From 41125eaff8fd4d47bd22b3cc423b9edc1b7b918c Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sun, 25 Feb 2018 16:06:24 +0100 Subject: gnu: Add maven-resolver-api. * gnu/packages/maven.scm: New file. (maven-resolver-api): New variable. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. --- gnu/local.mk | 1 + gnu/packages/maven.scm | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 gnu/packages/maven.scm diff --git a/gnu/local.mk b/gnu/local.mk index d091a89b82..d90d8a318d 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -281,6 +281,7 @@ GNU_SYSTEM_MODULES = \ %D%/packages/marst.scm \ %D%/packages/mate.scm \ %D%/packages/maths.scm \ + %D%/packages/maven.scm \ %D%/packages/mc.scm \ %D%/packages/mcrypt.scm \ %D%/packages/medical.scm \ diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm new file mode 100644 index 0000000000..7fcc7b4533 --- /dev/null +++ b/gnu/packages/maven.scm @@ -0,0 +1,50 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2018 Julien Lepiller +;;; +;;; 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 maven) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix download) + #:use-module (guix utils) + #:use-module (guix build-system ant) + #:use-module (gnu packages) + #:use-module (gnu packages java)) + +(define-public maven-resolver-api + (package + (name "maven-resolver-api") + (version "1.1.1") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/apache/maven-resolver/" + "archive/maven-resolver-" version ".tar.gz")) + (sha256 + (base32 + "0rpvdg3qr1j88gw0ankf0wnwfyq6238mdlm7s39vf5jrcvhdgwcl")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "maven-resolver-api.jar" + #:source-dir "maven-resolver-api/src/main/java" + #:test-dir "maven-resolver-api/src/test")) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core))) + (home-page "https://github.com/apache/maven-resolver") + (synopsis "Maven repository system API") + (description "This package contains the API for the maven repository system.") + (license license:asl2.0))) -- cgit 1.4.1 From d85cb53924ef648ab4ad373a664dc75f4e1c3d7a Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sun, 25 Feb 2018 16:08:57 +0100 Subject: gnu: Add maven-resolver-spi. * gnu/packages/maven.scm (maven-resolver-spi): New variable. --- gnu/packages/maven.scm | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 7fcc7b4533..8fa7ecc5b8 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -48,3 +48,18 @@ (synopsis "Maven repository system API") (description "This package contains the API for the maven repository system.") (license license:asl2.0))) + +(define-public maven-resolver-spi + (package + (inherit maven-resolver-api) + (name "maven-resolver-spi") + (arguments + `(#:jar-name "maven-resolver-spi.jar" + #:source-dir "maven-resolver-spi/src/main/java" + #:test-dir "maven-resolver-spi/src/test" + #:jdk ,icedtea-8)) + (inputs + `(("maven-resolver-api" ,maven-resolver-api))) + (synopsis "Maven repository system SPI") + (description "This package contains the service provider interface (SPI) +for repository system implementations and repository connectors."))) -- cgit 1.4.1 From 360537838ef77cdc45fc2433e108802461fa8410 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sun, 25 Feb 2018 16:17:40 +0100 Subject: gnu: Add maven-resolver-test-util. * gnu/packages/maven.scm (maven-resolver-test-util): New variable. --- gnu/packages/maven.scm | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 8fa7ecc5b8..8cc4938062 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -63,3 +63,19 @@ (synopsis "Maven repository system SPI") (description "This package contains the service provider interface (SPI) for repository system implementations and repository connectors."))) + +(define-public maven-resolver-test-util + (package + (inherit maven-resolver-api) + (name "maven-resolver-test-util") + (arguments + `(#:jar-name "maven-resolver-test-util.jar" + #:source-dir "maven-resolver-test-util/src/main/java" + #:test-dir "maven-resolver-test-util/src/test" + #:jdk ,icedtea-8)) + (inputs + `(("maven-resolver-api" ,maven-resolver-api) + ("maven-resolver-spi" ,maven-resolver-spi))) + (synopsis "Utility classes for testing the maven repository system") + (description "This package contains a collection of utility classes to +ease testing of the repository system."))) -- cgit 1.4.1 From bca6cf54f46692290aa759e3e741f812a82366ff Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sun, 25 Feb 2018 16:19:48 +0100 Subject: gnu: Add maven-resolver-util. gnu/packages/maven.scm (maven-resolver-util): New variable. --- gnu/packages/maven.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 8cc4938062..6c8f4b9319 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -79,3 +79,22 @@ for repository system implementations and repository connectors."))) (synopsis "Utility classes for testing the maven repository system") (description "This package contains a collection of utility classes to ease testing of the repository system."))) + +(define-public maven-resolver-util + (package + (inherit maven-resolver-api) + (name "maven-resolver-util") + (arguments + `(#:jar-name "maven-resolver-util.jar" + #:source-dir "maven-resolver-util/src/main/java" + #:test-dir "maven-resolver-util/src/test" + #:jdk ,icedtea-8)) + (inputs + `(("maven-resolver-api" ,maven-resolver-api))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core) + ("maven-resolver-test-util" ,maven-resolver-test-util))) + (synopsis "Utility classes for the maven repository system") + (description "This package contains a collection of utility classes to +ease usage of the repository system."))) -- cgit 1.4.1 From f70666c9ce4f463d47c4d1694ed608bfadb56cd7 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sun, 25 Feb 2018 16:22:49 +0100 Subject: gnu: Add maven-resolver-connector-basic. * gnu/packages/maven.scm (maven-resolver-connector-basic): New variable. --- gnu/packages/maven.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 6c8f4b9319..81021f6461 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -98,3 +98,33 @@ ease testing of the repository system."))) (synopsis "Utility classes for the maven repository system") (description "This package contains a collection of utility classes to ease usage of the repository system."))) + +(define-public maven-resolver-connector-basic + (package + (inherit maven-resolver-api) + (name "maven-resolver-connector-basic") + (arguments + `(#:jar-name "maven-resolver-connector-basic.jar" + #:source-dir "maven-resolver-connector-basic/src/main/java" + #:test-dir "maven-resolver-connector-basic/src/test" + #:jdk ,icedtea-8 + #:phases + (modify-phases %standard-phases + (add-before 'build 'generate-sisu + (lambda _ + (mkdir-p "build/classes/META-INF/sisu") + (with-output-to-file "build/classes/META-INF/sisu/javax.inject.Named" + (lambda _ + (display "org.eclipse.aether.connector.basic.BasicRepositoryConnectorFactory\n")))))))) + (inputs + `(("maven-resolver-api" ,maven-resolver-api) + ("maven-resolver-spi" ,maven-resolver-spi) + ("maven-resolver-util" ,maven-resolver-util) + ("java-javax-inject" ,java-javax-inject))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core) + ("maven-resolver-test-util" ,maven-resolver-test-util))) + (synopsis "Maven repository connector implementation") + (description "This package contains a repository connector implementation +for repositories using URI-based layouts."))) -- cgit 1.4.1 From 2468ca04882f27ac28a427e2445a20157b9b2802 Mon Sep 17 00:00:00 2001 From: Eric Bavier Date: Tue, 6 Mar 2018 23:33:57 -0600 Subject: gnu: thefuck: Update to 3.25. * gnu/packages/admin.scm (thefuck): Update to 3.25 [inputs]: Add python-pyte. [native-inputs]: Remove python-setuptools. * gnu/packages/patches/thefuck-test-environ.patch: Adjust to latest source. --- gnu/packages/admin.scm | 13 ++++++------- gnu/packages/patches/thefuck-test-environ.patch | 20 ++++++++++---------- 2 files changed, 16 insertions(+), 17 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 78b7b64dd1..26ee4aaabe 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès ;;; Copyright © 2013 Cyril Roelandt ;;; Copyright © 2014, 2015, 2016, 2018 Mark H Weaver -;;; Copyright © 2014, 2015, 2016, 2017 Eric Bavier +;;; Copyright © 2014, 2015, 2016, 2017, 2018 Eric Bavier ;;; Copyright © 2015, 2016 Taylan Ulrich Bayırlı/Kammer ;;; Copyright © 2015 Alex Sassmannshausen ;;; Copyright © 2015 Eric Dvorsak @@ -75,6 +75,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-web) + #:use-module (gnu packages terminals) #:use-module (gnu packages texinfo) #:use-module (gnu packages groff) #:use-module (gnu packages pciutils) @@ -1855,7 +1856,7 @@ throughput (in the same interval).") (define-public thefuck (package (name "thefuck") - (version "3.19") + (version "3.25") (source (origin (method url-fetch) (uri (string-append "https://github.com/nvbn/thefuck/archive/" @@ -1863,7 +1864,7 @@ throughput (in the same interval).") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "191zbvkyc02h0wwd46xwj4zzg7jhlr8xv0ji6knqkgjnk0nvqq01")) + "088bn2l1376qlndbpnjya4q1x3913nj3yj3wc7s2w3bz66d23skk")) (patches (search-patches "thefuck-test-environ.patch")))) (build-system python-build-system) (arguments @@ -1881,14 +1882,12 @@ throughput (in the same interval).") `(("python-colorama" ,python-colorama) ("python-decorator" ,python-decorator) ("python-psutil" ,python-psutil) + ("python-pyte" ,python-pyte) ("python-six" ,python-six))) (native-inputs `(("python-mock" ,python-mock) ("python-pytest" ,python-pytest) - ("python-pytest-mock" ,python-pytest-mock) - ;; Requires setuptools >= 17.1 due to some features used, while our - ;; python currently only includes 12.0. TODO: Remove this input. - ("python-setuptools" ,python-setuptools))) + ("python-pytest-mock" ,python-pytest-mock))) (home-page "https://github.com/nvbn/thefuck") (synopsis "Correct mistyped console command") (description diff --git a/gnu/packages/patches/thefuck-test-environ.patch b/gnu/packages/patches/thefuck-test-environ.patch index 0c602a38c4..54194d8928 100644 --- a/gnu/packages/patches/thefuck-test-environ.patch +++ b/gnu/packages/patches/thefuck-test-environ.patch @@ -1,14 +1,14 @@ Retain environment setting of "HOME" for tests that need os.path.expanduser() to return a readable directory in the build chroot. ---- thefuck-3.15/tests/test_conf.py -+++ thefuck-3.15/tests/test_conf.py -@@ -12,7 +12,7 @@ - - @pytest.fixture - def environ(monkeypatch): -- data = {} -+ data = {"HOME": os.environ.get("HOME")} - monkeypatch.setattr('thefuck.conf.os.environ', data) - return data +--- thefuck-3.25/tests/conftest.py ++++ thefuck-3.25/tests/conftest.py +@@ -64,6 +64,7 @@ def set_shell(monkeypatch): + @pytest.fixture(autouse=True) + def os_environ(monkeypatch): +- env = {'PATH': os.environ['PATH']} ++ env = {'PATH': os.environ['PATH'], ++ 'HOME': os.environ['HOME']} + monkeypatch.setattr('os.environ', env) + return env -- cgit 1.4.1 From 366ddc1ac549efee9acd1fddd30c9baee89ec18a Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 7 Mar 2018 09:58:40 +0100 Subject: services: dicod: Depend on 'user-processes'. * gnu/services/dict.scm (dicod-shepherd-service): Add 'requirement'. --- gnu/services/dict.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/services/dict.scm b/gnu/services/dict.scm index c8403c0135..70b05e8f80 100644 --- a/gnu/services/dict.scm +++ b/gnu/services/dict.