + (name "ocaml-compiler-libs") + (version "0.12.3") (home-page "https://github.com/janestreet/ocaml-compiler-libs") (source (origin (method git-fetch) (uri (git-reference - (url (string-append home-page ".git")) + (url home-page) (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 - "03jds7bszh8wwpfwxb3dg0gyr1j1872wxwx1xqhry5ir0i84bg0s")))) + "00nrar7h2pyflbdiq6wwwrb4k5jh9iff0jllihzm6ms8d5pspsg5")))) (build-system dune-build-system) - (arguments - `(#:tests? #f ;no tests - #:ocaml ,ocaml-4.07 - #:findlib ,ocaml4.07-findlib - #:dune ,ocaml4.07-dune)) - (properties `((upstream-name . "ocaml-compiler-libs"))) + (arguments `(#:tests? #f)) ;no tests + (properties `((upstream-name . "ocaml-compiler-libs") + (ocaml4.07-variant . ,(delay ocaml4.07-compiler-libs)))) (synopsis "Compiler libraries repackaged") (description "This package simply repackages the OCaml compiler libraries so they don't expose everything at toplevel. For instance, @code{Ast_helper} is now @code{Ocaml_common.Ast_helper}.") (license license:expat))) +(define-public ocaml4.07-compiler-libs + (package-with-ocaml4.07 + (package + (inherit ocaml-compiler-libs) + (name "ocaml-compiler-libs") + (version "0.11.0") + (home-page "https://github.com/janestreet/ocaml-compiler-libs") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03jds7bszh8wwpfwxb3dg0gyr1j1872wxwx1xqhry5ir0i84bg0s")))) + (properties `((upstream-name . "ocaml-compiler-libs")))))) + (define-public ocaml-stdio (package (name "ocaml-stdio") @@ -4789,7 +4805,7 @@ as part of the same ocaml-migrate-parsetree driver.") (build-system dune-build-system) (propagated-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-compiler-libs" ,ocaml4.07-compiler-libs) + ("ocaml-compiler-libs" ,(package-with-ocaml4.07 ocaml-compiler-libs)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) ("ocaml-ppx-derivers" ,(package-with-ocaml4.07 ocaml-ppx-derivers)) -- cgit 1.4.1 From 3c8899160b54823f8dbaa6af70468087b4028b13 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:22:53 +0000 Subject: gnu: ocaml-migrate-parsetree: Update to 2.1.0. * gnu/packages/ocaml.scm (ocaml-migrate-parsetree): Update to 2.1.0. (ocaml-migrate-parsetree-1): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 39 +++++++++++++++++++++++++++++---------- 1 file changed, 29 insertions(+), 10 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 08b62278d1..bf9311bf5d 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -1770,32 +1770,51 @@ module of this library is parameterised by the type of S-expressions.") (define-public ocaml-migrate-parsetree (package (name "ocaml-migrate-parsetree") - (version "1.7.3") + (version "2.1.0") (home-page "https://github.com/ocaml-ppx/ocaml-migrate-parsetree") (source (origin (method git-fetch) (uri (git-reference - (url (string-append home-page ".git")) + (url home-page) (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 - "0336vz0galjnsazbmkxjwdv1qvdqsx2rgrvp778xgq2fzasz45cx")))) + "1cpgdqcs624nd1p271ddakgyibl0ia4f6dzivnz9qdwszsinwr89")))) (build-system dune-build-system) - (arguments - `(#:tests? #f)) + (arguments `(#:tests? #f)) (propagated-inputs `(("ocaml-ppx-derivers" ,ocaml-ppx-derivers) ("ocamlbuild" ,ocamlbuild) ("ocaml-result" ,ocaml-result))) - (properties `((upstream-name . "ocaml-migrate-parsetree"))) + (properties `((upstream-name . "ocaml-migrate-parsetree") + ;; OCaml 4.07 packages require version 1.* + (ocaml4.07-variant . ,(delay (package-with-ocaml4.07 ocaml-migrate-parsetree-1))))) (synopsis "OCaml parsetree converter") (description "This library converts between parsetrees of different OCaml versions. For each version, there is a snapshot of the parsetree and conversion functions to the next and/or previous version.") (license license:lgpl2.1+))) - + +(define-public ocaml-migrate-parsetree-1 + (package + (inherit ocaml-migrate-parsetree) + (name "ocaml-migrate-parsetree-1") + (version "1.8.0") + (home-page "https://github.com/ocaml-ppx/ocaml-migrate-parsetree") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "16x8sxc4ygxrr1868qpzfqyrvjf3hfxvjzmxmf6ibgglq7ixa2nq")))) + (properties '((upstream-name . "ocaml-migrate-parsetree"))))) + (define-public ocaml-ppx-tools-versioned (package (name "ocaml-ppx-tools-versioned") @@ -1814,7 +1833,7 @@ functions to the next and/or previous version.") `(#:test-target "." #:package "ppx_tools_versioned")) (propagated-inputs - `(("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree))) + `(("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree-1))) (properties `((upstream-name . "ppx_tools_versioned"))) (home-page "https://github.com/let-def/ppx_tools_versioned") (synopsis "Variant of ppx_tools") @@ -6120,7 +6139,7 @@ combinators.") "0900vli5kw7s5kdam0n4cqsfsfqb7mdb3azn3i55595gilg1vyn8")))) (build-system dune-build-system) (propagated-inputs - `(("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree) + `(("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree-1) ("ocaml-ppx-tools-versioned" ,ocaml-ppx-tools-versioned) ("ocaml-ounit" ,ocaml-ounit))) (arguments @@ -6359,7 +6378,7 @@ variants.") ("ocaml-cmdliner" ,ocaml-cmdliner) ("ocaml-re" ,ocaml-re) ("ocaml-result" ,ocaml-result) - ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree) + ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree-1) ("ocaml-odoc" ,ocaml-odoc) ("ocaml-version" ,ocaml-version))) (native-inputs -- cgit 1.4.1 From 262683250cbfaaea61dd6bc6b627b6a73f578124 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:22:54 +0000 Subject: gnu: Add ocaml-ppxlib. * gnu/packages/ocaml.scm (ocaml-ppxlib): New variable. (ocaml4.07-ppxlib): Inherit from ocaml-ppxlib. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 144 +++++++++++++++++++++++++++---------------------- 1 file changed, 81 insertions(+), 63 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index bf9311bf5d..cc6e7422c6 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -4105,7 +4105,7 @@ syntax checking on dedukti files.") ("ocaml-compiler-libs" ,(package-with-ocaml4.07 ocaml-compiler-libs)) ("ocaml-sexplib0" ,(package-with-ocaml4.07 ocaml-sexplib0)) ("ocaml-stdio" ,(package-with-ocaml4.07 ocaml-stdio)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "ppx_inline_test"))) (synopsis "Syntax extension for writing in-line tests in ocaml code") (description "This package contains a syntax extension for writing @@ -4806,54 +4806,32 @@ ppx_deriving and ppx_type_conv to inter-operate gracefully when linked as part of the same ocaml-migrate-parsetree driver.") (license license:bsd-3))) -(define-public ocaml4.07-ppxlib +(define-public ocaml-ppxlib (package - (name "ocaml4.07-ppxlib") - (version "0.6.0") + (name "ocaml-ppxlib") + (version "0.22.0") (home-page "https://github.com/ocaml-ppx/ppxlib") (source (origin (method git-fetch) (uri (git-reference - (url (string-append home-page ".git")) + (url home-page) (commit version))) (file-name (git-file-name name version)) (sha256 (base32 - "0my9x7sxb329h0lzshppdaawiyfbaw6g5f41yiy7bhl071rnlvbv")))) + "0kf7lgcwygf6zlx7rwddqpqvasa6v7xiq0bqal8vxlib6lpg074q")))) (build-system dune-build-system) (propagated-inputs - `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-compiler-libs" ,(package-with-ocaml4.07 ocaml-compiler-libs)) - ("ocaml-migrate-parsetree" - ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppx-derivers" ,(package-with-ocaml4.07 ocaml-ppx-derivers)) - ("ocaml-stdio" ,(package-with-ocaml4.07 ocaml-stdio)) - ("ocaml-result" ,(package-with-ocaml4.07 ocaml-result)) - ("ocaml-sexplib0" ,(package-with-ocaml4.07 ocaml-sexplib0)))) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'check 'set-topfind - (lambda* (#:key inputs #:allow-other-keys) - ;; add the line #directory ".." at the top of each file - ;; using #use "topfind";; to be able to find topfind - (let* ((findlib-path (assoc-ref inputs "findlib")) - (findlib-libdir - (string-append findlib-path "/lib/ocaml/site-lib"))) - (substitute* '("test/base/test.ml" - "test/code_path/test.ml" - "test/deriving/test.ml" - "test/driver/attributes/test.ml" - "test/driver/non-compressible-suffix/test.ml" - "test/driver/transformations/test.ml") - (("#use \"topfind\";;" all) - (string-append "#directory \"" findlib-libdir "\"\n" - all)))) - #t))) - #:ocaml ,ocaml-4.07 - #:findlib ,ocaml4.07-findlib - #:dune ,ocaml4.07-dune)) + `(("ocaml-base" ,ocaml-base) + ("ocaml-compiler-libs" ,ocaml-compiler-libs) + ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree) + ("ocaml-stdlib-shims" ,ocaml-stdlib-shims) + ("ocaml-ppx-derivers" ,ocaml-ppx-derivers) + ("ocaml-stdio" ,ocaml-stdio) + ("ocaml-result" ,ocaml-result) + ("ocaml-sexplib0" ,ocaml-sexplib0))) + (properties `((ocaml4.07-variant . ,(delay ocaml4.07-ppxlib)))) (synopsis "Base library and tools for ppx rewriters") (description @@ -4871,6 +4849,46 @@ OCaml AST in the OCaml syntax; @end itemize") (license license:expat))) +(define-public ocaml4.07-ppxlib + (package-with-ocaml4.07 + (package + (inherit ocaml-ppxlib) + (name "ocaml-ppxlib") + (version "0.6.0") + (home-page "https://github.com/ocaml-ppx/ppxlib") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0my9x7sxb329h0lzshppdaawiyfbaw6g5f41yiy7bhl071rnlvbv")))) + (build-system dune-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'check 'set-topfind + (lambda* (#:key inputs #:allow-other-keys) + ;; add the line #directory ".." at the top of each file + ;; using #use "topfind";; to be able to find topfind + (let* ((findlib-path (assoc-ref inputs "findlib")) + (findlib-libdir + (string-append findlib-path "/lib/ocaml/site-lib"))) + (substitute* '("test/base/test.ml" + "test/code_path/test.ml" + "test/deriving/test.ml" + "test/driver/attributes/test.ml" + "test/driver/non-compressible-suffix/test.ml" + "test/driver/transformations/test.ml") + (("#use \"topfind\";;" all) + (string-append "#directory \"" findlib-libdir "\"\n" + all)))) + #t))))) + (properties '())))) + (define-public ocaml4.07-ppx-compare (package (name "ocaml4.07-ppx-compare") @@ -4889,7 +4907,7 @@ OCaml AST in the OCaml syntax; `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (arguments `(#:ocaml ,ocaml-4.07 #:findlib ,ocaml4.07-findlib @@ -4928,7 +4946,7 @@ by making sure that you only compare comparable values.") `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "fieldslib"))) (home-page "https://github.com/janestreet/fieldslib") (synopsis "Syntax extension to record fields") @@ -4960,7 +4978,7 @@ of a record and create new record values.") `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "variantslib"))) (home-page "https://github.com/janestreet/variantslib") (synopsis "OCaml variants as first class values") @@ -4986,7 +5004,7 @@ standard library.") ("ocaml-fieldslib" ,ocaml4.07-fieldslib) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (arguments `(#:ocaml ,ocaml-4.07 #:findlib ,ocaml4.07-findlib @@ -5018,7 +5036,7 @@ new record values.") `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (arguments `(#:ocaml ,ocaml-4.07 #:findlib ,ocaml4.07-findlib @@ -5049,7 +5067,7 @@ definitions.") ("ocaml-variantslib" ,ocaml4.07-variantslib) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (arguments `(#:ocaml ,ocaml-4.07 #:findlib ,ocaml4.07-findlib @@ -5082,7 +5100,7 @@ variant types.") ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (arguments `(#:ocaml ,ocaml-4.07 #:findlib ,ocaml4.07-findlib @@ -5182,7 +5200,7 @@ storage of large amounts of data.") ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (arguments `(#:ocaml ,ocaml-4.07 #:findlib ,ocaml4.07-findlib @@ -5217,7 +5235,7 @@ hash functions from type exrpessions and definitions.") `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "ppx_enumerate"))) (home-page "https://github.com/janestreet/ppx_enumerate") (synopsis "Generate a list containing all values of a finite type") @@ -5249,7 +5267,7 @@ many values).") `(("ocaml-ppx-inline-test" ,ocaml4.07-ppx-inline-test) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "ppx_bench"))) (home-page "https://github.com/janestreet/ppx_bench") (synopsis "Syntax extension for writing in-line benchmarks in ocaml code") @@ -5279,7 +5297,7 @@ many values).") `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "ppx_here"))) (home-page "https://github.com/janestreet/ppx_here") (synopsis "Expands [%here] into its location") @@ -5334,7 +5352,7 @@ many values).") ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "ppx_sexp_value"))) (home-page "https://github.com/janestreet/ppx_sexp_value") (synopsis "Simplify building s-expressions from ocaml values") @@ -5365,7 +5383,7 @@ ocaml values.") ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "ppx_sexp_message"))) (home-page "https://github.com/janestreet/ppx_sexp_message") (synopsis "A ppx rewriter for easy construction of s-expressions") @@ -5397,7 +5415,7 @@ context such as function arguments.") (propagated-inputs `(("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "ppx_pipebang"))) (home-page "https://github.com/janestreet/ppx_pipebang") (synopsis "Inline reverse application operators `|>` and `|!`") @@ -5428,7 +5446,7 @@ context such as function arguments.") `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "ppx_optional"))) (home-page "https://github.com/janestreet/ppx_optional") (synopsis "Pattern matching on flat options") @@ -5457,7 +5475,7 @@ else expression.") (propagated-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) ("ocaml-stdio" ,(package-with-ocaml4.07 ocaml-stdio)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "ppx_optcomp"))) (home-page "https://github.com/janestreet/ppx_optcomp") (synopsis "Optional compilation for OCaml") @@ -5487,7 +5505,7 @@ size, the version of the compiler, ...") `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "ppx_let"))) (home-page "https://github.com/janestreet/ppx_let") (synopsis "Monadic let-bindings") @@ -5517,7 +5535,7 @@ match expressions, and if expressions.") ("ocaml-ppx-here" ,ocaml4.07-ppx-here) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "ppx_fail"))) (home-page "https://github.com/janestreet/ppx_fail") (synopsis "Add location to calls to failwiths") @@ -5549,7 +5567,7 @@ position.") ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "ppx_assert"))) (home-page "https://github.com/janestreet/ppx_assert") (synopsis "Assert-like extension nodes that raise useful errors on failure") @@ -5588,7 +5606,7 @@ useful errors on failure.") ("ocaml-stdio" ,(package-with-ocaml4.07 ocaml-stdio)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)) ("ocaml-re" ,(package-with-ocaml4.07 ocaml-re)))) (properties `((upstream-name . "ppx_expect"))) (home-page "https://github.com/janestreet/ppx_expect") @@ -5624,7 +5642,7 @@ to denote the expected output.") ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) ("ocaml-octavius" ,(package-with-ocaml4.07 ocaml-octavius)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "ppx_js_style"))) (home-page "https://github.com/janestreet/ppx_js_style") (synopsis "Code style checker for Jane Street Packages") @@ -5657,7 +5675,7 @@ packages.") ("ocaml-typerep" ,ocaml4.07-typerep) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "ppx_typerep_conv"))) (home-page "https://github.com/janestreet/ppx_typerep_conv") (synopsis "Generation of runtime types from type declarations") @@ -5691,7 +5709,7 @@ from type definitions.") ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "ppx_base"))) (home-page "https://github.com/janestreet/ppx_base") (synopsis "Base set of ppx rewriters") @@ -5727,7 +5745,7 @@ verification tool.") ("ocaml-ppx-here" ,ocaml4.07-ppx-here) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "ppx_bin_prot"))) (home-page "https://github.com/janestreet/ppx_bin_prot") (synopsis "Generation of bin_prot readers and writers from types") @@ -5774,7 +5792,7 @@ functions from type definitions.") ("ocaml-ppx-variants-conv" ,ocaml4.07-ppx-variants-conv) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (properties `((upstream-name . "ppx_jane"))) (home-page "https://github.com/janestreet/ppx_jane") (synopsis "Standard Jane Street ppx rewriters") @@ -5957,7 +5975,7 @@ thousands of times faster than fork. ("ocaml-stdio" ,(package-with-ocaml4.07 ocaml-stdio)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,ocaml4.07-ppxlib))) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (home-page "https://github.com/janestreet/core") (synopsis "Alternative to OCaml's standard library") (description "The Core suite of libraries is an alternative to OCaml's -- cgit 1.4.1 From 59a39ec61b7c6a1de8bfaa50887b0ccaf245d4c7 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:22:55 +0000 Subject: gnu: Add ocaml-sedlex. * gnu/packages/ocaml.scm (ocaml-sedlex): New variable. (ocaml4.07-sedlex): Inherit from ocaml-sedlex. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 57 +++++++++++++++++++++++++++++++++----------------- 1 file changed, 38 insertions(+), 19 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index cc6e7422c6..9e9f1b6f21 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -2554,10 +2554,10 @@ representation of the data.") and consumable.") (license license:bsd-2))) -(define-public ocaml4.07-sedlex +(define-public ocaml-sedlex (package - (name "ocaml4.07-sedlex") - (version "2.1") + (name "ocaml-sedlex") + (version "2.3") (source (origin (method git-fetch) (uri (git-reference @@ -2566,36 +2566,37 @@ and consumable.") (file-name (git-file-name name version)) (sha256 (base32 - "05f6qa8x3vhpdz1fcnpqk37fpnyyq13icqsk2gww5idjnh6kng26")))) + "0iw3phlaqr27jdf857hmj5v5hdl0vngbb2h37p2ll18sw991fxar")))) (build-system dune-build-system) (arguments - `(#:tests? #f; no tests + `(#:tests? #f ; no tests #:package "sedlex" #:phases (modify-phases %standard-phases (add-before 'build 'copy-resources (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "src/generator/data" + ;; Newer versions of dune emit an error if files it wants to + ;; build already exist. Delete the dune file so dune doesn't + ;; complain. + (delete-file "dune") (for-each - (lambda (file) - (copy-file (assoc-ref inputs file) file)) - '("DerivedCoreProperties.txt" "DerivedGeneralCategory.txt" - "PropList.txt"))) + (lambda (file) + (copy-file (assoc-ref inputs file) file)) + '("DerivedCoreProperties.txt" "DerivedGeneralCategory.txt" + "PropList.txt"))) #t)) (add-before 'build 'chmod (lambda _ (for-each (lambda (file) (chmod file #o644)) (find-files "." ".*")) - #t))) - #:ocaml ,ocaml-4.07 - #:findlib ,ocaml4.07-findlib - #:dune ,ocaml4.07-dune)) + #t))))) (native-inputs - `(("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild)))) + `(("ocamlbuild" ,ocamlbuild))) (propagated-inputs - `(("ocaml-gen" ,(package-with-ocaml4.07 ocaml-gen)) - ("ocaml-ppx-tools-versioned" - ,(package-with-ocaml4.07 ocaml-ppx-tools-versioned)) - ("ocaml-uchar" ,(package-with-ocaml4.07 ocaml-uchar)))) + `(("ocaml-gen" ,ocaml-gen) + ("ocaml-ppxlib" ,ocaml-ppxlib) + ("ocaml-ppx-tools-versioned" ,ocaml-ppx-tools-versioned) + ("ocaml-uchar" ,ocaml-uchar))) ;; These three files are needed by src/generator/data/dune, but would be ;; downloaded using curl at build time. (inputs @@ -2620,11 +2621,29 @@ and consumable.") (sha256 (base32 "0gsb1jpj3mnqbjgbavi4l95gl6g4agq58j82km22fdfg63j3w3fk")))))) + (properties `((ocaml4.07-variant . ,(delay ocaml4.07-sedlex)))) (home-page "https://www.cduce.org/download.html#side") (synopsis "Lexer generator for Unicode and OCaml") (description "Lexer generator for Unicode and OCaml.") (license license:expat))) +(define-public ocaml4.07-sedlex + (package-with-ocaml4.07 + (package + (inherit ocaml-sedlex) + (name "ocaml-sedlex") + (version "2.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ocaml-community/sedlex") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "05f6qa8x3vhpdz1fcnpqk37fpnyyq13icqsk2gww5idjnh6kng26")))) + (properties '())))) + (define-public ocaml-uchar (package (name "ocaml-uchar") @@ -3472,7 +3491,7 @@ Format module of the OCaml standard library.") `(("which" ,which))) (propagated-inputs `(("ocaml-xmlm" ,(package-with-ocaml4.07 ocaml-xmlm)) - ("ocaml-sedlex" ,ocaml4.07-sedlex) + ("ocaml-sedlex" ,(package-with-ocaml4.07 ocaml-sedlex)) ("ocaml-easy-format" ,(package-with-ocaml4.07 ocaml-easy-format)) ("ocaml-base64" ,(package-with-ocaml4.07 ocaml-base64)))) (home-page "http://piqi.org") -- cgit 1.4.1 From ec31363e22c1b04528c17cd8210f469a732da3f2 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:22:56 +0000 Subject: gnu: Add ocaml-uunf. * gnu/packages/ocaml.scm (ocaml-uunf): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 45 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 9e9f1b6f21..a7558d7367 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -2707,6 +2707,51 @@ Functions are also provided to