From d5711017707b8e0e8a75c2e0b535fd73b8d78c6c Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Tue, 16 Jun 2015 12:30:26 +0200 Subject: gnu: calibre: Update to 2.30.0. * gnu/packages/ebook.scm (calibre): Update to 2.30.0. --- gnu/packages/ebook.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ebook.scm b/gnu/packages/ebook.scm index 2be5ea351a..670fc64de8 100644 --- a/gnu/packages/ebook.scm +++ b/gnu/packages/ebook.scm @@ -60,7 +60,7 @@ (define-public calibre (package (name "calibre") - (version "2.29.0") + (version "2.30.0") (source (origin (method url-fetch) @@ -69,7 +69,7 @@ version ".tar.xz")) (sha256 (base32 - "1n3cfnjnghhhsgzcbcvbr0gh191lhl6az09q1s68jhlcc2lski6l")) + "1k2rpn06nfzqjy5k6fh8pwfj8vbhpn7rgkpkkpz5n2fqg3z8ph1j")) ;; Remove non-free or doubtful code, see ;; https://lists.gnu.org/archive/html/guix-devel/2015-02/msg00478.html (modules '((guix build utils))) -- cgit 1.4.1 From 9e4552aac2919c5b1765fa260d4ca18dfd39971a Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Fri, 12 Jun 2015 12:01:26 +0800 Subject: gnu: talloc: Update to 2.1.2. * gnu/packages/samba.scm (talloc): Update to 2.1.2. --- gnu/packages/samba.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm index 8e53debcb3..35866304ef 100644 --- a/gnu/packages/samba.scm +++ b/gnu/packages/samba.scm @@ -168,14 +168,14 @@ Desktops into Active Directory environments using the winbind daemon.") (define-public talloc (package (name "talloc") - (version "2.1.0") + (version "2.1.2") (source (origin (method url-fetch) (uri (string-append "http://www.samba.org/ftp/talloc/talloc-" version ".tar.gz")) (sha256 (base32 - "13zh628hzlp2v9vj70knnfac2xbxqrdhgap30csq4zv4h8w3j087")))) + "13c365f7y8idjf2v1jxdjpkc3lxdmsxxfxjx1ymianm7zjiph393")))) (build-system gnu-build-system) (arguments '(#:phases (alist-replace -- cgit 1.4.1 From d22b9397e10e28f46f1fd2edff247ec6beb388bf Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Sun, 14 Jun 2015 14:40:07 +0800 Subject: gnu: qt-4: Update to 4.8.7. * gnu/packages/qt.scm (qt-4): Update to 4.8.7. --- gnu/packages/qt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 3bc3145e8d..84625bfea3 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -221,7 +221,7 @@ developers using C++ or QML, a CSS & JavaScript like language.") (define-public qt-4 (package (inherit qt) - (version "4.8.6") + (version "4.8.7") (source (origin (method url-fetch) (uri (string-append "http://download.qt-project.org/official_releases/qt/" @@ -231,7 +231,7 @@ developers using C++ or QML, a CSS & JavaScript like language.") version ".tar.gz")) (sha256 (base32 - "0b036iqgmbbv37dgwwfihw3mihjbnw3kb5kaisdy0qi8nn8xs54b")) + "183fca7n7439nlhxyg1z7aky0izgbyll3iwakw4gwivy16aj5272")) (patches (map search-patch '("qt4-ldflags.patch" "qt4-tests.patch"))))) (inputs `(,@(alist-delete "libjpeg" (package-inputs qt)) -- cgit 1.4.1 From a33b8449a069cf104cbcc4ba96f885edb03b947e Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Sun, 14 Jun 2015 16:50:55 +0800 Subject: gnu: qt: Update to 5.4.2. * gnu/packages/qt.scm (qt): Update to 5.4.2. --- gnu/packages/qt.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 84625bfea3..c92f7db79a 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -93,7 +93,7 @@ X11 (yet).") (define-public qt (package (name "qt") - (version "5.4.1") + (version "5.4.2") (source (origin (method url-fetch) (uri (string-append "http://download.qt-project.org/official_releases/qt/" @@ -103,7 +103,7 @@ X11 (yet).") version ".tar.xz")) (sha256 (base32 - "0q6qzakq8xihw91xv310qi3vyylq7x2bzdkjgy8sqxii2lgbjzhv")) + "09gay5cimfdb0apy60v7z4r4zkl2vjysdppzihpla8dp2c30fvcc")) (patches (list (search-patch "qt5-conflicting-typedefs.patch") (search-patch "qt5-runpath.patch"))) (snippet -- cgit 1.4.1 From b9ecd5ae24126c9b461ccb9ddb5a276bee425574 Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Tue, 16 Jun 2015 23:02:45 +0800 Subject: gnu: Add libmng. * gnu/packages/image.scm (libmng): New variable. --- gnu/packages/image.