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016 Sou Bunnbu -;;; Copyright © 2016, 2017 Ludovic Courtès +;;; Copyright © 2016, 2017, 2018 Ludovic Courtès ;;; Copyright © 2017 Huang Ying ;;; ;;; This file is part of GNU Guix. @@ -150,6 +150,7 @@ database { (gnu system file-systems))) (list (shepherd-service (provision '(dicod)) + (requirement '(user-processes)) (documentation "Run the dicod daemon.") (modules '((gnu build shepherd) (gnu system file-systems))) -- cgit 1.4.1 From 6c4458172d12dbda969c2eae5b3b6be19a068780 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 7 Mar 2018 10:00:07 +0100 Subject: services: file-systems: Include 'user-file-systems' service. Previously the KNOWN-FS value used in 'essential-services' would be incomplete: it would lack all the file systems provided by services that extend 'file-system-service-type' (/sys/fs/cgroup, /proc/sys/fs/binfmt_misc, etc.) Consequently, upon shutdown, 'user-processes' would unmount these file systems before their corresponding service had been stopped; when their corresponding (e.g., 'file-system-/proc/sys/fs/binfmt_misc') was stopped, its 'umount' call would fail. This was harmless in practice, but this patch makes sure things work as intended and file systems are unmounted in the right order. * gnu/services/base.scm (file-system-shepherd-services): Instantiate 'user-file-systems' Shepherd service from here. (user-unmount-service-type, user-unmount-service): Remove. * gnu/system.scm (essential-services): Remove call to 'user-unmount-service'. * gnu/system/install.scm (cow-store-service-type): Adjust comment. --- gnu/services/base.scm | 64 +++++++++++++++++++++++--------------------------- gnu/system.scm | 3 +-- gnu/system/install.scm | 2 +- 3 files changed, 32 insertions(+), 37 deletions(-) diff --git a/gnu/services/base.scm b/gnu/services/base.scm index 69e211ffa3..be30f2d9c3 100644 --- a/gnu/services/base.scm +++ b/gnu/services/base.scm @@ -55,7 +55,6 @@ #:export (fstab-service-type root-file-system-service file-system-service-type - user-unmount-service swap-service user-processes-service-type host-name-service @@ -464,7 +463,36 @@ FILE-SYSTEM." (start #~(const #t)) (stop #~(const #f)))) - (cons sink (map file-system-shepherd-service file-systems)))) + (define known-mount-points + (map file-system-mount-point file-systems)) + + (define user-unmount + (shepherd-service + (documentation "Unmount manually-mounted file systems.") + (provision '(user-file-systems)) + (start #~(const #t)) + (stop #~(lambda args + (define (known? mount-point) + (member mount-point + (cons* "/proc" "/sys" '#$known-mount-points))) + + ;; Make sure we don't keep the user's mount points busy. + (chdir "/") + + (for-each (lambda (mount-point) + (format #t "unmounting '~a'...~%" mount-point) + (catch 'system-error + (lambda () + (umount mount-point)) + (lambda args + (let ((errno (system-error-errno args))) + (format #t "failed to unmount '~a': ~a~%" + mount-point (strerror errno)))))) + (filter (negate known?) (mount-points))) + #f)))) + + (cons* sink user-unmount + (map file-system-shepherd-service file-systems)))) (define file-system-service-type (service-type (name 'file-systems) @@ -483,38 +511,6 @@ FILE-SYSTEM." "Provide Shepherd services to mount and unmount the given file systems, as well as corresponding @file{/etc/fstab} entries."))) -(define user-unmount-service-type - (shepherd-service-type - 'user-file-systems - (lambda (known-mount-points) - (shepherd-service - (documentation "Unmount manually-mounted file systems.") - (provision '(user-file-systems)) - (start #~(const #t)) - (stop #~(lambda args - (define (known? mount-point) - (member mount-point - (cons* "/proc" "/sys" '#$known-mount-points))) - - ;; Make sure we don't keep the user's mount points busy. - (chdir "/") - - (for-each (lambda (mount-point) - (format #t "unmounting '~a'...~%" mount-point) - (catch 'system-error - (lambda () - (umount mount-point)) - (lambda args - (let ((errno (system-error-errno args))) - (format #t "failed to unmount '~a': ~a~%" - mount-point (strerror errno)))))) - (filter (negate known?) (mount-points))) - #f)))))) - -(define (user-unmount-service known-mount-points) - "Return a service whose sole purpose is to unmount file systems not listed -in KNOWN-MOUNT-POINTS when it is stopped." - (service user-unmount-service-type known-mount-points)) ;;; diff --git a/gnu/system.scm b/gnu/system.scm index 1bcc1e1384..eb4b63c428 100644 --- a/gnu/system.scm +++ b/gnu/system.scm @@ -453,7 +453,6 @@ a container or that of a \"bare metal\" system." (let* ((mappings (device-mapping-services os)) (root-fs (root-file-system-service)) (other-fs (non-boot-file-system-service os)) - (unmount (user-unmount-service known-fs)) (swaps (swap-services os)) (procs (service user-processes-service-type)) (host-name (host-name-service (operating-system-host-name os))) @@ -478,7 +477,7 @@ a container or that of a \"bare metal\" system." (service fstab-service-type '()) (session-environment-service (operating-system-environment-variables os)) - host-name procs root-fs unmount + host-name procs root-fs (service setuid-program-service-type (operating-system-setuid-programs os)) (service profile-service-type diff --git a/gnu/system/install.scm b/gnu/system/install.scm index 37c591ec3a..97f5abe0b6 100644 --- a/gnu/system/install.scm +++ b/gnu/system/install.scm @@ -133,7 +133,7 @@ the given target.") (stop #~(lambda (target) ;; Delete the temporary directory, but leave everything ;; mounted as there may still be processes using it since - ;; 'user-processes' doesn't depend on us. The 'user-unmount' + ;; 'user-processes' doesn't depend on us. The 'user-file-systems' ;; service will unmount TARGET eventually. (delete-file-recursively (string-append target #$%backing-directory)))))))) -- cgit 1.4.1 From ca23693d280de5c4031058da4d3041d830080484 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 7 Mar 2018 10:41:06 +0100 Subject: linux-initrd: Factorize 'check-device-initrd-modules'. * gnu/system/mapped-devices.scm (check-device-initrd-modules): Move to... * gnu/system/linux-initrd.scm (check-device-initrd-modules): ... here. New procedure. * po/guix/POTFILES.in: Add it. * guix/scripts/system.scm (check-initrd-modules)[check-device]: Remove. Use 'check-device-initrd-modules' instead. --- gnu/system/linux-initrd.scm | 24 +++++++++++++++++++++++- gnu/system/mapped-devices.scm | 19 ++----------------- guix/scripts/system.scm | 23 +++++------------------ po/guix/POTFILES.in | 1 + 4 files changed, 31 insertions(+), 36 deletions(-) diff --git a/gnu/system/linux-initrd.scm b/gnu/system/linux-initrd.scm index e0cb59c009..d75caed83e 100644 --- a/gnu/system/linux-initrd.scm +++ b/gnu/system/linux-initrd.scm @@ -24,6 +24,7 @@ #:use-module (guix store) #:use-module (guix gexp) #:use-module (guix utils) + #:use-module (guix i18n) #:use-module ((guix store) #:select (%store-prefix)) #:use-module ((guix derivations) @@ -37,16 +38,22 @@ #:select (%guile-static-stripped)) #:use-module (gnu system file-systems) #:use-module (gnu system mapped-devices) + #:autoload (gnu build linux-modules) + (device-module-aliases matching-modules) #:use-module (ice-9 match) #:use-module (ice-9 regex) #:use-module (ice-9 vlist) + #:use-module (ice-9 format) #:use-module (srfi srfi-1) #:use-module (srfi srfi-26) + #:use-module (srfi srfi-34) + #:use-module (srfi srfi-35) #:export (expression->initrd %base-initrd-modules raw-initrd file-system-packages - base-initrd)) + base-initrd + check-device-initrd-modules)) ;;; Commentary: @@ -343,4 +350,19 @@ loaded at boot time in the order in which they appear." #:volatile-root? volatile-root? #:on-error on-error)) +(define (check-device-initrd-modules device linux-modules location) + "Raise an error if DEVICE needs modules beyond LINUX-MODULES to operate. +DEVICE must be a \"/dev\" file name." + (let ((modules (delete-duplicates + (append-map matching-modules + (device-module-aliases device))))) + (unless (every (cute member <> linux-modules) modules) + (raise (condition + (&message + (message (format #f (G_ "you may need these modules \ +in the initrd for ~a:~{ ~a~}") + device modules))) + (&error-location + (location (source-properties->location location)))))))) + ;;; linux-initrd.scm ends here diff --git a/gnu/system/mapped-devices.scm b/gnu/system/mapped-devices.scm index 5ceb5e658c..e6ac635231 100644 --- a/gnu/system/mapped-devices.scm +++ b/gnu/system/mapped-devices.scm @@ -29,9 +29,9 @@ #:use-module (gnu services) #:use-module (gnu services shepherd) #:use-module (gnu system uuid) + #:use-module ((gnu system linux-initrd) + #:select (check-device-initrd-modules)) #:autoload (gnu build file-systems) (find-partition-by-luks-uuid) - #:autoload (gnu build linux-modules) - (device-module-aliases matching-modules) #:autoload (gnu packages cryptsetup) (cryptsetup-static) #:autoload (gnu packages linux) (mdadm-static) #:use-module (srfi srfi-1) @@ -154,21 +154,6 @@ #~(zero? (system* #$(file-append cryptsetup-static "/sbin/cryptsetup") "close" #$target))) -(define (check-device-initrd-modules device linux-modules location) - "Raise an error if DEVICE needs modules beyond LINUX-MODULES to operate. -DEVICE must be a \"/dev\" file name." - (let ((modules (delete-duplicates - (append-map matching-modules - (device-module-aliases device))))) - (unless (every (cute member <> linux-modules) modules) - (raise (condition - (&message - (message (format #f (G_ "you may need these modules \ -in the initrd for ~a:~{ ~a~}") - device modules))) - (&error-location - (location (source-properties->location location)))))))) - (define* (check-luks-device md #:key needed-for-boot? (initrd-modules '()) diff --git a/guix/scripts/system.scm b/guix/scripts/system.scm index ff322ec785..acfccce96d 100644 --- a/guix/scripts/system.scm +++ b/guix/scripts/system.scm @@ -43,8 +43,7 @@ (find-partition-by-label find-partition-by-uuid) #:autoload (gnu build linux-modules) (device-module-aliases matching-modules) - #:autoload (gnu system linux-initrd) - (base-initrd default-initrd-modules) + #:use-module (gnu system linux-initrd) #:use-module (gnu system) #:use-module (gnu bootloader) #:use-module (gnu system file-systems) @@ -661,27 +660,15 @@ checking this by themselves in their 'check' procedure." ('uuid (find-partition-by-uuid device)) ('label (find-partition-by-label device))))) - (define (check-device device location) - (let ((modules (delete-duplicates - (append-map matching-modules - (device-module-aliases device))))) - (unless (every (cute member <> (operating-system-initrd-modules os)) - modules) - (raise (condition - (&message - (message (format #f (G_ "you need these modules \ -in the initrd for ~a:~{ ~a~}") - device modules))) - (&error-location (location location))))))) - (define file-systems (filter file-system-needed-for-boot? (operating-system-file-systems os))) (for-each (lambda (fs) - (check-device (file-system-/dev fs) - (source-properties->location - (file-system-location fs)))) + (check-device-initrd-modules (file-system-/dev fs) + (operating-system-initrd-modules os) + (source-properties->location + (file-system-location fs)))) file-systems)) diff --git a/po/guix/POTFILES.in b/po/guix/POTFILES.in index 6510b99e8f..ba09605375 100644 --- a/po/guix/POTFILES.in +++ b/po/guix/POTFILES.in @@ -5,6 +5,7 @@ gnu/packages.scm gnu/services.scm gnu/system.scm gnu/services/shepherd.scm +gnu/system/linux-initrd.scm gnu/system/shadow.scm guix/scripts.scm guix/scripts/build.scm -- cgit 1.4.1 From e1ba6d49ea4df327e4dde9a994c4a89b71484d69 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 7 Mar 2018 10:52:24 +0100 Subject: ui: Display fix hints in the case where we have location info. * guix/ui.scm (call-with-error-handling): Display fix-hints in the error + message case. --- guix/ui.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/guix/ui.scm b/guix/ui.scm index a4943c2a7f..5b87f1e29b 100644 --- a/guix/ui.scm +++ b/guix/ui.scm @@ -639,6 +639,8 @@ directories:~{ ~a~}~%") (G_ "~a: error: ~a~%") (location->string (error-location c)) (gettext (condition-message c) %gettext-domain)) + (when (fix-hint? c) + (display-hint (condition-fix-hint c))) (exit 1)) ((and (message-condition? c) (fix-hint? c)) (format (current-error-port) "~a: error: ~a~%" -- cgit 1.4.1 From 16de45557f782d23a87ae2fa394267d5826e834a Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 7 Mar 2018 10:53:16 +0100 Subject: ui: 'display-hint' preserves Texinfo formatting. The previous method would mess up with @example formatting, for instance. * guix/ui.scm (display-hint): Parameterize '%text-width' instead of using 'fill-paragraph'. --- guix/ui.