fold over the characters of UTF encoded OCaml string values and to directly encode characters in OCaml Buffer.t values.") (license license:isc))) +(define-public ocaml-uunf + (package + (name "ocaml-uunf") + (version "13.0.0") + (source + (origin + (method url-fetch) + (uri "https://erratique.ch/software/uunf/releases/uunf-13.0.0.tbz") + (sha256 + (base32 + "1qci04nkp24kdls1z4s8kz5dzgky4nwd5r8345nwdrgwmxhw7ksm")))) + (build-system ocaml-build-system) + (arguments + `(#:build-flags (list "build" "--tests" "true") + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'check 'check-data + (lambda* (#:key inputs #:allow-other-keys) + (copy-file (assoc-ref inputs "NormalizationTest.txt") + "test/NormalizationTest.txt") + #t))))) + (native-inputs + `(("ocamlbuild" ,ocamlbuild) + ("opam" ,opam) + ("topkg" ,ocaml-topkg) + ;; Test data is otherwise downloaded wit curl + ("NormalizationTest.txt" + ,(origin + (method url-fetch) + (uri (string-append "https://www.unicode.org/Public/" + version + "/ucd/NormalizationTest.txt")) + (sha256 + (base32 "07g0ya4f6zfzvpp24ccxkb2yq568kh83gls85rjl950nv5fya3nn")))))) + (propagated-inputs `(("ocaml-uutf" ,ocaml-uutf))) + (home-page "https://erratique.ch/software/uunf") + (synopsis "Unicode text normalization for OCaml") + (description + "Uunf is an OCaml library for normalizing Unicode text. It supports all +Unicode normalization forms. The library is independent from any +IO mechanism or Unicode text data structure and it can process text +without a complete in-memory representation.") + (license license:isc))) + (define-public ocaml-jsonm (package (name "ocaml-jsonm") -- cgit 1.4.1 From c729d9861041cfacc4edf48da11df6c96696fd1f Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:22:57 +0000 Subject: gnu: Add ocaml-ppx-sexp-conv. * gnu/packages/ocaml.scm (ocaml-ppx-sexp-conv): New variable. (ocaml4.07-ppx-sexp-conv): Inherit from ocaml-ppx-sexp-conv. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 98 ++++++++++++++++++++++++++++---------------------- 1 file changed, 56 insertions(+), 42 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index a7558d7367..e05d8fd88f 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -3442,7 +3442,7 @@ JSON.") #:dune ,ocaml4.07-dune)) (native-inputs `(("ocaml-ounit" ,(package-with-ocaml4.07 ocaml-ounit)) - ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv))) + ("ocaml-ppx-sexp-conv" ,(package-with-ocaml4.07 ocaml-ppx-sexp-conv)))) (propagated-inputs `(("ocaml-re" ,(package-with-ocaml4.07 ocaml-re)) ("ocaml-sexplib0" ,(package-with-ocaml4.07 ocaml-sexplib0)) @@ -5082,36 +5082,50 @@ and set record fields, iterate and fold over all fields of a record and create new record values.") (license license:asl2.0))) -(define-public ocaml4.07-ppx-sexp-conv +(define-public ocaml-ppx-sexp-conv (package - (name "ocaml4.07-ppx-sexp-conv") - (version "0.11.2") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/janestreet/ppx_sexp_conv") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0pqwnqy1xp309wvdcaax4lg02yk64lq2w03mbgfvf6ps5ry4gis9")))) + (name "ocaml-ppx-sexp-conv") + (version "0.14.3") + (home-page "https://github.com/janestreet/ppx_sexp_conv") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0dbri9d00ydi0dw1cavswnqdmhjaaz80vap29ns2lr6mhhlvyjmj")))) (build-system dune-build-system) (propagated-inputs - `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-migrate-parsetree" - ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) - (arguments - `(#:ocaml ,ocaml-4.07 - #:findlib ,ocaml4.07-findlib - #:dune ,ocaml4.07-dune)) - (properties `((upstream-name . "ppx_sexp_conv"))) - (home-page "https://github.com/janestreet/ppx_sexp_conv") + `(("ocaml-base" ,ocaml-base) + ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree) + ("ocaml-ppxlib" ,ocaml-ppxlib))) + (properties `((upstream-name . "ppx_sexp_conv") + (ocaml4.07-variant . ,(delay ocaml4.07-ppx-sexp-conv)))) (synopsis "Generation of S-expression conversion functions from type definitions") (description "This package generates S-expression conversion functions from type definitions.") (license license:asl2.0))) +(define-public ocaml4.07-ppx-sexp-conv + (package-with-ocaml4.07 + (package + (inherit ocaml-ppx-sexp-conv) + (name "ocaml-ppx-sexp-conv") + (version "0.11.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/janestreet/ppx_sexp_conv") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0pqwnqy1xp309wvdcaax4lg02yk64lq2w03mbgfvf6ps5ry4gis9")))) + (properties `((upstream-name . "ppx_sexp_conv")))))) + (define-public ocaml4.07-ppx-variants-conv (package (name "ocaml4.07-ppx-variants-conv") @@ -5119,30 +5133,30 @@ definitions.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/janestreet/ppx_variants_conv") - (commit (string-append "v" version)))) + (url "https://github.com/janestreet/ppx_variants_conv") + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1yc0gsds5m2nv39zga8nnrca2n75rkqy5dz4xj1635ybz20hhbjd")))) (build-system dune-build-system) (propagated-inputs - `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-variantslib" ,ocaml4.07-variantslib) - ("ocaml-migrate-parsetree" - ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) + `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) + ("ocaml-variantslib" ,ocaml4.07-variantslib) + ("ocaml-migrate-parsetree" + ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) + ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (arguments `(#:ocaml ,ocaml-4.07 #:findlib ,ocaml4.07-findlib #:dune ,ocaml4.07-dune)) (properties - `((upstream-name . "ppx_variants_conv"))) + `((upstream-name . "ppx_variants_conv"))) (home-page - "https://github.com/janestreet/ppx_variants_conv") + "https://github.com/janestreet/ppx_variants_conv") (synopsis "Generation of accessor and iteration functions for OCaml variant types") (description - "This package generates accessors and iteration functions for OCaml + "This package generates accessors and iteration functions for OCaml variant types.") (license license:asl2.0))) @@ -5161,7 +5175,7 @@ variant types.") (build-system dune-build-system) (propagated-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv) + ("ocaml-ppx-sexp-conv" ,(package-with-ocaml4.07 ocaml-ppx-sexp-conv)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) @@ -5194,7 +5208,7 @@ string conversion.") ("ocaml-ppx-compare" ,ocaml4.07-ppx-compare) ("ocaml-ppx-custom-printf" ,ocaml4.07-ppx-custom-printf) ("ocaml-ppx-fields-conv" ,ocaml4.07-ppx-fields-conv) - ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv) + ("ocaml-ppx-sexp-conv" ,(package-with-ocaml4.07 ocaml-ppx-sexp-conv)) ("ocaml-ppx-variants-conv" ,ocaml4.07-ppx-variants-conv) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)))) @@ -5261,7 +5275,7 @@ storage of large amounts of data.") (propagated-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) ("ocaml-ppx-compare" ,ocaml4.07-ppx-compare) - ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv) + ("ocaml-ppx-sexp-conv" ,(package-with-ocaml4.07 ocaml-ppx-sexp-conv)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) @@ -5413,7 +5427,7 @@ many values).") (propagated-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) ("ocaml-ppx-here" ,ocaml4.07-ppx-here) - ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv) + ("ocaml-ppx-sexp-conv" ,(package-with-ocaml4.07 ocaml-ppx-sexp-conv)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) @@ -5444,7 +5458,7 @@ ocaml values.") (propagated-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) ("ocaml-ppx-here" ,ocaml4.07-ppx-here) - ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv) + ("ocaml-ppx-sexp-conv" ,(package-with-ocaml4.07 ocaml-ppx-sexp-conv)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) @@ -5628,7 +5642,7 @@ position.") `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) ("ocaml-ppx-compare" ,ocaml4.07-ppx-compare) ("ocaml-ppx-here" ,ocaml4.07-ppx-here) - ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv) + ("ocaml-ppx-sexp-conv" ,(package-with-ocaml4.07 ocaml-ppx-sexp-conv)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) @@ -5665,7 +5679,7 @@ useful errors on failure.") ("ocaml-ppx-fields-conv" ,ocaml4.07-ppx-fields-conv) ("ocaml-ppx-here" ,ocaml4.07-ppx-here) ("ocaml-ppx-inline-test" ,ocaml4.07-ppx-inline-test) - ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv) + ("ocaml-ppx-sexp-conv" ,(package-with-ocaml4.07 ocaml-ppx-sexp-conv)) ("ocaml-ppx-variants-conv" ,ocaml4.07-ppx-variants-conv) ("ocaml-stdio" ,(package-with-ocaml4.07 ocaml-stdio)) ("ocaml-migrate-parsetree" @@ -5770,7 +5784,7 @@ from type definitions.") ("ocaml-ppx-enumerate" ,ocaml4.07-ppx-enumerate) ("ocaml-ppx-hash" ,ocaml4.07-ppx-hash) ("ocaml-ppx-js-style" ,ocaml4.07-ppx-js-style) - ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv) + ("ocaml-ppx-sexp-conv" ,(package-with-ocaml4.07 ocaml-ppx-sexp-conv)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) @@ -6079,7 +6093,7 @@ standard library that was developed by Jane Street.") ("ocaml-ppx-hash" ,ocaml4.07-ppx-hash) ("ocaml-ppx-inline-test" ,ocaml4.07-ppx-inline-test) ("ocaml-ppx-jane" ,ocaml4.07-ppx-jane) - ("ocaml-ppx-sexp-conv" ,ocaml4.07-ppx-sexp-conv) + ("ocaml-ppx-sexp-conv" ,(package-with-ocaml4.07 ocaml-ppx-sexp-conv)) ("ocaml-ppx-sexp-message" ,ocaml4.07-ppx-sexp-message) ("ocaml-sexplib" ,(package-with-ocaml4.07 ocaml-sexplib)) ("ocaml-splittable-random" ,ocaml4.07-splittable-random) -- cgit 1.4.1 From 6f4f9c4d5519979740de9d74b343414349cab79a Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:22:58 +0000 Subject: gnu: Add ocaml-bigstringaf. * gnu/ocaml/packages.scm (ocaml-bigstringaf): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index e05d8fd88f..a8d7828359 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -6591,3 +6591,37 @@ provides support to program with time varying values: declarative events and signals. React doesn't define any primitive event or signal, it lets the client chooses the concrete timeline.") (license license:lgpl2.1+))) + +(define-public ocaml-bigstringaf + (package + (name "ocaml-bigstringaf") + (version "0.7.0") + (home-page "https://github.com/inhabitedtype/bigstringaf") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1q1sqxzdnlrpl95ccrhl7lwy3zswgd9rbn19ildclh0lyi2vazbj")))) + (build-system dune-build-system) + (arguments + '(#:test-target ".")) + (propagated-inputs + `(("ocaml-bigarray-compat" ,ocaml-bigarray-compat))) + (native-inputs + `(("ocaml-alcotest" ,ocaml-alcotest) + ("pkg-config" ,pkg-config))) + (synopsis + "Bigstring intrinsics and fast blits based on memcpy/memmove") + (description + "The OCaml compiler has a bunch of intrinsics for Bigstrings, but they're +not widely-known, sometimes misused, and so programs that use Bigstrings are +slower than they have to be. And even if a library got that part right and +exposed the intrinsics properly, the compiler doesn't have any fast blits +between Bigstrings and other string-like types. @code{bigstringaf} provides +these missing pieces.") + (license license:bsd-3))) -- cgit 1.4.1 From 3649c56a5f23501a5bb3418dc6047b71d494f0fa Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:22:59 +0000 Subject: gnu: Add ocaml-ppx-let. * gnu/packages/ocaml.scm (ocaml-ppx-let): New variable. (ocaml4.07-ppx-let): Inherit from ocaml-ppx-let. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 44 +++++++++++++++++++++++--------------------- 1 file changed, 23 insertions(+), 21 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index a8d7828359..b378708844 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -5562,35 +5562,37 @@ used to handle optional compilations of pieces of code depending of the word size, the version of the compiler, ...") (license license:asl2.0))) -(define-public ocaml4.07-ppx-let +(define-public ocaml-ppx-let (package - (name "ocaml4.07-ppx-let") - (version "0.11.0") - (source (origin - (method url-fetch) - (uri (string-append "https://ocaml.janestreet.com/ocaml-core/v" - (version-major+minor version) - "/files/ppx_let-v" version ".tar.gz")) - (sha256 - (base32 - "1wdfw6w4xbg97a35yg6bif9gggxniy9ddnrjfw1a0inkl2yamxkj")))) + (name "ocaml-ppx-let") + (version "0.14.0") + (source + (janestreet-origin "ppx_let" version + "1qcrnd86pbr1di5m6z4ps4p15qawwa02jxwz3xfd82hdbjmdwf1s")) (build-system dune-build-system) - (arguments - `(#:ocaml ,ocaml-4.07 - #:findlib ,ocaml4.07-findlib - #:dune ,ocaml4.07-dune)) (propagated-inputs - `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-migrate-parsetree" - ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) - (properties `((upstream-name . "ppx_let"))) + `(("ocaml-base" ,ocaml-base) + ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree) + ("ocaml-ppxlib" ,ocaml-ppxlib))) + (properties `((upstream-name . "ppx_let") + (ocaml4.07-variant . ,(delay ocaml4.07-ppx-let)))) (home-page "https://github.com/janestreet/ppx_let") (synopsis "Monadic let-bindings") (description "A ppx rewriter for monadic and applicative let bindings, match expressions, and if expressions.") (license license:asl2.0))) +(define-public ocaml4.07-ppx-let + (package-with-ocaml4.07 + (package + (inherit ocaml-ppx-let) + (version "0.11.0") + (source + (janestreet-origin "ppx_let" version + "1wdfw6w4xbg97a35yg6bif9gggxniy9ddnrjfw1a0inkl2yamxkj")) + + (properties `(upstream-name . "ppx_let"))))) + (define-public ocaml4.07-ppx-fail (package (name "ocaml4.07-ppx-fail") @@ -5860,7 +5862,7 @@ functions from type definitions.") ("ocaml-ppx-fields-conv" ,ocaml4.07-ppx-fields-conv) ("ocaml-ppx-here" ,ocaml4.07-ppx-here) ("ocaml-ppx-inline-test" ,ocaml4.07-ppx-inline-test) - ("ocaml-ppx-let" ,ocaml4.07-ppx-let) + ("ocaml-ppx-let" ,(package-with-ocaml4.07 ocaml-ppx-let)) ("ocaml-ppx-optcomp" ,ocaml4.07-ppx-optcomp) ("ocaml-ppx-optional" ,ocaml4.07-ppx-optional) ("ocaml-ppx-pipebang" ,ocaml4.07-ppx-pipebang) -- cgit 