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 89590cc5ad..17da5f6391 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -563,3 +563,26 @@ with lossy compression and typically provides 3x smaller file sizes compared to PNG when lossy compression is acceptable for the red/green/blue color channels.") (license license:bsd-3))) + +(define-public libmng + (package + (name "libmng") + (version "2.0.3") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/libmng/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "1lvxnpds0vcf0lil6ia2036ghqlbl740c4d2sz0q5g6l93fjyija")))) + (build-system gnu-build-system) + (propagated-inputs + ;; These are all in the 'Libs.private' field of libmng.pc. + `(("lcms" ,lcms) + ("libjpeg" ,libjpeg) + ("zlib" ,zlib))) + (home-page "http://www.libmng.com/") + (synopsis "Library for handling MNG files") + (description + "Libmng is the MNG (Multiple-image Network Graphics) reference library.") + (license license:bsd-3))) -- cgit 1.4.1 From 2cba3d6f9e8a0ca6a3be36383f9f1c49c001cd6d Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Tue, 16 Jun 2015 23:27:10 +0800 Subject: gnu: qt: Add more inputs. * gnu/packages/qt.scm (qt)[inputs]: Add cups, libmng, postgresql and unixodbc. --- gnu/packages/qt.scm | 6 ++++++ 1 file changed, 6 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index c92f7db79a..1cf72e1586 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -29,6 +29,8 @@ #:use-module (gnu packages) #:use-module (gnu packages bison) #:use-module (gnu packages compression) + #:use-module (gnu packages cups) + #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) #:use-module (gnu packages flex) #:use-module (gnu packages gl) @@ -119,12 +121,14 @@ webrtc/tools/e2e_quality/audio/perf"))))) (inputs `(("alsa-lib" ,alsa-lib) ("dbus" ,dbus) + ("cups" ,cups) ("expat" ,expat) ("fontconfig" ,fontconfig) ("freetype" ,freetype) ("glib" ,glib) ("icu4c" ,icu4c) ("libjpeg" ,libjpeg) + ("libmng" ,libmng) ("libpci" ,pciutils) ("libpng" ,libpng) ("libx11" ,libx11) @@ -143,10 +147,12 @@ webrtc/tools/e2e_quality/audio/perf"))))) ("mysql" ,mysql) ("nss" ,nss) ("openssl" ,openssl) + ("postgresql" ,postgresql) ("pulseaudio" ,pulseaudio) ("pcre" ,pcre) ("sqlite" ,sqlite) ("udev" ,eudev) + ("unixodbc" ,unixodbc) ("xcb-util" ,xcb-util) ("xcb-util-image" ,xcb-util-image) ("xcb-util-keysyms" ,xcb-util-keysyms) -- cgit 1.4.1 From 01e64ef50434e663b0f3488dcba0b99bf6ed7a83 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Tue, 16 Jun 2015 14:20:06 -0400 Subject: gnu: talloc: Change source URI to use https. * gnu/packages/samba.scm (talloc)[source]: Change URI to use https. --- gnu/packages/samba.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm index 35866304ef..d7223bc0ba 100644 --- a/gnu/packages/samba.scm +++ b/gnu/packages/samba.scm @@ -171,7 +171,7 @@ Desktops into Active Directory environments using the winbind daemon.") (version "2.1.2") (source (origin (method url-fetch) - (uri (string-append "http://www.samba.org/ftp/talloc/talloc-" + (uri (string-append "https://www.samba.org/ftp/talloc/talloc-" version ".tar.gz")) (sha256 (base32 -- cgit 1.4.1 From f5a9ffa006687c6759e3d329159dc938b4a705ea Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Mon, 15 Jun 2015 13:18:20 +0300 Subject: system: Rename 'sudoers' into 'sudoers-file'. * gnu/system.scm (): Rename record field. (etc-directory): Rename argument. (operating-system-etc-directory): Adjust accordingly. * doc/guix.texi (operating-system Reference): Likewise. --- doc/guix.texi | 4 ++-- gnu/system.scm | 15 ++++++++------- 2 files changed, 10 insertions(+), 9 deletions(-) (limited to 'gnu') diff --git a/doc/guix.texi b/doc/guix.texi index f707b5c58f..1c7f4e1232 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -4606,8 +4606,8 @@ Linux @dfn{pluggable authentication module} (PAM) services. List of string-valued G-expressions denoting setuid programs. @xref{Setuid Programs}. -@item @code{sudoers} (default: @var{%sudoers-specification}) -@cindex sudoers +@item @code{sudoers-file} (default: @var{%sudoers-specification}) +@cindex sudoers file The contents of the @file{/etc/sudoers} file as a file-like object (@pxref{G-Expressions, @code{local-file} and @code{plain-file}}). diff --git a/gnu/system.scm b/gnu/system.scm index 92ed454b2c..565d6c10c7 100644 --- a/gnu/system.scm +++ b/gnu/system.