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/guix/ui.scm b/guix/ui.scm index 5b87f1e29b..cb49a15c4d 100644 --- a/guix/ui.scm +++ b/guix/ui.scm @@ -299,8 +299,10 @@ VARIABLE and return it, or #f if none was found." "Display MESSAGE, a l10n message possibly containing Texinfo markup, to PORT." (format port (G_ "hint: ~a~%") - (fill-paragraph (texi->plain-text message) - (terminal-columns) 8))) + ;; XXX: We should arrange so that the initial indent is wider. + (parameterize ((%text-width (max 15 + (- (terminal-columns) 5)))) + (texi->plain-text message)))) (define* (report-load-error file args #:optional frame) "Report the failure to load FILE, a user-provided Scheme file. -- cgit 1.4.1 From abfbdafd0ee331770f783a75cff29aada9fbf4ae Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 7 Mar 2018 11:00:44 +0100 Subject: linux-initrd: Add a hint for the missing module error. * gnu/system/linux-initrd.scm (check-device-initrd-modules): Add a '&fix-hint'. --- gnu/system/linux-initrd.scm | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/gnu/system/linux-initrd.scm b/gnu/system/linux-initrd.scm index d75caed83e..1eb5f5130d 100644 --- a/gnu/system/linux-initrd.scm +++ b/gnu/system/linux-initrd.scm @@ -362,6 +362,18 @@ DEVICE must be a \"/dev\" file name." (message (format #f (G_ "you may need these modules \ in the initrd for ~a:~{ ~a~}") device modules))) + (&fix-hint + (hint (format #f (G_ "Try adding them to the +@code{initrd-modules} field of your @code{operating-system} declaration, along +these lines: + +@example + (operating-system + ;; @dots{} + (initrd-modules (append (list~{ ~s~}) + %base-initrd-modules))) +@end example\n") + modules))) (&error-location (location (source-properties->location location)))))))) -- cgit 1.4.1 From 270750d440b4b2c5f88694b5abc2c2b48046d173 Mon Sep 17 00:00:00 2001 From: Charlie Ritter Date: Tue, 6 Mar 2018 10:59:47 -0500 Subject: gnu: Add IBM Plex font. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fonts.scm (font-ibm-plex): New variable. Co-authored-by: Ludovic Courtès --- gnu/packages/fonts.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index 8af4f8dc83..aa9e466ebb 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -21,6 +21,7 @@ ;;; Copyright © 2017 Brendan Tildesley ;;; Copyright © 2017 Arun Isaac ;;; Copyright © 2017 Mohammed Sadiq +;;; Copyright © 2018 Charlie Ritter ;;; ;;; This file is part of GNU Guix. ;;; @@ -55,6 +56,27 @@ #:use-module (gnu packages python) #:use-module (gnu packages xorg)) +(define-public font-ibm-plex + (package + (name "font-ibm-plex") + (version "1.0.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/IBM/plex/releases/download/" + "v" version "/OpenType.zip")) + (sha256 + (base32 + "0nzxw9z6waixslam248yr26ci3fbk83c7jf6m90hncnaj6zxx795")))) + (build-system font-build-system) + (home-page "https://github.com/IBM/plex") + (synopsis "IBM Plex typeface") + (description "This package provides the Plex font family. It comes in a +Sans, Serif, Mono and Sans Condensed, all with roman and true italics. The +fonts have been designed to work well in user interface (UI) environments as +well as other mediums.") + (license license:silofl1.1))) + (define-public font-inconsolata (package (name "font-inconsolata") -- cgit 1.4.1 From 63d99002961c8845cd16ae4b5e9ae6b273d43a80 Mon Sep 17 00:00:00 2001 From: Alex Vong Date: Fri, 2 Mar 2018 21:22:59 +0800 Subject: gnu: youtube-viewer: Add '$out/lib/perl5/site_perl/' to search path. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fixes . Reported by Ricardo Wurmus . * gnu/packages/video.scm (youtube-viewer)[arguments]: In 'wrap-program' phase, add '$out/lib/perl5/site_perl/' to search path. Signed-off-by: Ludovic Courtès --- gnu/packages/video.scm | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index e4e71e9dcc..7d072009a0 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1344,16 +1344,18 @@ audio, images) from the Web. It can use either mpv or vlc for playback.") (guix build utils) (srfi srfi-26)) #:module-build-flags '("--gtk") - #:phases (modify-phases %standard-phases - (add-after 'install 'wrap-program - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin-dir (string-append (assoc-ref outputs "out") - "/bin/")) - (perl-path (getenv "PERL5LIB"))) - (for-each (cut wrap-program <> - `("PERL5LIB" ":" prefix (,perl-path))) - (find-files bin-dir)) - #t)))))) + #:phases + (modify-phases %standard-phases + (add-after 'install 'wrap-program + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin-dir (string-append out "/bin/")) + (site-dir (string-append out "/lib/perl5/site_perl/")) + (lib-path (getenv "PERL5LIB"))) + (for-each (cut wrap-program <> + `("PERL5LIB" ":" prefix (,lib-path ,site-dir))) + (find-files bin-dir)) + #t)))))) (synopsis "Lightweight application for searching and streaming videos from YouTube") (description -- cgit 1.4.1 From 06c15ee5856442f5520a185d0f1934b6afb1c01b Mon Sep 17 00:00:00 2001 From: Oleg Pykhalov Date: Fri, 9 Feb 2018 17:33:42 +0300 Subject: gnu: Add r-colorout. * gnu/packages/statistics.scm (r-colorout): New public variable. --- gnu/packages/statistics.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 8ebdce1376..0ae4dddb64 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5564,6 +5564,38 @@ inferring an appropriate positioning method.") shaped points? Now you can!") (license license:asl2.0)))) +(define-public r-colorout + (package + (name "r-colorout") + (version "1.2-0") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/jalvesaq/colorout/archive/" + "v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "07vqx5ihgnq4dzn5jnfjfhdm3957v4prvf8vhnb3cwvlly4l7p9v")))) + (build-system r-build-system) + (home-page "https://github.com/jalvesaq/colorout") + (synopsis "Colorize output in the R REPL") + (description "@code{colorout} is an R package that colorizes R output when +running in terminal emulator. + +R STDOUT is parsed and numbers, negative numbers, dates in the standard +format, strings, and R constants are identified and wrapped by special ANSI +scape codes that are interpreted by terminal emulators as commands to colorize +the output. R STDERR is also parsed to identify the expressions warning and +error and their translations to many languages. If these expressions are +found, the output is colorized accordingly; otherwise, it is colorized as +STDERROR (blue, by default). + +You can customize the colors according to your taste, guided by the color +table made by the command @code{show256Colors()}. You can also set the colors +to any arbitrary string. In this case, it is up to you to set valid values.") + (license license:gpl3+))) + (define-public java-jdistlib (package (name "java-jdistlib") -- cgit 1.4.1 From 7700c6ca205d6a0594a036cbbab783dca24874f1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 7 Mar 2018 12:57:31 +0100 Subject: gnu: glibmm: Update to 2.54.1. * gnu/packages/glib.scm (glibmm): Update to 2.54.1. [arguments]: Add #:configure-flags. --- gnu/packages/glib.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index a64407a36f..e09351a788 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -499,7 +499,7 @@ has an ease of use unmatched by other C++ callback libraries.") (define glibmm (package (name "glibmm") - (version "2.50.1") + (version "2.54.1") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/glibmm/" @@ -507,10 +507,13 @@ has an ease of use unmatched by other C++ callback libraries.") "/glibmm-" version ".tar.xz")) (sha256 (base32 - "1926b3adx903hzvdp8glblsgjyadzqnwgkj8hg605d4wv98m1n0z")))) + "0jkapw18icz59cmlmsl00nwwz0wh291kb4hc9z9hxmq45drqrhkw")))) (build-system gnu-build-system) (arguments - `(#:phases + `(;; XXX: Some tests uses C++14 features. Remove this when the default + ;; compiler is >= GCC6. + #:configure-flags '("CXXFLAGS=-std=gnu++14") + #:phases (modify-phases %standard-phases (add-before 'build 'pre-build (lambda _ -- cgit 1.4.1 From 29c7b4d6389d7d0ae70f2d87f27433431ac74890 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 7 Mar 2018 13:10:07 +0100 Subject: gnu: gtkmm: Update to 3.22.2. * gnu/packages/gtk.scm (gtkmm): Update to 3.22.2. [arguments]: Set #:configure-flags. --- gnu/packages/gtk.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index ceb3f4dc4e..3a67e84d2a 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -1053,7 +1053,7 @@ toolkit.") (define-public gtkmm (package (name "gtkmm") - (version "3.22.0") + (version "3.22.2") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -1061,7 +1061,7 @@ toolkit.") name "-" version ".tar.xz")) (sha256 (base32 - "1x8l0ny6r3ym53z82q9d5fan4m9vi93xy3b3hj1hrclgc95lvnh5")))) + "1400535lhyya462pfx8bp11k3mg3jsbdghlpygskd5ai665dkbwi")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config) ("glib" ,glib "bin") ;for 'glib-compile-resources' @@ -1073,7 +1073,10 @@ toolkit.") ("gtk+" ,gtk+) ("glibmm" ,glibmm))) (arguments - '(#:phases (modify-phases %standard-phases + '(;; XXX: Tests require C++14 or later. Remove this when the default + ;; compiler is >= GCC6. + #:configure-flags '("CXXFLAGS=-std=gnu++14") + #:phases (modify-phases %standard-phases (add-before 'check 'run-xvfb (lambda* (#:key inputs #:allow-other-keys) (let ((xorg-server (assoc-ref inputs "xorg-server"))) -- cgit 1.4.1 From 6a49ae786487013cecd97a372514b75c77282b50 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 7 Mar 2018 13:10:57 +0100 Subject: gnu: gtkmm: Use the for-test xorg variant for tests. * gnu/packages/gtk.scm (gtkmm)[native-inputs]: Replace XORG-SERVER with XORG-SERVER-1.19.3. [arguments]: Add #:disallowed-references. --- gnu/packages/gtk.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index 3a67e84d2a..9fc9fd6015 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -1065,7 +1065,7 @@ toolkit.") (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config) ("glib" ,glib "bin") ;for 'glib-compile-resources' - ("xorg-server" ,xorg-server))) + ("xorg-server" ,xorg-server-1.19.3))) (propagated-inputs `(("pangomm" ,pangomm) ("cairomm" ,cairomm) @@ -1073,9 +1073,10 @@ toolkit.") ("gtk+" ,gtk+) ("glibmm" ,glibmm))) (arguments - '(;; XXX: Tests require C++14 or later. Remove this when the default + `(;; XXX: Tests require C++14 or later. Remove this when the default ;; compiler is >= GCC6. #:configure-flags '("CXXFLAGS=-std=gnu++14") + #:disallowed-references (,xorg-server-1.19.3) #:phases (modify-phases %standard-phases (add-before 'check 'run-xvfb (lambda* (#:key inputs #:allow-other-keys) -- cgit 1.4.1 From 8e933cb36aa08843fd0187ec4c441179a1ed3695 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 7 Mar 2018 13:15:15 +0100 Subject: gnu: Use HTTPS on gtkmm.org home pages. * gnu/packages/gtk.scm (atkmm, gtkmm)[home-page]: Use HTTPS. * gnu/packages/gnome.scm (libgnomecanvasmm)[home-page]: Likewise. * gnu/packages/glib.scm (glibmm)[home-page]: Likewise. --- gnu/packages/glib.scm | 2 +- gnu/packages/gnome.scm | 2 +- gnu/packages/gtk.scm | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index e09351a788..366d615e58 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -535,7 +535,7 @@ has an ease of use unmatched by other C++ callback libraries.") (propagated-inputs `(("libsigc++" ,libsigc++) ("glib" ,glib))) - (home-page "http://gtkmm.org/") + (home-page "https://gtkmm.org/") (synopsis "C++ interface to the GLib library") (description "Glibmm provides a C++ programming interface to the part of GLib that are diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index d6f7e9e281..2384bf2381 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -1595,7 +1595,7 @@ creating interactive structured graphics.") (native-inputs `(("gtkmm-2" ,gtkmm-2) ("pkg-config" ,pkg-config))) - (home-page "http://gtkmm.org") + (home-page "https://gtkmm.org") (synopsis "C++ bindings to the GNOME Canvas library") (description "C++ bindings to the GNOME Canvas library.") (license license:lgpl2.0+))) diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index 9fc9fd6015..a1d7e548aa 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -1043,7 +1043,7 @@ library.") (native-inputs `(("pkg-config" ,pkg-config))) (propagated-inputs `(("glibmm" ,glibmm) ("atk" ,atk))) - (home-page "http://www.gtkmm.org") + (home-page "https://www.gtkmm.org") (synopsis "C++ interface to the ATK accessibility library") (description "ATKmm provides a C++ programming interface to the ATK accessibility @@ -1088,7 +1088,7 @@ toolkit.") ;; Don't fail because of the missing /etc/machine-id. (setenv "DBUS_FATAL_WARNINGS" "0") #t)))))) - (home-page "http://gtkmm.org/") + (home-page "https://gtkmm.org/") (synopsis "C++ interface to the GTK+ graphical user interface library") (description -- cgit 1.4.1 From e07a44891cd906aa071e88e355b9cc8f93b047f7 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 7 Mar 2018 13:27:09 +0100 Subject: gnu: Add gtksourceviewmm. * gnu/packages/gtk.scm (gtksourceviewmm): New public variable. --- gnu/packages/gtk.