1.4.1 From 5b61a1472b998c39b069e9a557c3029e1351d0a7 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:23:00 +0000 Subject: gnu: Add ocaml-syntax-shims. * gnu/packages/ocaml.scm (ocaml-syntax-shims): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index b378708844..4f94273695 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -6627,3 +6627,28 @@ exposed the intrinsics properly, the compiler doesn't have any fast blits between Bigstrings and other string-like types. @code{bigstringaf} provides these missing pieces.") (license license:bsd-3))) + +(define-public ocaml-syntax-shims + (package + (name "ocaml-syntax-shims") + (version "1.0.0") + (home-page "https://github.com/ocaml-ppx/ocaml-syntax-shims") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0l1i8z95qgb0lxlrv3yb5nkp391hqsiyi4r91p12k3xmggqixagf")))) + (build-system dune-build-system) + (properties + `((upstream-name . "ocaml-syntax-shims"))) + (synopsis + "Backport new syntax to older OCaml versions") + (description + "This packages backports new features of the language to older +compilers, such as let+.") + (license license:expat))) -- cgit 1.4.1 From c35fd0374dd6e0f67eaaee34f52bb70453e2a93a Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:23:01 +0000 Subject: gnu: Add ocaml-ppx-compare. * gnu/packages/ocaml.scm (ocaml-ppx-compare): New variable. (ocaml4.07-ppx-compare): Inherit from ocaml-ppx-compare. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 64 ++++++++++++++++++++++++++++++-------------------- 1 file changed, 38 insertions(+), 26 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 4f94273695..2f642abf0d 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -4953,30 +4953,24 @@ OCaml AST in the OCaml syntax; #t))))) (properties '())))) -(define-public ocaml4.07-ppx-compare +(define-public ocaml-ppx-compare (package - (name "ocaml4.07-ppx-compare") - (version "0.11.1") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/janestreet/ppx_compare") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "06bq4m1bsm4jlx4g7wh5m99qky7xm4c2g52kaz6pv25hdn5agi2m")))) + (name "ocaml-ppx-compare") + (version "0.14.0") + (source + (janestreet-origin "ppx_compare" version + "0mqxa2s194nif7x4fjn1p5gd9i3bakr8nv27gf8x1g5nmi8q9pmp")) (build-system dune-build-system) - (propagated-inputs - `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-migrate-parsetree" - ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) (arguments - `(#:ocaml ,ocaml-4.07 - #:findlib ,ocaml4.07-findlib - #:dune ,ocaml4.07-dune)) - (properties `((upstream-name . "ppx_compare"))) + ;; Tests are currenlty failing + ;; (see https://github.com/janestreet/ppx_compare/issues/10) + '(#:tests? #f)) + (propagated-inputs + `(("ocaml-base" ,ocaml-base) + ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree) + ("ocaml-ppxlib" ,ocaml-ppxlib))) + (properties `((upstream-name . "ppx_compare") + (ocaml4.07-variant . ,(delay ocaml4.07-ppx-compare)))) (home-page "https://github.com/janestreet/ppx_compare") (synopsis "Generation of comparison functions from types") (description "Generation of fast comparison functions from type expressions @@ -4987,6 +4981,24 @@ flexibility by allowing you to override them for a specific type and more safety by making sure that you only compare comparable values.") (license license:asl2.0))) +(define-public ocaml4.07-ppx-compare + (package-with-ocaml4.07 + (package + (inherit ocaml-ppx-compare) + (name "ocaml-ppx-compare") + (version "0.11.1") + (home-page "https://github.com/janestreet/ppx_compare") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "06bq4m1bsm4jlx4g7wh5m99qky7xm4c2g52kaz6pv25hdn5agi2m")))) + (properties `((upstream-name . "ppx_compare")))))) + (define-public ocaml4.07-fieldslib (package (name "ocaml4.07-fieldslib") @@ -5205,7 +5217,7 @@ string conversion.") (build-system dune-build-system) (inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-ppx-compare" ,ocaml4.07-ppx-compare) + ("ocaml-ppx-compare" ,(package-with-ocaml4.07 ocaml-ppx-compare)) ("ocaml-ppx-custom-printf" ,ocaml4.07-ppx-custom-printf) ("ocaml-ppx-fields-conv" ,ocaml4.07-ppx-fields-conv) ("ocaml-ppx-sexp-conv" ,(package-with-ocaml4.07 ocaml-ppx-sexp-conv)) @@ -5274,7 +5286,7 @@ storage of large amounts of data.") (build-system dune-build-system) (propagated-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-ppx-compare" ,ocaml4.07-ppx-compare) + ("ocaml-ppx-compare" ,(package-with-ocaml4.07 ocaml-ppx-compare)) ("ocaml-ppx-sexp-conv" ,(package-with-ocaml4.07 ocaml-ppx-sexp-conv)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) @@ -5642,7 +5654,7 @@ position.") #:dune ,ocaml4.07-dune)) (propagated-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-ppx-compare" ,ocaml4.07-ppx-compare) + ("ocaml-ppx-compare" ,(package-with-ocaml4.07 ocaml-ppx-compare)) ("ocaml-ppx-here" ,ocaml4.07-ppx-here) ("ocaml-ppx-sexp-conv" ,(package-with-ocaml4.07 ocaml-ppx-sexp-conv)) ("ocaml-migrate-parsetree" @@ -5676,7 +5688,7 @@ useful errors on failure.") (propagated-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) ("ocaml-ppx-assert" ,ocaml4.07-ppx-assert) - ("ocaml-ppx-compare" ,ocaml4.07-ppx-compare) + ("ocaml-ppx-compare" ,(package-with-ocaml4.07 ocaml-ppx-compare)) ("ocaml-ppx-custom-printf" ,ocaml4.07-ppx-custom-printf) ("ocaml-ppx-fields-conv" ,ocaml4.07-ppx-fields-conv) ("ocaml-ppx-here" ,ocaml4.07-ppx-here) @@ -5782,7 +5794,7 @@ from type definitions.") #:findlib ,ocaml4.07-findlib #:dune ,ocaml4.07-dune)) (propagated-inputs - `(("ocaml-ppx-compare" ,ocaml4.07-ppx-compare) + `(("ocaml-ppx-compare" ,(package-with-ocaml4.07 ocaml-ppx-compare)) ("ocaml-ppx-enumerate" ,ocaml4.07-ppx-enumerate) ("ocaml-ppx-hash" ,ocaml4.07-ppx-hash) ("ocaml-ppx-js-style" ,ocaml4.07-ppx-js-style) -- cgit 1.4.1 From 7cf518ee8506ae5e5ff2c7846ca402b88de78c27 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:23:02 +0000 Subject: gnu: Add ocaml-ppx-here. * gnu/packages/ocaml.scm (ocaml-ppx-here): New variable. (ocaml4.07-ppx-here): Inherit from ocaml-ppx-here. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 56 ++++++++++++++++++++++++++------------------------ 1 file changed, 29 insertions(+), 27 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 2f642abf0d..79537bfa93 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -5364,37 +5364,39 @@ many values).") (description "Syntax extension for writing in-line benchmarks in ocaml code.") (license license:asl2.0))) -(define-public ocaml4.07-ppx-here +(define-public ocaml-ppx-here (package - (name "ocaml4.07-ppx-here") - (version "0.11.0") - (source (origin - (method url-fetch) - (uri (string-append "https://ocaml.janestreet.com/ocaml-core/v" - (version-major+minor version) - "/files/ppx_here-v" version ".tar.gz")) - (sha256 - (base32 - "0wxcak3ay4jpigm3pfdcpr65qw4hxfa8whhkryhcd8gy71x056z5")))) + (name "ocaml-ppx-here") + (version "0.14.0") + (source + (janestreet-origin "ppx_here" version + "0b444djy68v6ji0ypwv5l02pkl151qzrgg96lyhl8dxfrzvj1zkj")) (build-system dune-build-system) (arguments ;; broken tests - `(#:tests? #f - #:ocaml ,ocaml-4.07 - #:findlib ,ocaml4.07-findlib - #:dune ,ocaml4.07-dune)) + `(#:tests? #f)) (propagated-inputs - `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-migrate-parsetree" - ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) - ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) - (properties `((upstream-name . "ppx_here"))) + `(("ocaml-base" ,ocaml-base) + ("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree) + ("ocaml-ppxlib" ,ocaml-ppxlib))) + (properties `((upstream-name . "ppx_here") + (ocaml4.07-variant . ,(delay ocaml4.07-ppx-here)))) (home-page "https://github.com/janestreet/ppx_here") (synopsis "Expands [%here] into its location") (description "Part of the Jane Street's PPX rewriters collection.") (license license:asl2.0))) +(define-public ocaml4.07-ppx-here + (package-with-ocaml4.07 + (package + (inherit ocaml-ppx-here) + (version "0.11.0") + (source + (janestreet-origin "ppx_here" version + "0wxcak3ay4jpigm3pfdcpr65qw4hxfa8whhkryhcd8gy71x056z5")) + (properties `((upstream-name . "ppx_here")))))) + (define-public ocaml4.07-typerep (package (name "ocaml4.07-typerep") @@ -5438,7 +5440,7 @@ many values).") #:dune ,ocaml4.07-dune)) (propagated-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-ppx-here" ,ocaml4.07-ppx-here) + ("ocaml-ppx-here" ,(package-with-ocaml4.07 ocaml-ppx-here)) ("ocaml-ppx-sexp-conv" ,(package-with-ocaml4.07 ocaml-ppx-sexp-conv)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) @@ -5469,7 +5471,7 @@ ocaml values.") #:dune ,ocaml4.07-dune)) (propagated-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-ppx-here" ,ocaml4.07-ppx-here) + ("ocaml-ppx-here" ,(package-with-ocaml4.07 ocaml-ppx-here)) ("ocaml-ppx-sexp-conv" ,(package-with-ocaml4.07 ocaml-ppx-sexp-conv)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) @@ -5624,7 +5626,7 @@ match expressions, and if expressions.") #:dune ,ocaml4.07-dune)) (propagated-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("ocaml-ppx-here" ,ocaml4.07-ppx-here) + ("ocaml-ppx-here" ,(package-with-ocaml4.07 ocaml-ppx-here)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) @@ -5655,7 +5657,7 @@ position.") (propagated-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) ("ocaml-ppx-compare" ,(package-with-ocaml4.07 ocaml-ppx-compare)) - ("ocaml-ppx-here" ,ocaml4.07-ppx-here) + ("ocaml-ppx-here" ,(package-with-ocaml4.07 ocaml-ppx-here)) ("ocaml-ppx-sexp-conv" ,(package-with-ocaml4.07 ocaml-ppx-sexp-conv)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) @@ -5691,7 +5693,7 @@ useful errors on failure.") ("ocaml-ppx-compare" ,(package-with-ocaml4.07 ocaml-ppx-compare)) ("ocaml-ppx-custom-printf" ,ocaml4.07-ppx-custom-printf) ("ocaml-ppx-fields-conv" ,ocaml4.07-ppx-fields-conv) - ("ocaml-ppx-here" ,ocaml4.07-ppx-here) + ("ocaml-ppx-here" ,(package-with-ocaml4.07 ocaml-ppx-here)) ("ocaml-ppx-inline-test" ,ocaml4.07-ppx-inline-test) ("ocaml-ppx-sexp-conv" ,(package-with-ocaml4.07 ocaml-ppx-sexp-conv)) ("ocaml-ppx-variants-conv" ,ocaml4.07-ppx-variants-conv) @@ -5834,7 +5836,7 @@ verification tool.") (propagated-inputs `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) ("ocaml-bin-prot" ,ocaml4.07-bin-prot) - ("ocaml-ppx-here" ,ocaml4.07-ppx-here) + ("ocaml-ppx-here" ,(package-with-ocaml4.07 ocaml-ppx-here)) ("ocaml-migrate-parsetree" ,(package-with-ocaml4.07 ocaml-migrate-parsetree)) ("ocaml-ppxlib" ,(package-with-ocaml4.07 ocaml-ppxlib)))) @@ -5872,7 +5874,7 @@ functions from type definitions.") ("ocaml-ppx-expect" ,ocaml4.07-ppx-expect) ("ocaml-ppx-fail" ,ocaml4.07-ppx-fail) ("ocaml-ppx-fields-conv" ,ocaml4.07-ppx-fields-conv) - ("ocaml-ppx-here" ,ocaml4.07-ppx-here) + ("ocaml-ppx-here" ,(package-with-ocaml4.07 ocaml-ppx-here)) ("ocaml-ppx-inline-test" ,ocaml4.07-ppx-inline-test) ("ocaml-ppx-let" ,(package-with-ocaml4.07 ocaml-ppx-let)) ("ocaml-ppx-optcomp" ,ocaml4.07-ppx-optcomp) -- cgit 1.4.1 From 52dc188e12fe80dfe13ba04f995081beedde6358 Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Tue, 1 Jun 2021 20:23:03 +0000 Subject: gnu: Add ocaml-ppx-cold. * gnu/packages/ocaml.scm (ocaml-ppx-cold): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 79537bfa93..2b4673882b 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -5637,6 +5637,28 @@ match expressions, and if expressions.") position.") (license license:asl2.0))) +(define-public ocaml-ppx-cold + (package + (name "ocaml-ppx-cold") + (version "0.14.0") + (home-page "https://github.com/janestreet/ppx_cold") + (source + (janestreet-origin "ppx_cold" version + "1madfzhpir9amnxmg530n70vll0jrl59vyp71miji73i6b9sy6n2")) + (build-system dune-build-system) + (arguments `(#:test-target "tests")) + (propagated-inputs + `(("ocaml-base" ,ocaml-base) + ("ocaml-ppxlib" ,ocaml-ppxlib))) + (properties `((upstream-name . "ppx_cold"))) + (synopsis "Syntax extension for indicating cold path") + (description + "This package contains an syntax extension to indicate that the code is +on the cold path and should be kept out of the way to avoid polluting the +instruction cache on the hot path. See also +https://github.com/ocaml/ocaml/issues/8563.") + (license license:expat))) + (define-public ocaml4.07-ppx-assert (package (name "ocaml4.07-ppx-assert") -- cgit 1.4.1 From d8fed768a899bd0a3a84a88572135a1d7bde2400 Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Tue, 25 May 2021 10:17:20 +0200 Subject: gnu: Add python-asn1tools. * gnu/packages/python-xyz.scm (python-asn1tools): New variable. --- gnu/packages/python-xyz.scm | 26 +++++++++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a4fe31a01f..6a6d7f4b26 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19,7 +19,7 @@ ;;; Copyright © 2015, 2016 Chris Marusich ;;; Copyright © 2016 Danny Milosavljevic ;;; Copyright © 2016 Lukas Gradl -;;; Copyright © 2016, 2018, 2019 Hartmut Goebel +;;; Copyright © 2016, 2018, 2019, 2021 Hartmut Goebel ;;; Copyright © 2016 Daniel Pimentel ;;; Copyright © 2016 Sou Bunnbu ;;; Copyright © 2016, 2017 Troy Sankey @@ -10471,6 +10471,30 @@ implementations of ASN.1-based codecs and protocols.") module to older versions of Python.") (license license:psfl))) +(define-public python-asn1tools + (package + (name "python-asn1tools") + (version "0.158.