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013, 2014, 2015 Ludovic Courtès ;;; Copyright © 2015 Mark H Weaver +;;; Copyright © 2015 Alex Kost ;;; ;;; This file is part of GNU Guix. ;;; @@ -148,8 +149,8 @@ (setuid-programs operating-system-setuid-programs (default %setuid-programs)) ; list of string-valued gexps - (sudoers operating-system-sudoers ; file-like - (default %sudoers-specification))) + (sudoers-file operating-system-sudoers-file ; file-like + (default %sudoers-specification))) ;;; @@ -440,7 +441,7 @@ on SHELLS. /etc/shells is used by xterm, polkit, and other programs." (pam-services '()) (profile "/run/current-system/profile") hosts-file nss (shells '()) - (sudoers (plain-file "sudoers" ""))) + (sudoers-file (plain-file "sudoers" ""))) "Return a derivation that builds the static part of the /etc directory." (mlet* %store-monad ((pam.d (pam-services->directory pam-services)) @@ -540,7 +541,7 @@ fi\n")) ("hosts" ,#~#$hosts-file) ("localtime" ,#~(string-append #$tzdata "/share/zoneinfo/" #$timezone)) - ("sudoers" ,sudoers))))) + ("sudoers" ,sudoers-file))))) (define (operating-system-profile os) "Return a derivation that builds the system profile of OS." @@ -624,9 +625,9 @@ use 'plain-file' instead~%") #:timezone (operating-system-timezone os) #:hosts-file /etc/hosts #:shells shells - #:sudoers (maybe-string->file - "sudoers" - (operating-system-sudoers os)) + #:sudoers-file (maybe-string->file + "sudoers" + (operating-system-sudoers-file os)) #:profile profile-drv))) (define %setuid-programs -- cgit 1.4.1 From 6178d94706cb3000859bc3f84bdbf7e796375d55 Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Wed, 17 Jun 2015 18:27:37 +0800 Subject: gnu: Add wayland. * gnu/packages/freedesktop.scm (wayland): New variable. --- gnu/packages/freedesktop.scm | 37 ++++++++++++++++++++++++++++++++++++- 1 file changed, 36 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index c5b55f30a2..eeb97cdc85 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -38,7 +38,9 @@ #:use-module (gnu packages docbook) #:use-module (gnu packages glib) ;intltool #:use-module (gnu packages xdisorg) - #:use-module (gnu packages xorg)) + #:use-module (gnu packages xorg) + #:use-module (gnu packages doxygen) + #:use-module (gnu packages libffi)) (define-public xdg-utils (package @@ -197,3 +199,36 @@ Python") (define-public python2-pyxdg (package-with-python2 python-pyxdg)) + +(define-public wayland + (package + (name "wayland") + (version "1.8.1") + (source (origin + (method url-fetch) + (uri (string-append "http://wayland.freedesktop.org/releases/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "1j3gfzn8i0xhk3j34mwb2srrscjxfyi279jhyq80mz943j6r6z7i")))) + (build-system gnu-build-system) + (native-inputs + `(("doxygen" ,doxygen) + ("pkg-config" ,pkg-config) + ("xmlto" ,xmlto) + ("xsltproc" ,libxslt))) + (inputs + `(("docbook-xml" ,docbook-xml) + ("docbook-xsl" ,docbook-xsl) + ("expat" ,expat) + ("libffi" ,libffi) + ("libxml2" ,libxml2))) ; for XML_CATALOG_FILES + (home-page "http://wayland.freedesktop.org/") + (synopsis "Display server protocol") + (description + "Wayland is a protocol for a compositor to talk to its clients as well as +a C library implementation of that protocol. The compositor can be a standalone +display server running on Linux kernel modesetting and evdev input devices, an X +application, or a wayland client itself. The clients can be traditional +applications, X servers (rootless or fullscreen) or other display servers.") + (license license:x11))) -- cgit 1.4.1 From 1bbc3b1d2c0be680a902a7745dc34f43d5bc4f9c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 17 Jun 2015 14:36:32 +0200 Subject: gnu: bedops: Update to 2.4.14. * gnu/packages/bioinformatics.scm (bedops): Update to 2.4.14. --- 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 0d8a6d518c..53e53ace58 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -87,7 +87,7 @@ BAM files.") (define-public bedops (package (name "bedops") - (version "2.4.5") + (version "2.4.14") (source (origin (method url-fetch) (uri (string-append "https://github.com/bedops/bedops/archive/v" @@ -95,7 +95,7 @@ BAM files.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0wmg6j0icimlrnsidaxrzf3hfgjvlkkcwvpdg7n4gg7hdv2m9ni5")))) + "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v")))) (build-system gnu-build-system) (arguments '(#:tests? #f -- cgit 1.4.1 From 86517de69c0626f60f60b81c42747cb19bafa69b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 17 Jun 2015 12:16:40 +0200 Subject: gnu: miso: Use HTTPS URL. * gnu/packages/bioinformatics.scm (miso)[source]: Use "https" protocol for downloading the source tarball. --- 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 53e53ace58..22a775f41f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1063,7 +1063,7 @@ sequencing tag position and orientation.") (source (origin (method url-fetch) (uri (string-append - "http://pypi.python.org/packages/source/m/misopy/misopy-" + "https://pypi.python.org/packages/source/m/misopy/misopy-" version ".tar.gz")) (sha256 (base32 -- cgit 1.4.1 From ba981db2933e47d20e22098ef1bc93db3461cebc Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Wed, 17 Jun 2015 16:25:48 -0400 Subject: gnu: guix: Update snapshot. * gnu/packages/package-management.scm (guix-devel): Update to 2c04921. --- gnu/packages/package-management.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 7f6ec56151..e8852caf24 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -166,7 +166,7 @@ the Nix package manager.") ;; ;; Note: use a short commit id; when using the long one, the limit on socket ;; file names is exceeded while running the tests. - (let ((commit "a43b55f")) + (let ((commit "2c04921")) (package (inherit guix-0.8.2) (version (string-append "0.8.2." commit)) (source (origin @@ -176,7 +176,7 @@ the Nix package manager.") (commit commit))) (sha256 (base32 - "1r0l8gfh5nxc1j0sqj8ywkg280k9qbj7zsk33z84rvl7l0nwnk88")) + "1yxb6vnpglcwl3z0djap333b2ifl8s4ncpmmkb8ylba19ij7v0bw")) (file-name (string-append "guix-" version "-checkout")))) (arguments (substitute-keyword-arguments (package-arguments guix-0.8.2) -- cgit 1.4.1 From 2f6d3e417fb99d264f0147a81771874860dcaf10 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 17 Jun 2015 09:13:04 +0200 Subject: gnu: ocaml: Don't rely on (gnu packages commencement). * gnu/packages/ocaml.scm (ocaml)[inputs]: Use (canonical-package gcc-4.8) instead of GCC-FINAL. --- gnu/packages/ocaml.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 5baf24cac0..84841d017c 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -24,12 +24,12 @@ #:use-module (guix utils) #:use-module (guix build-system gnu) #:use-module (gnu packages) + #:use-module (gnu packages gcc) #:use-module (gnu packages base) #:use-module (gnu packages emacs) #:use-module (gnu packages texinfo) #:use-module (gnu packages pkg-config) #:use-module (gnu packages compression) - #:use-module (gnu packages commencement) #:use-module (gnu packages xorg) #:use-module (gnu packages texlive) #:use-module (gnu packages perl) @@ -57,8 +57,9 @@ ("pkg-config" ,pkg-config))) (inputs `(("libx11" ,libx11) - ("gcc:lib" ,gcc-final "lib") ; for libiberty, needed for objdump support - ("zlib" ,zlib))) ; also needed