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index a1d7e548aa..a96cb96470 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -1122,6 +1122,38 @@ extensive documentation, including API reference and a tutorial.") ("gtk+" ,gtk+-2) ("glibmm" ,glibmm))))) +(define-public gtksourceviewmm + (package + (name "gtksourceviewmm") + (version "3.18.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://gnome/sources/" name "/" + (version-major+minor version) "/" + name "-" version ".tar.xz")) + (sha256 + (base32 "0fgvmhm4h4qmxig87qvangs6ijw53mi40siz7pixlxbrsgiil22i")))) + (build-system gnu-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (propagated-inputs + ;; In 'Requires' of gtksourceviewmm-3.0.pc. + `(("glibmm" ,glibmm) + ("gtkmm" ,gtkmm) + ("gtksourceview" ,gtksourceview))) + (synopsis "C++ interface to the GTK+ 'GtkTextView' widget") + (description + "gtksourceviewmm is a portable C++ library that extends the standard GTK+ +framework for multiline text editing with support for configurable syntax +highlighting, unlimited undo/redo, search and replace, a completion framework, +printing and other features typical of a source code editor.") + (license license:lgpl2.1+) + (home-page "https://developer.gnome.org/gtksourceview/"))) + +;;; +;;; Python bindings. +;;; + (define-public python-pycairo (package (name "python-pycairo") -- cgit 1.4.1 From 0cf985d615c6447b12ea3c784ffc3515c59ef99f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 7 Mar 2018 13:56:26 +0100 Subject: gnu: imagemagick: Update to 6.9.9-37. * gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.9-37. --- gnu/packages/imagemagick.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm index cc03f8fc2d..d798833742 100644 --- a/gnu/packages/imagemagick.scm +++ b/gnu/packages/imagemagick.scm @@ -47,14 +47,14 @@ ;; The 7 release series has an incompatible API, while the 6 series is still ;; maintained. Don't update to 7 until we've made sure that the ImageMagick ;; users are ready for the 7-series API. - (version "6.9.9-36") + (version "6.9.9-37") (source (origin (method url-fetch) (uri (string-append "mirror://imagemagick/ImageMagick-" version ".tar.xz")) (sha256 (base32 - "1nhv3cmg4npqibhchp3qgm9pld3n94xwwzv5hgn2s7lqz0zc0vd8")))) + "1hmfw0jcpc3s3gz9zrzjy9amyrfz6gzzjdsyaw3xw994aq9qf4lq")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch") -- cgit 1.4.1 From 5668a365d66d7150920822aadb12dd47ffb8d49f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 7 Mar 2018 14:10:42 +0100 Subject: gnu: mkfontscale: Update to 1.1.3. * gnu/packages/xorg.scm (mkfontscale): Update to 1.1.3. --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 3ae936923c..9ee7ef5bec 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -1558,7 +1558,7 @@ input from UTF-8 into the locale's encoding.") (define-public mkfontscale (package (name "mkfontscale") - (version "1.1.2") + (version "1.1.3") (source (origin (method url-fetch) @@ -1568,7 +1568,7 @@ input from UTF-8 into the locale's encoding.") ".tar.bz2")) (sha256 (base32 - "081z8lwh9c1gyrx3ad12whnpv3jpfbqsc366mswpfm48mwl54vcc")))) + "0siag28jpm8hj62bgjvw81sjfgrc7vcy2h7127bl4iazxrlxz60y")))) (build-system gnu-build-system) (inputs `(("zlib" ,zlib) -- cgit 1.4.1 From b5ebc1bf8cf35ae2579012319083aff29d74b9bf Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 7 Mar 2018 14:12:55 +0100 Subject: gnu: twm: Update to 1.0.10. * gnu/packages/xorg.scm (twm): Update to 1.0.10. [source]: Use bzip-compressed tarball. --- gnu/packages/xorg.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 9ee7ef5bec..3bf2266034 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -5421,17 +5421,17 @@ Intrinsics (Xt) Library.") (define-public twm (package (name "twm") - (version "1.0.9") + (version "1.0.10") (source (origin (method url-fetch) (uri (string-append "mirror://xorg/individual/app/" name "-" version - ".tar.gz")) + ".tar.bz2")) (sha256 (base32 - "1s1r00x8add3f27xjqxg6q7mwplwrb72gakbh4y6j052as25wchw")))) + "1ms5cj1w3g26zg6bxdv1j9hl0pxr4300qnv003cz1q3cl7ffljb4")))) (build-system gnu-build-system) (inputs `(("libxt" ,libxt) -- cgit 1.4.1 From 9dda6dadf103d6241b54ac652ccd5dec82caca00 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 7 Mar 2018 14:14:34 +0100 Subject: gnu: xdriinfo: Update to 1.0.6. * gnu/packages/xorg.scm (xdriinfo): Update to 1.0.6. --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 3bf2266034..d1671ba8c1 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -2276,7 +2276,7 @@ available.") (define-public xdriinfo (package (name "xdriinfo") - (version "1.0.5") + (version "1.0.6") (source (origin (method url-fetch) @@ -2286,7 +2286,7 @@ available.") ".tar.bz2")) (sha256 (base32 - "0681d0y8liqakkpz7mmsf689jcxrvs5291r20qi78mc9xxk3gfjc")))) + "0lcx8h3zd11m4w8wf7dyp89826d437iz78cyrix436bqx31x5k6r")))) (build-system gnu-build-system) (inputs `(("mesa" ,mesa) -- cgit 1.4.1 From eaa8292e41b573adc7d4a338c8ee76918becbb9c Mon Sep 17 00:00:00 2001 From: Mark Meyer Date: Fri, 15 Dec 2017 10:09:28 +0100 Subject: gnu: Add python-pycurl. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python-web.scm (python-pycurl, python2-pycurl): New variables. Co-authored-by: Ludovic Courtès --- gnu/packages/python-web.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index d9721f1375..dce651246c 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -22,6 +22,7 @@ ;;; Copyright © 2016 David Craven ;;; Copyright © 2017 Oleg Pykhalov ;;; Copyright © 2015, 2016 David Thompson +;;; Copyright © 2017 Mark Meyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -45,11 +46,13 @@ #:use-module (gnu packages) #:use-module (gnu packages check) #:use-module (gnu packages compression) + #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages django) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-crypto) + #:use-module (gnu packages tls) #:use-module (gnu packages time) #:use-module (gnu packages xml) #:use-module ((guix licenses) #:prefix license:) @@ -238,6 +241,40 @@ C, yielding parse times that can be a thirtieth of the html5lib parse times.") (define-public python2-html5-parser (package-with-python2 python-html5-parser)) +(define-public python-pycurl + (package + (name "python-pycurl") + (version "7.43.0.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://dl.bintray.com/pycurl/pycurl/pycurl-" + version ".tar.gz")) + (sha256 + (base32 "1ali1gjs9iliwjra7w0y5hwg79a2fd0f4ydvv6k27sgxpbr1n8s3")))) + (build-system python-build-system) + (arguments + ;; The tests attempt to access external web servers, so we cannot run + ;; them. Furthermore, they are skipped altogether when using Python 2. + '(#:tests? #f)) + (native-inputs + `(("python-nose" ,python-nose) + ("python-bottle" ,python-bottle))) + (inputs + `(("curl" ,curl) + ("gnutls" ,gnutls))) + (home-page "http://pycurl.io/") + (synopsis "Lightweight Python wrapper around libcurl") + (description "Pycurl is a lightweight wrapper around libcurl. It provides +high-speed transfers via libcurl and frequently outperforms alternatives.") + + ;; Per 'README.rst', this is dual-licensed: users can redistribute pycurl + ;; under the terms of LGPLv2.1+ or Expat. + (license (list license:lgpl2.1+ license:expat)))) + +(define-public python2-pycurl + (package-with-python2 python-pycurl)) + (define-public python-webencodings (package (name "python-webencodings") -- cgit 1.4.1 From 30e43e816b15caab97183362235d2c39ea18ec7f Mon Sep 17 00:00:00 2001 From: Mark Meyer Date: Sat, 16 Dec 2017 10:57:21 +0100 Subject: gnu: python2-gobject@2: Update to 2.28.7 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/glib.scm (python2-gobject-2): Update to 2.28.7. Signed-off-by: Ludovic Courtès --- gnu/packages/glib.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index 366d615e58..30a22d7d59 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -547,7 +547,7 @@ useful for C++.") (name "python2-pygobject") ;; This was the last version to declare the 2.0 platform number, i.e. its ;; pkg-config files were named pygobject-2.0.pc - (version "2.28.6") + (version "2.28.7") (source (origin (method url-fetch) @@ -556,7 +556,7 @@ useful for C++.") "/pygobject-" version ".tar.xz")) (sha256 (base32 - "1f5dfxjnil2glfwxnqr14d2cjfbkghsbsn8n04js2c2icr7iv2pv")) + "0nkam61rsn7y3wik3vw46wk5q2cjfh2iph57hl9m39rc8jijb7dv")) (patches (search-patches "python2-pygobject-2-gi-info-type-error-domain.patch")))) (build-system gnu-build-system) -- cgit 1.4.1 From 2b30af95416f37f8e371d59f6a7dd8607aea6e2a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 7 Mar 2018 13:27:48 +0100 Subject: gnu: c-reduce: Update to 2.6.0. * gnu/packages/debug.scm (c-reduce): Update to 2.6.0. --- gnu/packages/debug.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm index 6b566b0097..92d635332f 100644 --- a/gnu/packages/debug.scm +++ b/gnu/packages/debug.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015, 2016, 2017 Eric Bavier ;;; Copyright © 2016, 2017, 2018 Efraim Flashner +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -85,10 +86,11 @@ program to exhibit a bug.") ;; home-page pointing to a bsd-2 license. (license bsd-3))) +;; Newer versions depend on LLVM and Clang >= 4, which have yet to be packaged. (define-public c-reduce (package (name "c-reduce") - (version "2.5.0") + (version "2.6.0") (source (origin (method url-fetch) @@ -97,12 +99,12 @@ program to exhibit a bug.") "creduce-" version ".tar.gz"))) (sha256 (base32 - "1r23lhzq3dz8vi2dalxk5las8bf0av2w94hxxbs61pr73m77ik9d")))) + "0pf5q0n8vkdcr1wrkxn2jzxv0xkrir13bwmqfw3jpbm3dh2c3b6d")))) (build-system gnu-build-system) (inputs `(("astyle" ,astyle) - ("llvm" ,llvm) - ("clang" ,clang) + ("llvm" ,llvm-3.9.1) + ("clang" ,clang-3.9.1) ("flex" ,flex) ("indent" ,indent) ("perl" ,perl) -- cgit 1.4.1 From 7649e4269ef2107da5fbbb1e112f4be00338d0e9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 7 Mar 2018 13:28:32 +0100 Subject: gnu: c-reduce: Use HTTPS home page. * gnu/packages/debug.scm (c-reduce)[home-page]: Use HTTPS. --- gnu/packages/debug.