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "asn1tools" version)) + (sha256 + (base32 "1k88a1azmyvp2ab6qcf2i40dig5abhyn7cmlyhmwwh8kr3syvma0")))) + (build-system python-build-system) + (propagated-inputs + `(("python-bitstruct" ,python-bitstruct) + ("python-diskcache" ,python-diskcache) + ("python-prompt-toolkit" ,python-prompt-toolkit) + ("python-pyparsing" ,python-pyparsing))) + (home-page "https://github.com/eerimoq/asn1tools") + (synopsis "ASN.1 parsing, encoding and decoding") + (description "This package provides ASN.1 parsing, encoding and decoding +for Python, including constraints checking. It supports several +codecs (e.g. BER, PER, UPER, XER) as well as limited C source code generating +for OER and UPER.") + (license license:expat))) + (define-public python2-ipaddr (package (name "python2-ipaddr") -- cgit 1.4.1 From 5d4bd2ee94075a1c9abb12d16c62edddf9bb006c Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Tue, 25 May 2021 10:17:53 +0200 Subject: gnu: Add python-pytest-mp. * gnu/packages/python-check.scm (python-pytest-mp): New variable. --- gnu/packages/python-check.scm | 39 ++++++++++++++++++++++++++++++++++++++- 1 file changed, 38 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm index 1206dda5c4..122098ae17 100644 --- a/gnu/packages/python-check.scm +++ b/gnu/packages/python-check.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020 Efraim Flashner ;;; Copyright © 2019, 2020, 2021 Maxim Cournoyer -;;; Copyright © 2019 Hartmut Goebel +;;; Copyright © 2019, 2021 Hartmut Goebel ;;; Copyright © 2020 Julien Lepiller ;;; Copyright © 2020 Marius Bakke ;;; Copyright © 2020 Edouard Klein @@ -1482,3 +1482,40 @@ allows one to create a set of tests using @emph{pairwise combinations} method, reducing a number of combinations of variables into a lesser set that covers most situations.") (license license:expat))) + +(define-public python-pytest-mp + (package + (name "python-pytest-mp") + (version "0.0.4p2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ansible/pytest-mp") + (commit "49a8ff2ca9ef62d8c86854ab31d6b5d5d6cf3f28"))) + (file-name (git-file-name name version)) + (sha256 + (base32 "01v98b6n3yvkfmxf2v38xk5ijqlk6ika0yljwkhl5bh6qhq23498")))) + (build-system python-build-system) + (propagated-inputs + `(("python-pytest" ,python-pytest) + ("python-psutil" ,python-psutil))) + (arguments + ;; tests require setuptools-markdown, which is deprecated and not in guix + '(#:tests? #f + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-useless-requirements + (lambda _ + (substitute* "setup.py" + ((" setup_requires=") " #"))))))) + (home-page "https://github.com/ansible/pytest-mp") + (synopsis "Segregate tests into several processes") + (description "pytest-mp is a minimalist approach to distribute and +segregate pytest tests across processes using python's multiprocessing library +and is heavily inspired by pytest-concurrent and pytest-xdist. As a very +early beta, it doesn't pledge or intend to support the majority of platforms +or use cases. Design is based on supporting slow, io-bound testing with often +tedious system under test configuration that can benefit from running several +tests at one time.") + (license license:expat))) -- cgit 1.4.1 From 3c401ca6df385b737363e5caea7396d3aa55863f Mon Sep 17 00:00:00 2001 From: Denis 'GNUtoo' Carikli Date: Fri, 4 Jun 2021 18:11:41 +0200 Subject: gnu: Add matterbridge. * gnu/packages/messaging.scm (matterbridge): New variable. Signed-off-by: Mathieu Othacehe --- gnu/packages/messaging.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 96cbf95fe9..1713aa7ceb 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -28,6 +28,7 @@ ;;; Copyright © 2020 Raghav Gururajan ;;; Copyright © 2020, 2021 Robert Karszniewicz ;;; Copyright © 2020 Giacomo Leidi +;;; Copyright © 2021 Denis 'GNUtoo' Carikli ;;; ;;; This file is part of GNU Guix. ;;; @@ -123,6 +124,7 @@ #:use-module (gnu packages xml) #:use-module (gnu packages xorg) #:use-module (guix build-system cmake) + #:use-module (guix build-system go) #:use-module (guix build-system glib-or-gtk) #:use-module (guix build-system gnu) #:use-module (guix build-system meson) @@ -2967,4 +2969,31 @@ designed for experienced users.") (description "This package contains Zulip's official terminal client.") (license license:asl2.0))) +(define-public matterbridge + (package + (name "matterbridge") + (version "1.22.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/42wim/matterbridge") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "07rgdc4v043fhzsalmlhickqizk6xjlpjkzn6l5v9ryp5gmv580z")))) + (build-system go-build-system) + (arguments + `(#:import-path "github.com/42wim/matterbridge" + #:unpack-path "github.com/42wim/matterbridge")) + (synopsis "Bridge together various messaging networks and protocols") + (description "Relays messages between different channels from various +messaging networks and protocols. So far it supports mattermost, IRC, gitter, +xmpp, slack, discord, telegram, rocketchat, twitch, ssh-chat, zulip, whatsapp, +keybase, matrix, microsoft teams, nextcloud, mumble, vk and more with REST +API. Mattermost is not required.") + (home-page "https://github.com/42wim/matterbridge") + (license license:asl2.0))) + ;;; messaging.scm ends here -- cgit 1.4.1 From d00713d49ec144987cf59c94a462f0245834e6b0 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 6 Jun 2021 18:32:41 +0200 Subject: gnu: git: Update to 2.32.0. * gnu/packages/version-control.scm (git): Update to 2.32.0. --- gnu/packages/version-control.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 4156c97cea..5900779de8 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -175,14 +175,14 @@ as well as the classic centralized workflow.") (define-public git (package (name "git") - (version "2.31.1") + (version "2.32.0") (source (origin (method url-fetch) (uri (string-append "mirror://kernel.org/software/scm/git/git-" version ".tar.xz")) (sha256 (base32 - "10367n5sv4nsgaxy486pbp7nscx34vjk8vrb06jm9ffm8ix42qcz")))) + "08rnm3ipjqdd2n31dw7mxl3iv9g4nxgc409krmz892a37kd43a38")))) (build-system gnu-build-system) (native-inputs `(("native-perl" ,perl) @@ -202,7 +202,7 @@ as well as the classic centralized workflow.") version ".tar.xz")) (sha256 (base32 - "00n7vbfmd3ywgjksgwrszwj0l2niba64qkaq07ra4p8mawy483ax")))) + "1hba3wh1fmhrwzw93a0m7q4kb3kwwwi1bx4457c4lkf94l2cpqqr")))) ;; For subtree documentation. ("asciidoc" ,asciidoc) ("docbook-xsl" ,docbook-xsl) -- cgit 1.4.1 From e2ad110f4c2a54cecaa8fed3792ba2dbe5fa2af4 Mon Sep 17 00:00:00 2001 From: Solene Rapenne via Guix-patches via Date: Sun, 6 Jun 2021 11:02:07 +0200 Subject: gnu: vlc: Update to 3.0.14. * gnu/packages/video.scm (vlc): Update to 3.0.14. Signed-off-by: Tobias Geerinckx-Rice --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 7d072dd7ec..e352cbf6fd 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1763,7 +1763,7 @@ videoformats depend on the configuration flags of ffmpeg.") (define-public vlc (package (name "vlc") - (version "3.0.12") + (version "3.0.14") (source (origin (method url-fetch) (uri (string-append @@ -1772,7 +1772,7 @@ videoformats depend on the configuration flags of ffmpeg.") "/vlc-" version ".tar.xz")) (sha256 (base32 - "0ygqihw2c5vvzv8950dlf7rdwz1cpz1668jgyja604ljibrmix7g")))) + "19imhm6wd85nm2r4xwa7g500rmya021aj93b1q33gany6ddkxfa9")))) (build-system gnu-build-system) (native-inputs `(("flex" ,flex) -- cgit 1.4.1