for objdump support + ;; For libiberty, needed for objdump support. + ("gcc:lib" ,(canonical-package gcc-4.8) "lib") + ("zlib" ,zlib))) ;also needed for objdump support (arguments `(#:modules ((guix build gnu-build-system) (guix build utils) -- cgit 1.4.1 From 08fa76131e71dc12f5d669480d74e9183008d71a Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 17 Jun 2015 09:49:22 +0200 Subject: install: Turn off deduplication for the binary tarball. * gnu/build/install.scm (register-closure): Add #:deduplicate? parameter and honor it. (populate-single-profile-directory): Likewise. * gnu/system/install.scm (self-contained-tarball): Pass #:deduplicate? #f. Invoke tar with --check-links. --- gnu/build/install.scm | 20 ++++++++++++++------ gnu/system/install.scm | 6 +++++- 2 files changed, 19 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/build/install.scm b/gnu/build/install.scm index 32fbe8efbc..9085e22e09 100644 --- a/gnu/build/install.scm +++ b/gnu/build/install.scm @@ -161,20 +161,27 @@ as created and modified at the Epoch." (utime file 0 0 0 0)))) (find-files directory ""))) -(define (register-closure store closure) +(define* (register-closure store closure + #:key (deduplicate? #t)) "Register CLOSURE in STORE, where STORE is the directory name of the target store and CLOSURE is the name of a file containing a reference graph as used -by 'guix-register'. As a side effect, this resets timestamps on store files." - (let ((status (system* "guix-register" "--prefix" store - closure))) +by 'guix-register'. As a side effect, this resets timestamps on store files +and, if DEDUPLICATE? is true, deduplicates files common to CLOSURE and the +rest of STORE." + (let ((status (apply system* "guix-register" "--prefix" store + (append (if deduplicate? '() '("--no-deduplication")) + (list closure))))) (unless (zero? status) (error "failed to register store items" closure)))) (define* (populate-single-profile-directory directory - #:key profile closure) + #:key profile closure + deduplicate?) "Populate DIRECTORY with a store containing PROFILE, whose closure is given in the file called CLOSURE (as generated by #:references-graphs.) DIRECTORY is initialized to contain a single profile under /root pointing to PROFILE. +DEDUPLICATE? determines whether to deduplicate files in the store. + This is used to create the self-contained Guix tarball." (define (scope file) (string-append directory "/" file)) @@ -190,7 +197,8 @@ This is used to create the self-contained Guix tarball." ;; Populate the store. (populate-store (list closure) directory) - (register-closure (canonicalize-path directory) closure) + (register-closure (canonicalize-path directory) closure + #:deduplicate? deduplicate?) ;; XXX: 'guix-register' registers profiles as GC roots but the symlink ;; target uses $TMPDIR. Fix that. diff --git a/gnu/system/install.scm b/gnu/system/install.scm index e8a36b3def..6f4116ef9b 100644 --- a/gnu/system/install.scm +++ b/gnu/system/install.scm @@ -63,15 +63,19 @@ under /root/.guix-profile where GUIX is installed." (setenv "PATH" (string-append #$guix "/sbin:" #$tar "/bin:" #$xz "/bin")) + ;; Note: there is not much to gain here with deduplication and there + ;; is the overhead of the '.links' directory, so turn it off. (populate-single-profile-directory %root #:profile #$profile - #:closure "profile") + #:closure "profile" + #:deduplicate? #f) ;; Create the tarball. Use GNU format so there's no file name ;; length limitation. (with-directory-excursion %root (zero? (system* "tar" "--xz" "--format=gnu" "--owner=root:0" "--group=root:0" + "--check-links" "-cvf" #$output ;; Avoid adding / and /var to the tarball, ;; so that the ownership and permissions of those -- cgit 1.4.1 From 84189ebc66266f03b9ca7e8b912d529886436851 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 17 Jun 2015 10:49:29 +0200 Subject: Move 