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm index 92d635332f..112c656ff8 100644 --- a/gnu/packages/debug.scm +++ b/gnu/packages/debug.scm @@ -133,7 +133,7 @@ program to exhibit a bug.") "file-which" "getopt-tabular" "regex-common" "sys-cpu"))))) #t))))) - (home-page "http://embed.cs.utah.edu/creduce") + (home-page "https://embed.cs.utah.edu/creduce") (synopsis "Reducer for interesting code") (description "C-Reduce is a tool that takes a large C or C++ program that has a -- cgit 1.4.1 From b11481a5428ce04da690735b24cf7fa0e994c263 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 6 Mar 2018 21:02:39 +0100 Subject: gnu: mg: Update to 20171014. * gnu/packages/text-editors.scm (mg): Update to 20171014. --- gnu/packages/text-editors.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm index 0207ca36ab..64f13dd998 100644 --- a/gnu/packages/text-editors.scm +++ b/gnu/packages/text-editors.scm @@ -239,14 +239,14 @@ Wordstar-, EMACS-, Pico, Nedit or vi-like key bindings. e3 can be used on (define-public mg (package (name "mg") - (version "20170401") + (version "20171014") (source (origin (method url-fetch) (uri (string-append "https://homepage.boetes.org/software/mg/mg-" version ".tar.gz")) (sha256 (base32 - "1arasswgdadbb265rahq3867r9s54jva6k4m3p5n0f8mgjqhhdha")) + "0hakfikzsml7z0hja8m8mcahrmfy2piy81bq9nccsjplyfc9clai")) (modules '((guix build utils))) (snippet '(begin -- cgit 1.4.1 From c3d828855ade0d9742754339f5683ca1317baa19 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 6 Mar 2018 21:02:44 +0100 Subject: gnu: mg: Use HTTPS home page. * gnu/packages/text-editors.scm (mg)[home-page]: Use HTTPS. --- gnu/packages/text-editors.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm index 64f13dd998..f1ccab9af9 100644 --- a/gnu/packages/text-editors.scm +++ b/gnu/packages/text-editors.scm @@ -283,7 +283,7 @@ Wordstar-, EMACS-, Pico, Nedit or vi-like key bindings. e3 can be used on (doc (string-append out "/share/doc/mg"))) (install-file "tutorial" doc) #t)))))) - (home-page "http://homepage.boetes.org/software/mg/") + (home-page "https://homepage.boetes.org/software/mg/") (synopsis "Microscopic GNU Emacs clone") (description "Mg (mg) is a GNU Emacs style editor, with which it is \"broadly\" -- cgit 1.4.1 From 0e6c242bb7589938388983028ff55953b45d89fc Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 7 Mar 2018 00:57:40 +0100 Subject: gnu: pam-krb5: Update to 4.8. * gnu/packages/admin.scm (pam-krb5): Update to 4.8. --- gnu/packages/admin.scm | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 26ee4aaabe..4b97d04804 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1992,12 +1992,10 @@ shortcut syntax and completion options.") (home-page "https://github.com/TrilbyWhite/interrobang") (license license:gpl3+)))) - - (define-public pam-krb5 (package (name "pam-krb5") - (version "4.7") + (version "4.8") (source (origin (method url-fetch) (uri (string-append @@ -2005,7 +2003,7 @@ shortcut syntax and completion options.") version ".tar.xz")) (sha256 (base32 - "0abf8cfpkprmhw5ca8iyqgrggh65lgqvmfllc1y6qz7zw1gas894")))) + "1qjp8i1s9bz7g6kiqrkzzkxn5pfspa4sy53b6z40fqmdf9przdfb")))) (build-system gnu-build-system) (arguments `(#:phases @@ -2042,8 +2040,6 @@ Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.") ;; clause requiring us to give all recipients a copy. (license license:gpl1+))) -;;http://archives.eyrie.org/software/kerberos/pam-krb5-4.7.tar.xz - (define-public sunxi-tools (package (name "sunxi-tools") -- cgit 1.4.1 From 45298300e43d314f9001c2bdbd72f1189e20eb70 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 7 Mar 2018 01:23:55 +0100 Subject: gnu: pam-krb5: Mark up description. * gnu/packages/admin.scm (pam-krb5)[description]: Use @code. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 4b97d04804..9116835d04 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -2029,8 +2029,8 @@ It supports ticket refreshing by screen savers, configurable authorization handling, authentication of non-local accounts for network services, password changing, and password expiration, as well as all the standard expected PAM features. It works correctly with OpenSSH, even -with ChallengeResponseAuthentication and PrivilegeSeparation enabled, -and supports extensive configuration either by PAM options or in +with @code{ChallengeResponseAuthentication} and @code{PrivilegeSeparation} +enabled, and supports extensive configuration either by PAM options or in krb5.conf or both. PKINIT is supported with recent versions of both MIT Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.") (home-page "http://www.eyrie.org/~eagle/software/pam-krb5") -- cgit 1.4.1 From d4f5e68e55d15f851ad4d820a5384123d9b51441 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 7 Mar 2018 02:49:23 +0100 Subject: gnu: cmdtest: Update to 0.32. * gnu/packages/check.scm (cmdtest): Update to 0.32. --- gnu/packages/check.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 50b4afcaf0..686c2e2b27 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -16,7 +16,7 @@ ;;; Copyright © 2016 Troy Sankey ;;; Copyright © 2016 Lukas Gradl ;;; Copyright © 2016 Hartmut Goebel -;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice +;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2017 Julien Lepiller ;;; Copyright © 2017 Thomas Danckaert ;;; Copyright © 2017 Arun Isaac @@ -202,14 +202,14 @@ multi-paradigm automated test framework for C++ and Objective-C.") (define-public cmdtest (package (name "cmdtest") - (version "0.29") + (version "0.32") (source (origin (method url-fetch) (uri (string-append "http://git.liw.fi/cmdtest/snapshot/" name "-" version ".tar.gz")) (sha256 (base32 - "1i6gi4yp4qqx1liax098c7nwdb24pghh11xqlrcs7lnhh079rqhb")))) + "1jmfiyrrqmpvwdb273bkb8hjaf4rwx9njblx29pmr7giyahskwi5")))) (build-system python-build-system) (arguments `(#:python ,python-2 -- cgit 1.4.1 From 925102bb98f3b501d5168a42ed0d7646f311257c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 7 Mar 2018 03:23:38 +0100 Subject: gnu: cppcheck: Update to 1.82. * gnu/packages/check.scm (cppcheck): Update to 1.82. --- gnu/packages/check.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 686c2e2b27..73d3efd9e1 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -271,13 +271,13 @@ format.") (define-public cppcheck (package (name "cppcheck") - (version "1.81") + (version "1.82") (source (origin (method url-fetch) (uri (string-append "https://github.com/danmar/cppcheck/archive/" version ".tar.gz")) (sha256 - (base32 "0miamqk7pa2dzmnmi5wb6hjp2a3zya1x8afnlcxby8jb6gp6wf8j")) + (base32 "0zywpd9hbsx23aj33pk5mbr0fz1ijhqzxlnqgwjfwgg6g2k48i2j")) (file-name (string-append name "-" version ".tar.gz")))) (build-system cmake-build-system) (home-page "http://cppcheck.sourceforge.net") -- cgit 1.4.1 From b9499508b4aa6055c01cc9f2d7ff776dd5a53c1c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 7 Mar 2018 03:31:49 +0100 Subject: gnu: keyutils: Update to 1.5.10. * gnu/packages/crypto.scm (keyutils): Update to 1.5.10. --- gnu/packages/crypto.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index b498aabf4d..7716205947 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -258,7 +258,7 @@ the wrong hands.") (define-public keyutils (package (name "keyutils") - (version "1.5.9") + (version "1.5.10") (source (origin (method url-fetch) @@ -267,7 +267,7 @@ the wrong hands.") version ".tar.bz2")) (sha256 (base32 - "1bl3w03ygxhc0hz69klfdlwqn33jvzxl1zfl2jmnb2v85iawb8jd")) + "1dmgjcf7mnwc6h72xkvpaqpzxw8vmlnsmzz0s27pg0giwzm3sp0i")) (modules '((guix build utils))) ;; Create relative symbolic links instead of absolute ones to /lib/* (snippet '(substitute* "Makefile" (("\\$\\(LNS\\) \\$\\(LIBDIR\\)/") -- cgit 1.4.1 From b8b34be61c663ba3dc0cefa002b7051fc47ed4c0 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 7 Mar 2018 00:52:02 +0100 Subject: gnu: links, lynx, qutebrowser: Update phase style. * gnu/packages/web-browsers.scm (links, lynx, qutebrowser)[arguments]: Substitute INVOKE for SYSTEM and end phases with #t. --- gnu/packages/web-browsers.scm | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index bd4c34efb6..ef39d71411 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2015, 2016 Efraim Flashner ;;; Copyright © 2016 Kei Kebreau ;;; Copyright © 2017 Eric Bavier +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -102,10 +103,10 @@ older or slower computers and embedded systems.") `((setenv "CHOST" ,(%current-target-system))) '()) (setenv "CONFIG_SHELL" (which "bash")) - (zero? - (system* "./configure" - (string-append "--prefix=" out) - "--enable-graphics")))))))) + (invoke "./configure" + (string-append "--prefix=" out) + "--enable-graphics") + #t)))))) (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("zlib" ,zlib) ("openssl" ,openssl) @@ -175,7 +176,8 @@ features including, tables, builtin image display, bookmarks, SSL and more.") #t)) (replace 'install (lambda* (#:key (make-flags '()) #:allow-other-keys) - (zero? (apply system* "make" "install-full" make-flags))))))) + (apply invoke "make" "install-full" make-flags) + #t))))) (synopsis "Text Web Browser") (description "Lynx is a fully-featured World Wide Web (WWW) client for users running @@ -223,7 +225,7 @@ access.") (let* ((out (assoc-ref outputs "out")) (app (string-append out "/share/applications")) (hicolor (string-append out "/share/icons/hicolor"))) - (system* "a2x" "-f" "manpage" "doc/qutebrowser.1.asciidoc") + (invoke "a2x" "-f" "manpage" "doc/qutebrowser.1.asciidoc") (install-file "doc/qutebrowser.1" (string-append out "/share/man/man1")) -- cgit 1.4.1 From 6c4da3b76a7c1a92b04983a93790f3a5f3bf8284 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 7 Mar 2018 01:31:27 +0100 Subject: gnu: meson: Mark up description. * gnu/packages/build-tools.scm (meson)[description]: Use @dfn. --- gnu/packages/build-tools.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm index 7c0faca9a2..2abb44fdb8 100644 --- a/gnu/packages/build-tools.scm +++ b/gnu/packages/build-tools.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017 Ricardo Wurmus ;;; Copyright © 2017 Corentin Bocquillon -;;; Copyright © 2017 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -90,8 +90,8 @@ makes a few sacrifices to acquire fast full and incremental build times.") It can compile code written in C, C++, Fortran, Java, Rust, and other languages. Meson provides features comparable to those of the Autoconf/Automake/make combo. Build specifications, also known as @dfn{Meson -files}, are written in a custom domain-specific language (DSL) that resembles -Python.") +files}, are written in a custom domain-specific language (@dfn{DSL}) that +resembles Python.") (license license:asl2.0))) (define-public meson-for-build -- cgit 1.4.1 From 9dae73c31cf18779dec656fe2fb7e5eed24a35c6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 7 Mar 2018 02:28:28 +0100 Subject: gnu: pigz: Update to 2.4. * gnu/packages/compression.scm (pigz): Update to 2.4. --- gnu/packages/compression.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 423d3989aa..d77d06a642 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -844,14 +844,14 @@ extract such file systems.") (define-public pigz (package (name "pigz") - (version "2.3.3") + (version "2.4") (source (origin (method url-fetch) (uri (string-append "http://zlib.net/pigz/" name "-" version ".tar.gz")) (sha256 (base32 - "172hdf26k4zmm7z8md7nl0dph2a7mhf3x7slb9bhfyff6as6g2sf")))) + "0wsgw5vwl23jrnpsvd8v3xcp5k4waw5mk0164fynjhkv58i1dy54")))) (build-system gnu-build-system) (arguments `(#:phases -- cgit 1.4.1 From 7f1773eaee2f10990c9c4002d383e96deb2b95c3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 7 Mar 2018 02:31:05 +0100 Subject: gnu: Use HTTPS for zlib.net home pages. * gnu/packages/compression.scm (zlib, pigz)[home-page]: Use HTTPS. --- gnu/packages/compression.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index d77d06a642..d44ae2d259 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -99,7 +99,7 @@ (zero? (system* "./configure" (string-append "--prefix=" out))))))))) - (home-page "http://zlib.net/") + (home-page "https://zlib.net/") (synopsis "Compression library") (description "zlib is designed to be a free, general-purpose, legally unencumbered -- @@ -869,7 +869,7 @@ extract such file systems.") #:make-flags (list "CC=gcc") #:test-target "tests")) (inputs `(("zlib" ,zlib))) - (home-page "http://zlib.net/pigz/") + (home-page "https://zlib.net/pigz/") (synopsis "Parallel implementation of gzip") (description "This package provides a parallel implementation of gzip that exploits -- cgit 1.4.1 From f35843674ecdfd08be710888e6e7bb1cdc0ee309 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 7 Mar 2018 13:34:47 +0100 Subject: gnu: znc: Update to 1.6.6. * gnu/packages/messaging.scm (znc): Update to 1.6.6. --- gnu/packages/messaging.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 7a4c370c99..b6323c39b2 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -449,14 +449,14 @@ compromised.") (define-public znc (package (name "znc") - (version "1.6.5") + (version "1.6.6") (source (origin (method url-fetch) (uri (string-append "http://znc.in/releases/archive/znc-" version ".tar.gz")) (sha256 (base32 - "1jia6kq6bp8yxfj02d5vj9vqb4pylqcldspyjj6iz82kkka2a0ig")))) + "09cmsnxvi7jg9a0dicf60fxnxdff4aprw7h8vjqlj5ywf6y43f3z")))) (build-system gnu-build-system) (arguments `(#:phases -- cgit 1.4.1 From 021caafa2cd213f773386af8a3226a4ad41683da Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Mar 2018 18:11:33 +0100 Subject: gnu: Add r-heatmaply. * gnu/packages/cran.scm (r-heatmaply): New variable. --- gnu/packages/cran.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f8d17e1ad2..b5471d703b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2738,3 +2738,44 @@ ordered factor data types.") "This package provides tools for the computation of matrix and scalar exponentiation.") (license license:gpl2))) + +(define-public r-heatmaply + (package + (name "r-heatmaply") + (version "0.14.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "heatmaply" version)) + (sha256 + (base32 + "03p2caclhfgqgpx3wwck5h06jy3mxgs05gjmwkb7hmwghkjh41jc")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-colorspace" ,r-colorspace) + ("r-dendextend" ,r-dendextend) + ("r-ggplot2" ,r-ggplot2) + ("r-gplots" ,r-gplots) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-magrittr" ,r-magrittr) + ("r-plotly" ,r-plotly) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape2" ,r-reshape2) + ("r-scales" ,r-scales) + ("r-seriation" ,r-seriation) + ("r-viridis" ,r-viridis) + ("r-webshot" ,r-webshot))) + (home-page "https://cran.r-project.org/package=heatmaply") + (synopsis "Interactive cluster heat maps using plotly") + (description + "This package enables you to create interactive cluster heatmaps that can +be saved as a stand-alone HTML file, embedded in R Markdown documents or in a +Shiny app, and made available in the RStudio viewer pane. Hover the mouse +pointer over a cell to show details or drag a rectangle to zoom. A heatmap is +a popular graphical method for visualizing high-dimensional data, in which a +table of numbers is encoded as a grid of colored cells. The rows and columns +of the matrix are ordered to highlight patterns and are often accompanied by +dendrograms.") + ;; Either version of the license. + (license (list license:gpl2 license:gpl3)))) -- cgit 1.4.1 From 0fccb24765dfda3e90d7ce6981d9204f05aa6117 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 7 Mar 2018 16:57:20 +0100 Subject: gnu: commencement: 'glibc-final' now inherits from 'glibc'. * gnu/packages/commencement.scm (glibc-final): Inherit from GLIBC instead of GLIBC-FINAL-WITH-BOOTSTRAP-BASH. [propagated-inputs]: New fields. --- gnu/packages/commencement.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm index c38f40f618..1584f000d4 100644 --- a/gnu/packages/commencement.scm +++ b/gnu/packages/commencement.scm @@ -673,7 +673,12 @@ exec ~a/bin/~a-~a -B~a/lib -Wl,-dynamic-linker -Wl,~a/~a \"$@\"~%" (define glibc-final ;; The final glibc, which embeds the statically-linked Bash built above. - (package (inherit glibc-final-with-bootstrap-bash) + (package (inherit glibc) + (package + (inherit (package + (inherit glibc) + ;; Use the source patched with %BOOTSTRAP-GUILE. + (source (package-source glibc-final-with-bootstrap-bash)))) (name "glibc") (inputs `(("static-bash" ,static-bash-for-glibc) ,@(alist-delete @@ -684,6 +689,9 @@ exec ~a/bin/~a-~a -B~a/lib -Wl,-dynamic-linker -Wl,~a/~a \"$@\"~%" (native-inputs `(,@(package-native-inputs glibc-final-with-bootstrap-bash) ("gettext" ,gettext-boot0))) + (propagated-inputs + (package-propagated-inputs glibc-final-with-bootstrap-bash)) + ;; The final libc only refers to itself, but the 'debug' output contains ;; references to GCC-BOOT0 and to the Linux headers. XXX: Would be great ;; if 'allowed-references' were per-output. -- cgit 1.4.1 From 7c788ed2276957ea52858d80faeca2962cd26f8d Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 7 Mar 2018 21:30:41 +0100 Subject: gnu: commencement: 'glibc-final' inherits the replacement of 'glibc'. That was the intent of commit b672a8160755bab07fb3c13dbc43dcc26525a7b7, but that commit left 'glibc-final' ungrafted. Reported by Ricardo Wurmus at . * gnu/packages/commencement.scm (glibc-final): Use 'package/inherit' so that we inherit the 'replacement' of GLIBC. --- gnu/packages/commencement.scm | 53 ++++++++++++++++++++----------------------- 1 file changed, 25 insertions(+), 28 deletions(-) diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm index 1584f000d4..fe9fbebcc2 100644 --- a/gnu/packages/commencement.scm +++ b/gnu/packages/commencement.scm @@ -673,35 +673,32 @@ exec ~a/bin/~a-~a -B~a/lib -Wl,-dynamic-linker -Wl,~a/~a \"$@\"~%" (define glibc-final ;; The final glibc, which embeds the statically-linked Bash built above. - (package (inherit glibc) - (package - (inherit (package - (inherit glibc) - ;; Use the source patched with %BOOTSTRAP-GUILE. - (source (package-source glibc-final-with-bootstrap-bash)))) - (name "glibc") - (inputs `(("static-bash" ,static-bash-for-glibc) - ,@(alist-delete - "static-bash" - (package-inputs glibc-final-with-bootstrap-bash)))) - - ;; This time we need 'msgfmt' to install all the libc.mo files. - (native-inputs `(,@(package-native-inputs glibc-final-with-bootstrap-bash) - ("gettext" ,gettext-boot0))) - - (propagated-inputs - (package-propagated-inputs glibc-final-with-bootstrap-bash)) - - ;; The final libc only refers to itself, but the 'debug' output contains - ;; references to GCC-BOOT0 and to the Linux headers. XXX: Would be great - ;; if 'allowed-references' were per-output. - (arguments - `(#:allowed-references - ,(cons* `(,gcc-boot0 "lib") (kernel-headers-boot0) - static-bash-for-glibc - (package-outputs glibc-final-with-bootstrap-bash)) + ;; Use 'package/inherit' so we get the 'replacement' of 'glibc', if any. + (let ((glibc (package-with-bootstrap-guile glibc))) + (package/inherit glibc + (name "glibc") + (inputs `(("static-bash" ,static-bash-for-glibc) + ,@(alist-delete + "static-bash" + (package-inputs glibc-final-with-bootstrap-bash)))) + + ;; This time we need 'msgfmt' to install all the libc.mo files. + (native-inputs `(,@(package-native-inputs glibc-final-with-bootstrap-bash) + ("gettext" ,gettext-boot0))) + + (propagated-inputs + (package-propagated-inputs glibc-final-with-bootstrap-bash)) + + ;; The final libc only refers to itself, but the 'debug' output contains + ;; references to GCC-BOOT0 and to the Linux headers. XXX: Would be great + ;; if 'allowed-references' were per-output. + (arguments + `(#:allowed-references + ,(cons* `(,gcc-boot0 "lib") (kernel-headers-boot0) + static-bash-for-glibc + (package-outputs glibc-final-with-bootstrap-bash)) - ,@(package-arguments glibc-final-with-bootstrap-bash))))) + ,@(package-arguments glibc-final-with-bootstrap-bash)))))) (define gcc-boot0-wrapped ;; Make the cross-tools GCC-BOOT0 and BINUTILS-BOOT0 available under the -- cgit 1.4.1 From 036ed3a8305ba0fb113666d52989cb4b009c5b72 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 7 Mar 2018 21:34:18 +0100 Subject: gnu: glibc-2.26-patch: Remove unneeded 'replacement' field. * gnu/packages/base.scm (glibc-2.26-patched): Remove unneeded 'replacement' field. --- gnu/packages/base.scm | 1 - 1 file changed, 1 deletion(-) diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index 23107a823e..e91f7d43ef 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -844,7 +844,6 @@ GLIBC/HURD for a Hurd host" (define glibc-2.26-patched (package (inherit glibc) - (replacement #f) (source (origin (inherit (package-source glibc)) (patches (cons (search-patch "glibc-allow-kernel-2.6.32.patch") -- cgit 1.4.1 From 12ff7f3fc77ce6a7a3d7be9555e602be3c63704d Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 7 Mar 2018 21:36:30 +0100 Subject: gnu: glibc: Add a comment in the patch. * gnu/packages/patches/glibc-allow-kernel-2.6.32.patch: Add a comment. --- gnu/packages/patches/glibc-allow-kernel-2.6.32.patch | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch b/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch index ce18b874c4..c03807323f 100644 --- a/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch +++ b/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch @@ -1,3 +1,10 @@ +This patch allows libc to be used with the heavily-patched kernel found +on CentOS 6, which identifies itself as 2.6.32. + +See . + +Patch taken from Nixpkgs. + diff --git a/sysdeps/unix/sysv/linux/configure b/sysdeps/unix/sysv/linux/configure index cace758c01..38fe7fe0b0 100644 --- a/sysdeps/unix/sysv/linux/configure -- cgit 1.4.1 From b2dc4cb41ce107199c8899b89e1c4104d410370b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Mar 2018 18:52:18 +0100 Subject: gnu: Add r-cgdsr. * gnu/packages/cran.scm (r-cgdsr): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b5471d703b..7281caf7a6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2779,3 +2779,26 @@ of the matrix are ordered to highlight patterns and are often accompanied by dendrograms.") ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) + +(define-public r-cgdsr + (package + (name "r-cgdsr") + (version "1.2.10") + (source + (origin + (method url-fetch) + (uri (cran-uri "cgdsr" version)) + (sha256 + (base32 + "1xyhw7mhmjichr1l6f9y1qvfj9wm87kfbm87ji7lcwf36gxh5g23")))) + (build-system r-build-system) + (propagated-inputs + `(("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo))) + (home-page "https://github.com/cBioPortal/cgdsr") + (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server") + (description + "This package provides a basic set of R functions for querying the Cancer +Genomics Data Server (CGDS), hosted by the Computational Biology Center at +Memorial-Sloan-Kettering Cancer Center (MSKCC).") + (license license:lgpl3))) -- cgit 1.4.1 From a00968b7a878ab5aa0d0afb000f29e713b880674 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Mar 2018 20:12:47 +0100 Subject: gnu: Add r-import. * gnu/packages/cran.scm (r-import): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7281caf7a6..b256d228d8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2802,3 +2802,27 @@ dendrograms.") Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).") (license license:lgpl3))) + +(define-public r-import + (package + (name "r-import") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "import" version)) + (sha256 + (base32 + "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji")))) + (build-system r-build-system) + (home-page "https://github.com/smbache/import") + (synopsis "Import mechanism for R") + (description + "This is an alternative mechanism for importing objects from packages. +The syntax allows for importing multiple objects from a package with a single +command in an expressive way. The import package bridges some of the gap +between using @code{library} (or @code{require}) and direct (single-object) +imports. Furthermore the imported objects are not placed in the current +environment. It is also possible to import objects from stand-alone @code{.R} +files.") + (license license:expat))) -- cgit 1.4.1 From 5d9b82acfc597edfcf8ae0cce0f897c3764bb9b9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Mar 2018 20:12:54 +0100 Subject: gnu: Add r-shinyace. * gnu/packages/cran.scm (r-shinyace): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b256d228d8..d0033e1685 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2826,3 +2826,25 @@ imports. Furthermore the imported objects are not placed in the current environment. It is also possible to import objects from stand-alone @code{.R} files.") (license license:expat))) + +(define-public r-shinyace + (package + (name "r-shinyace") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinyAce" version)) + (sha256 + (base32 + "0ycka8rsw0178q9klfid97vdn5cbyx3r778nis5s3dqipdyazdm9")))) + (properties `((upstream-name . "shinyAce"))) + (build-system r-build-system) + (propagated-inputs + `(("r-shiny" ,r-shiny))) + (home-page "http://cran.r-project.org/web/packages/shinyAce") + (synopsis "Ace editor bindings for Shiny") + (description + "This package provides Ace editor bindings to enable a rich text editing +environment within Shiny.") + (license license:expat))) -- cgit 1.4.1 From f64fea1d2cbfe76882abc31f1ce1e7b917352dfb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Mar 2018 20:13:06 +0100 Subject: gnu: Add r-radiant-data. * gnu/packages/cran.scm (r-radiant-data): New variable. --- gnu/packages/cran.scm | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d0033e1685..708afc0be5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2848,3 +2848,56 @@ files.") "This package provides Ace editor bindings to enable a rich text editing environment within Shiny.") (license license:expat))) + +(define-public r-radiant-data + (package + (name "r-radiant-data") + (version "0.8.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "radiant.data" version)) + (sha256 + (base32 + "1ylina1jlrmvjkj8pwg0ip5jv1038vnzyckmf542xl7g11x8rvw1")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete files that are under CC-NC-SA. + (delete-file-recursively "inst/app/tools/help") + #t)))) + (properties `((upstream-name . "radiant.data"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-broom" ,r-broom) + ("r-car" ,r-car) + ("r-curl" ,r-curl) + ("r-dplyr" ,r-dplyr) + ("r-dt" ,r-dt) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-import" ,r-import) + ("r-jsonlite" ,r-jsonlite) + ("r-knitr" ,r-knitr) + ("r-lubridate" ,r-lubridate) + ("r-magrittr" ,r-magrittr) + ("r-markdown" ,r-markdown) + ("r-pryr" ,r-pryr) + ("r-psych" ,r-psych) + ("r-readr" ,r-readr) + ("r-rmarkdown" ,r-rmarkdown) + ("r-rstudioapi" ,r-rstudioapi) + ("r-scales" ,r-scales) + ("r-shiny" ,r-shiny) + ("r-shinyace" ,r-shinyace) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/radiant-rstats/radiant.data") + (synopsis "Data menu for Radiant: business analytics using R and Shiny") + (description + "The Radiant Data menu includes interfaces for loading, saving, viewing, +visualizing, summarizing, transforming, and combining data. It also contains +functionality to generate reproducible reports of the analyses conducted in +the application.") + (license license:agpl3))) -- cgit 1.4.1 From e2cafc2449df16ccc3ca1555d5e9ed66908d846e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Mar 2018 22:43:38 +0100 Subject: gnu: Add r-algdesign. * gnu/packages/cran.scm (r-algdesign): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 708afc0be5..c4cf394e6e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2901,3 +2901,26 @@ visualizing, summarizing, transforming, and combining data. It also contains functionality to generate reproducible reports of the analyses conducted in the application.") (license license:agpl3))) + +(define-public r-algdesign + (package + (name "r-algdesign") + (version "1.1-7.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "AlgDesign" version)) + (sha256 + (base32 + "0bl7mx4dnmkgs2x1fj7cqnrp7jx18mqwxyga0rzlniq12h8mc3fz")))) + (properties `((upstream-name . "AlgDesign"))) + (build-system r-build-system) + (home-page "https://github.com/jvbraun/AlgDesign") + (synopsis "Algorithmic experimental design") + (description + "This package provides tools to calculate exact and approximate theory +experimental designs for D, A, and I criteria. Very large designs may be +created. Experimental designs may be blocked or blocked designs created from +a candidate list, using several criteria. The blocking can be done when whole +and within plot factors interact.") + (license license:gpl2+))) -- cgit 1.4.1 From 0bdd5b8ab7c5e618a63cac6d9aa55f9cf674deea Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Mar 2018 23:07:23 +0100 Subject: gnu: Add pigx-rnaseq. * gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable. --- gnu/packages/bioinformatics.scm | 67 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 67 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 546b240f84..d6c7c05dd5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12646,3 +12646,70 @@ contains analyze RNA expression genome-wide in thousands of individual cells at once. This package provides tools to perform Drop-seq analyses.") (license license:expat))) + +(define-public pigx-rnaseq + (package + (name "pigx-rnaseq") + (version "0.0.2") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/" + "releases/download/v" version + "/pigx_rnaseq-" version ".tar.gz")) + (sha256 + (base32 + "168hx2ig3rarphx3l21ay9yyg8ipaakzixnrhpbdi0sknhyvrrk8")))) + (build-system gnu-build-system) + (arguments + `(#:parallel-tests? #f ; not supported + #:phases + (modify-phases %standard-phases + (add-after 'install 'wrap-executable + ;; Make sure the executable finds all R modules. + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (wrap-program (string-append out "/bin/pigx-rnaseq") + `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) + `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) + #t))))) + (inputs + `(("snakemake" ,snakemake) + ("fastqc" ,fastqc) + ("multiqc" ,multiqc) + ("star" ,star) + ("trim-galore" ,trim-galore) + ("htseq" ,htseq) + ("samtools" ,samtools) + ("bedtools" ,bedtools) + ("r-minimal" ,r-minimal) + ("r-rmarkdown" ,r-rmarkdown) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-gprofiler" ,r-gprofiler) + ("r-deseq2" ,r-deseq2) + ("r-dt" ,r-dt) + ("r-knitr" ,r-knitr) + ("r-pheatmap" ,r-pheatmap) + ("r-corrplot" ,r-corrplot) + ("r-reshape2" ,r-reshape2) + ("r-plotly" ,r-plotly) + ("r-scales" ,r-scales) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-crosstalk" ,r-crosstalk) + ("r-tximport" ,r-tximport) + ("r-rtracklayer" ,r-rtracklayer) + ("r-rjson" ,r-rjson) + ("salmon" ,salmon) + ("ghc-pandoc" ,ghc-pandoc) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("python-wrapper" ,python-wrapper) + ("python-pyyaml" ,python-pyyaml))) + (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (synopsis "Analysis pipeline for RNA sequencing experiments") + (description "PiGX RNAseq is an analysis pipeline for preprocessing and +reporting for RNA sequencing experiments. It is easy to use and produces high +quality reports. The inputs are reads files from the sequencing experiment, +and a configuration file which describes the experiment. In addition to +quality control of the experiment, the pipeline produces a differential +expression report comparing samples in an easily configurable manner.") + (license license:gpl3+))) -- cgit 1.4.1 From f43857d65d35ba90cfe675d8e44ef05a0a593a4d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Mar 2018 01:24:02 +0100 Subject: gnu: emacs-slack: Update to 0-3.9272460. * gnu/packages/emacs.scm (emacs-slack): Update to 0-3.9272460. --- gnu/packages/emacs.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index a6f398ac3b..c2c162c75c 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -6787,8 +6787,8 @@ want to use it.") (license license:gpl3+))) (define-public emacs-slack - (let ((commit "02ee1d7339e48c64946041f6f4e09447c3f53e82") - (revision "2")) + (let ((commit "92724604879149cf331fa8778d089813a9d4ce1a") + (revision "3")) (package (name "emacs-slack") (version (string-append "0-" revision "." (string-take commit 7))) @@ -6800,7 +6800,7 @@ want to use it.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0grx95xxf314m2k35m1kf20l2pwc6j11ibvrngx4pis7wqwjas3h")))) + "1fdf8s3ca356k7m7f5kqzfamfl2nrqjj2pynjv3kkrr0ad15nxmw")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-alert" ,emacs-alert) -- cgit 1.4.1 From e7988175d9a3871315fe83b9824b1be56bb18e5a Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 8 Mar 2018 00:39:58 +0100 Subject: gnu: sunxi-tools: Improve build error reporting. * gnu/packages/admin.scm (sunxi-tools)[arguments]<#:phases>[set-environment-up]: Improve build error reporting. --- gnu/packages/admin.scm | 29 +++++++++++++++++++---------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 9116835d04..b35fd8fdd4 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -2080,25 +2080,34 @@ Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.") (lambda* (#:key make-flags #:allow-other-keys) (define (cross? x) (string-contains x "cross-arm-linux")) + (define (filter-environment! filter-predicate + environment-variable-names) + (for-each + (lambda (env-name) + (let* ((env-value (getenv env-name)) + (search-path (search-path-as-string->list env-value)) + (new-search-path (filter filter-predicate + search-path)) + (new-env-value (list->search-path-as-string + new-search-path ":"))) + (setenv env-name new-env-value))) + environment-variable-names)) (setenv "CROSS_C_INCLUDE_PATH" (getenv "C_INCLUDE_PATH")) (setenv "CROSS_CPLUS_INCLUDE_PATH" (getenv "CPLUS_INCLUDE_PATH")) (setenv "CROSS_LIBRARY_PATH" (getenv "LIBRARY_PATH")) - (for-each - (lambda (env-name) - (let* ((env-value (getenv env-name)) - (search-path (search-path-as-string->list env-value)) - (new-search-path (filter (lambda (e) (not (cross? e))) - search-path)) - (new-env-value (list->search-path-as-string - new-search-path ":"))) - (setenv env-name new-env-value))) - '("C_INCLUDE_PATH" "CPLUS_INCLUDE_PATH" "LIBRARY_PATH")) + (filter-environment! cross? + '("CROSS_C_INCLUDE_PATH" "CROSS_CPLUS_INCLUDE_PATH" + "CROSS_LIBRARY_PATH")) + (filter-environment! (lambda (e) (not (cross? e))) + '("C_INCLUDE_PATH" "CPLUS_INCLUDE_PATH" + "LIBRARY_PATH")) #t)) (replace 'build (lambda* (#:key make-flags #:allow-other-keys) (zero? (apply system* "make" "tools" "misc" make-flags)))) (add-after 'build 'build-armhf (lambda* (#:key make-flags #:allow-other-keys) + (setenv "LIBRARY_PATH" #f) (zero? (apply system* "make" "target-tools" make-flags)))) (replace 'install (lambda* (#:key make-flags #:allow-other-keys) -- cgit 1.4.1 From e2d0cf033eb894fa8c786d0bf039fc54685d5559 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 8 Mar 2018 00:47:46 +0100 Subject: gnu: sunxi-tools: Add cross-libc's "static" output. * gnu/packages/admin.scm (sunxi-tools)[native-inputs]: Add cross-libc's "static" output. --- gnu/packages/admin.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index b35fd8fdd4..7623693722 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -2062,7 +2062,8 @@ Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.") ("cross-gcc" ,(cross-gcc "arm-linux-gnueabihf" #:xbinutils (cross-binutils "arm-linux-gnueabihf") #:libc (cross-libc "arm-linux-gnueabihf"))) - ("cross-libc" ,(cross-libc "arm-linux-gnueabihf")))) + ("cross-libc" ,(cross-libc "arm-linux-gnueabihf")) ; header files + ("cross-libc-static" ,(cross-libc "arm-linux-gnueabihf") "static"))) (inputs `(("libusb" ,libusb))) (build-system gnu-build-system) -- cgit 1.4.1 From a89bf3318f81e9b190188f5f9ab9b1fa94c318db Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Thu, 8 Mar 2018 08:51:56 +0100 Subject: gnu: vulkan-icd-loader: Update to 1.1.70.0. * gnu/packages/vulkan.scm (vulkan-icd-loader): Update to 1.1.70.0. --- gnu/packages/vulkan.