'specification->package+output' to (gnu packages). * guix/scripts/package.scm (specification->package+output): Move to... * gnu/packages.scm (specification->package+output): ... here * guix/scripts/archive.scm (guix): Adjust accordingly. --- gnu/packages.scm | 36 +++++++++++++++++++++++++++++++++++- guix/scripts/archive.scm | 4 ++-- guix/scripts/package.scm | 36 +----------------------------------- 3 files changed, 38 insertions(+), 38 deletions(-) (limited to 'gnu') diff --git a/gnu/packages.scm b/gnu/packages.scm index 9eb4877be8..6e46a890bb 100644 --- a/gnu/packages.scm +++ b/gnu/packages.scm @@ -51,7 +51,8 @@ check-package-freshness - specification->package)) + specification->package + specification->package+output)) ;;; Commentary: ;;; @@ -418,3 +419,36 @@ present, return the preferred newest version." (leave (_ "~A: package not found for version ~a~%") name version) (leave (_ "~A: unknown package~%") name)))))) + +(define* (specification->package+output spec #:optional (output "out")) + "Return the package and output specified by SPEC, or #f and #f; SPEC may +optionally contain a version number and an output name, as in these examples: + + guile + guile-2.0.9 + guile:debug + guile-2.0.9:debug + +If SPEC does not specify a version number, return the preferred newest +version; if SPEC does not specify an output, return OUTPUT." + (define (ensure-output p sub-drv) + (if (member sub-drv (package-outputs p)) + sub-drv + (leave (_ "package `~a' lacks output `~a'~%") + (package-full-name p) + sub-drv))) + + (let-values (((name version sub-drv) + (package-specification->name+version+output spec output))) + (match (find-best-packages-by-name name version) + ((p) + (values p (ensure-output p sub-drv))) + ((p p* ...) + (warning (_ "ambiguous package specification `~a'~%") + spec) + (warning (_ "choosing ~a from ~a~%") + (package-full-name p) + (location->string (package-location p))) + (values p (ensure-output p sub-drv))) + (() + (leave (_ "~a: package not found~%") spec))))) diff --git a/guix/scripts/archive.scm b/guix/scripts/archive.scm index ea6801a6eb..ab2fc46c31 100644 --- a/guix/scripts/archive.scm +++ b/guix/scripts/archive.scm @@ -27,6 +27,8 @@ #:use-module (guix ui) #:use-module (guix pki) #:use-module (guix pk-crypto) + #:use-module (guix scripts build) + #:use-module (gnu packages) #:use-module (ice-9 match) #:use-module (ice-9 format) #:use-module (ice-9 rdelim) @@ -34,8 +36,6 @@ #:use-module (srfi srfi-11) #:use-module (srfi srfi-26) #:use-module (srfi srfi-37) - #:use-module (guix scripts build) - #:use-module (guix scripts package) #:use-module (rnrs io ports) #:export (guix-archive)) diff --git a/guix/scripts/package.scm b/guix/scripts/package.scm index d9f38fb8bc..56a6e2db64 100644 --- a/guix/scripts/package.scm +++ b/guix/scripts/package.scm @@ -47,8 +47,7 @@ #:use-module (gnu packages base) #:use-module (gnu packages guile) #:use-module ((gnu packages bootstrap) #:select (%bootstrap-guile)) - #:export (specification->package+output - switch-to-generation + #:export (switch-to-generation switch-to-previous-generation roll-back delete-generation @@ -324,39 +323,6 @@ similar." (primitive-_exit 0) (apply throw args))))) -(define* (specification->package+output spec #:optional (output "out")) - "Return the package and output specified by SPEC, or #f and #f; SPEC may -optionally contain a version number and an output name, as in these examples: - - guile - guile-2.0.9 - guile:debug - guile-2.0.9:debug - -If SPEC does not specify a version number, return the preferred newest -version; if SPEC does not specify an output, return OUTPUT." - (define (ensure-output p sub-drv) - (if (member sub-drv (package-outputs p)) - sub-drv - (leave (_ "package `~a' lacks output `~a'~%") - (package-full-name p) - sub-drv))) - - (let-values (((name version sub-drv) - (package-specification->name+version+output spec output))) - (match (find-best-packages-by-name name version) - ((p) - (values p (ensure-output p sub-drv))) - ((p p* ...) - (warning (_ "ambiguous package specification `~a'~%") - spec) - (warning (_ "choosing ~a from ~a~%") - (package-full-name p) - (location->string (package-location p))) - (values p (ensure-output p sub-drv))) - (() - (leave (_ "~a: package not found~%") spec))))) - (define (upgradeable? name current-version current-path) "Return #t if there's a version of package NAME newer than CURRENT-VERSION, or if the newest available version is equal to CURRENT-VERSION but would have -- cgit 1.4.1 From 684bf7c7f14bde59059093f2c6e4f79c5d6f0fec Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Wed, 17 Jun 2015 19:21:22 +1000 Subject: gnu: Add diamond. * gnu/packages/bioinformatics.scm (diamond): New variable. --- gnu/packages/bioinformatics.scm | 52 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 22a775f41f..12c9175ed3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015 Ricardo Wurmus +;;; Copyright © 2015 Ben Woodcroft ;;; ;;; This file is part of GNU Guix. ;;; @@ -28,6 +29,7 @@ #:use-module (guix build-system python) #:use-module (guix build-system trivial) #:use-module (gnu packages) + #:use-module (gnu packages algebra) #:use-module (gnu packages base) #:use-module (gnu packages boost) #:use-module (gnu packages compression) @@ -615,6 +617,56 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") other types of unwanted sequence from high-throughput sequencing reads.") (license license:expat))) +(define-public diamond + (package + (name "diamond") + (version "0.7.9") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/bbuchfink/diamond/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15")) + (snippet '(begin + (delete-file "bin/diamond") + #t)))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f ;no "check" target + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'enter-source-dir + (lambda _ + (chdir "src") + #t)) + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin"))) + (mkdir-p bin) + (copy-file "../bin/diamond" + (string-append bin "/diamond")) + #t)))))) + (native-inputs + `(("bc" ,bc))) + (inputs + `(("boost" ,boost) + ("zlib" ,zlib))) + (home-page "https://github.com/bbuchfink/diamond") + (synopsis "Accelerated BLAST compatible local sequence aligner") + (description + "DIAMOND is a BLAST-compatible local aligner for mapping protein and +translated DNA query sequences against a protein reference database (BLASTP +and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short +reads at a typical sensitivity of 90-99% relative to BLAST depending on the +data and settings.") + (license (license:non-copyleft "file://src/COPYING" + "See src/COPYING in the distribution.")))) + (define-public edirect (package (name "edirect") -- cgit 1.4.1 From 040ca34f7e7a9eff51363b72aad62cbcb3ad5b20 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 18 Jun 2015 00:08:52 -0400 Subject: gnu: guix: Update snapshot. * gnu/packages/package-management.scm (guix-devel): Update to 684bf7c. --- gnu/packages/package-management.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index e8852caf24..3da9df92cc 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -166,7 +166,7 @@ the Nix package manager.") ;; ;; Note: use a short commit id; when using the long one, the limit on socket ;; file names is exceeded while running the tests. - (let ((commit "2c04921")) + (let ((commit "684bf7c")) (package (inherit guix-0.8.2) (version (string-append "0.8.2." commit)) (source (origin @@ -176,7 +176,7 @@ the Nix package manager.") (commit commit))) (sha256 (base32 - "1yxb6vnpglcwl3z0djap333b2ifl8s4ncpmmkb8ylba19ij7v0bw")) + "0fq9ajj17kbb0f1p79al2vcqah9sl0imayhggcp31c3vq0ahya9g")) (file-name (string-append "guix-" version "-checkout")))) (arguments (substitute-keyword-arguments (package-arguments guix-0.8.2) -- cgit 1.4.1