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/vulkan.scm b/gnu/packages/vulkan.scm index 1d83b6f363..478de6a444 100644 --- a/gnu/packages/vulkan.scm +++ b/gnu/packages/vulkan.scm @@ -158,7 +158,7 @@ interpretation of the specifications for these languages.") (define-public vulkan-icd-loader (package (name "vulkan-icd-loader") - (version "1.0.68.0") + (version "1.1.70.0") (source (origin (method url-fetch) @@ -167,7 +167,7 @@ interpretation of the specifications for these languages.") "archive/sdk-" version ".tar.gz")) (sha256 (base32 - "1n5gry5zxpwi7330fmi06snalra8hkbbw68gnwbp531kd5ycyinh")))) + "15qkh77596v3xivnbb3l0q9zbmmsdglnaza2m1g7f8q7bbigyc5x")))) (build-system cmake-build-system) (arguments `(#:tests? #f ;FIXME: 23/39 tests fail. Try "tests/run_all_tests.sh". -- cgit 1.4.1 From 254a88199f32d35e39c8913bc557ea2db69bd04e Mon Sep 17 00:00:00 2001 From: Clément Lassieur Date: Thu, 8 Mar 2018 08:58:38 +0100 Subject: gnu: global: Replace GLOBAL with GNU GLOBAL in description. * gnu/packages/code.scm (global)[description]: Replace GLOBAL with GNU GLOBAL. --- gnu/packages/code.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 8d9c661302..13a89c7bcc 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -139,10 +139,10 @@ highlighting your own code that seemed comprehensible when you wrote it.") (home-page "https://www.gnu.org/software/global/") (synopsis "Cross-environment source code tag system") (description - "GLOBAL is a source code tagging system that functions in the same way -across a wide array of environments, such as different text editors, shells -and web browsers. The resulting tags are useful for quickly moving around in -a large, deeply nested project.") + "GNU GLOBAL is a source code tagging system that functions in the same +way across a wide array of environments, such as different text editors, +shells and web browsers. The resulting tags are useful for quickly moving +around in a large, deeply nested project.") (license license:gpl3+))) (define-public sloccount -- cgit 1.4.1 From 6e076b3d50f131252822286f2f9b427ae32754d8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 8 Mar 2018 07:26:27 +0100 Subject: gnu: slurm: Update to 17.11.3. * gnu/packages/parallel.scm (slurm): Update to 17.11.3. --- gnu/packages/parallel.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm index 17423856aa..c110fab086 100644 --- a/gnu/packages/parallel.scm +++ b/gnu/packages/parallel.scm @@ -94,7 +94,7 @@ and they are executed on lists of files, hosts, users or other items.") (define-public slurm (package (name "slurm") - (version "17.11.2") + (version "17.11.3") (source (origin (method url-fetch) (uri (string-append @@ -102,7 +102,7 @@ and they are executed on lists of files, hosts, users or other items.") version ".tar.bz2")) (sha256 (base32 - "18yakb8kmhb16n0cv3zhjv8ahvsk9p0max8mmr2flb2c65fawks6")) + "1x3i6z03d9m46fvj1cslrapm1drvgyqch9pn4xf23kvbz4gkhaps")) (modules '((guix build utils))) (snippet '(begin -- cgit 1.4.1 From f95e9a6bca75332fb71f9618b1a03a6fd455c4cf Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 8 Mar 2018 07:27:01 +0100 Subject: gnu: keepassxc: Update to 2.3.1. * gnu/packages/password-utils.scm (keepassxc): Update to 2.3.1. --- gnu/packages/password-utils.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index 96a51f0dd4..0dde8808b6 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -92,7 +92,7 @@ human.") (define-public keepassxc (package (name "keepassxc") - (version "2.3.0") + (version "2.3.1") (source (origin (method url-fetch) @@ -101,7 +101,7 @@ human.") version "-src.tar.xz")) (sha256 (base32 - "1v6v59fnbbsssbwy4is6hh2l4qqwy3ddb6dp2jk8clx0xbd5hn7c")))) + "1gdrbpzwbs56anc3k5vklvcackcn214pc8gm5xh5zcymsi8q4zff")))) (build-system cmake-build-system) (arguments '(#:configure-flags '("-DWITH_XC_NETWORKING=YES" -- cgit 1.4.1 From 3d63422c92c6931fbc688770073214b561eab723 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 8 Mar 2018 09:03:47 +0100 Subject: gnu: yapet: Update to 1.1. * gnu/packages/password-utils.scm (yapet): Update to 1.1. --- gnu/packages/password-utils.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index 0dde8808b6..46b6e795ab 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -200,7 +200,7 @@ applications, there is xclip integration." ) (define-public yapet (package (name "yapet") - (version "1.0") + (version "1.1") (source (origin (method url-fetch) (uri (string-append "http://www.guengel.ch/myapps/yapet/downloads/yapet-" @@ -208,7 +208,7 @@ applications, there is xclip integration." ) ".tar.bz2")) (sha256 (base32 - "0ydbnqw6icdh07pnv2w6dhvq501bdfvrklv4xmyr8znca9d753if")))) + "1lq46mpxdsbl6qw4cj58hp9q7jckmyvbsi08p5zr77rjgqadxyyy")))) (build-system gnu-build-system) (inputs `(("ncurses" ,ncurses) -- cgit 1.4.1 From ef20a6f0b469b7d86fb0d7502ecb6f7f8a78603a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 7 Mar 2018 17:15:45 +0100 Subject: gnu: python-ddt: Mark up description. * gnu/packages/python.scm (python-ddt)[description]: Use @dfn. --- gnu/packages/python.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 970c835de6..b9f6749797 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10426,8 +10426,9 @@ convering text with ANSI color codes to HTML or LaTeX.") (home-page "https://github.com/txels/ddt") (synopsis "Data-Driven Tests") (description - "DDT (Data-Driven Tests) allows you to multiply one test case by running -it with different test data, and make it appear as multiple test cases.") + "Data-Driven Tests (@dfn{DDT}) allow you to multiply one test case by +running it with different test data, and make it appear as multiple test +cases.") (license license:expat))) (define-public python2-ddt -- cgit 1.4.1 From 338e2852b5d12a6d8b83e5fea1278a8a8453370f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 7 Mar 2018 17:15:17 +0100 Subject: gnu: python-ddt: Update to 1.1.2. * gnu/packages/python.scm (python-ddt): Update to 1.1.2. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index b9f6749797..eb25e893ff 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10408,14 +10408,14 @@ convering text with ANSI color codes to HTML or LaTeX.") (define-public python-ddt (package (name "python-ddt") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (pypi-uri "ddt" version)) (sha256 (base32 - "1c00ikkxr7lha97c81k938bzhgd4pbwamkjn0h4nkhr3xk00zp6n")))) + "1wqkmz0yhanly8sif5vb02p2iik7mwxwph8ywph2kbb8ws8szdpx")))) (build-system python-build-system) (native-inputs `(("python-mock" ,python-mock) -- cgit 1.4.1 From ca1499ce2064c1d1015ef517cdd2ad7961160070 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Thu, 8 Mar 2018 09:43:15 +0100 Subject: gnu: intelmetool, me-cleaner: Restrict to Intel platforms. * gnu/packages/flashing-tools.scm (intelmetool)[supported-systems]: New field. (me-cleaner)[supported-systems]: New field. --- gnu/packages/flashing-tools.scm | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/gnu/packages/flashing-tools.scm b/gnu/packages/flashing-tools.scm index 5309510d40..192f84c36c 100644 --- a/gnu/packages/flashing-tools.scm +++ b/gnu/packages/flashing-tools.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2014 Mark H Weaver ;;; Copyright © 2014 Manolis Fragkiskos Ragkousis ;;; Copyright © 2016 Hartmut Goebel -;;; Copyright © 2016 Ludovic Courtès +;;; Copyright © 2016, 2018 Ludovic Courtès ;;; Copyright © 2016 Efraim Flashner ;;; Copyright © 2017 Jonathan Brielmaier ;;; Copyright © 2017 Julien Lepiller @@ -402,7 +402,10 @@ dump Intel Firmware Descriptor data of an image file.") Management Engine (ME). You need to @code{sudo rmmod mei_me} and @code{sudo rmmod mei} before using this tool. Also pass @code{iomem=relaxed} to the Linux kernel command line.") - (license license:gpl2))) + (license license:gpl2) + + ;; This is obviously an Intel thing, plus it requires . + (supported-systems '("x86_64-linux" "i686-linux")))) (define-public me-cleaner (package @@ -420,7 +423,7 @@ Management Engine (ME). You need to @code{sudo rmmod mei_me} and (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'create-setup.py + (add-after 'unpack 'create-setup.py (lambda _ (call-with-output-file "setup.py" (lambda (port) @@ -433,4 +436,7 @@ setup(name='me_cleaner', version='~a', scripts=['me_cleaner.py']) (synopsis "Intel ME cleaner") (description "This package provides tools for disabling Intel ME as far as possible (it only edits ME firmware image files).") - (license license:gpl3+))) + (license license:gpl3+) + + ;; This is an Intel thing. + (supported-systems '("x86_64-linux" "i686-linux")))) -- cgit 1.4.1 From 3aab8851442713f6ad748ffebb055c5e9eae1bd4 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Thu, 8 Mar 2018 11:46:55 +0100 Subject: gnu: guile: Add 2.2.2. * gnu/packages/guile.scm (guile-2.2.2): New variable. --- gnu/packages/guile.scm | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 5dc66c1625..91a440d928 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès +;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès ;;; Copyright © 2014, 2015 Mark H Weaver ;;; Copyright © 2015, 2017 Christopher Allan Webber ;;; Copyright © 2016 Alex Sassmannshausen @@ -281,6 +281,21 @@ without requiring the source code to be rewritten.") ; when heavily loaded) (replacement #f))) +(define-public guile-2.2.2 + ;; Keep it so that, when 'guix' runs on 2.2.2, 'guix pull' compiles objects + ;; with 2.2.2, thereby avoiding the ABI incompatibility issues described in + ;; . + (package + (inherit guile-2.2) + (version "2.2.2") + (source (origin + (inherit (package-source guile-2.2)) + (uri (string-append "mirror://gnu/guile/guile-" version + ".tar.xz")) + (sha256 + (base32 + "1azm25zcmxif0skxfrp11d2wc89nrzpjaann9yxdw6pvjxhs948w")))))) + (define-public guile-next (deprecated-package "guile-next" guile-2.2)) -- cgit 1.4.1 From 33286075b9c2ecd27607b5674c68909dd528473a Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Thu, 8 Mar 2018 11:47:28 +0100 Subject: hash: Add 'sha1'. * guix/hash.scm (GCRY_MD_SHA1): New macro. (bytevector-hash): New procedure. (sha256): Express in terms of 'bytevector-hash'. (sha1): New procedure. * tests/hash.scm ("sha1, empty", "sha1, hello"): New tests. --- guix/hash.scm | 23 +++++++++++++++++------ tests/hash.scm | 8 ++++++++ 2 files changed, 25 insertions(+), 6 deletions(-) diff --git a/guix/hash.scm b/guix/hash.scm index 773b9d4777..39834043e1 100644 --- a/guix/hash.scm +++ b/guix/hash.scm @@ -23,7 +23,9 @@ #:use-module (system foreign) #:use-module ((guix build utils) #:select (dump-port)) #:use-module (srfi srfi-11) - #:export (sha256 + #:use-module (srfi srfi-26) + #:export (sha1 + sha256 open-sha256-port port-sha256 file-sha256 @@ -44,17 +46,26 @@ ;; Value as of Libgcrypt 1.5.2. (identifier-syntax 8)) -(define sha256 +(define-syntax GCRY_MD_SHA1 + (identifier-syntax 2)) + +(define bytevector-hash (let ((hash (pointer->procedure void (libgcrypt-func "gcry_md_hash_buffer") `(,int * * ,size_t)))) - (lambda (bv) - "Return the SHA256 of BV as a bytevector." - (let ((digest (make-bytevector (/ 256 8)))) - (hash GCRY_MD_SHA256 (bytevector->pointer digest) + (lambda (bv type size) + "Return the hash TYPE, of SIZE bytes, of BV as a bytevector." + (let ((digest (make-bytevector size))) + (hash type (bytevector->pointer digest) (bytevector->pointer bv) (bytevector-length bv)) digest)))) +(define sha1 + (cut bytevector-hash <> GCRY_MD_SHA1 20)) + +(define sha256 + (cut bytevector-hash <> GCRY_MD_SHA256 (/ 256 8))) + (define open-sha256-md (let ((open (pointer->procedure int (libgcrypt-func "gcry_md_open") diff --git a/tests/hash.scm b/tests/hash.scm index b4cf2b61d6..da87616eec 100644 --- a/tests/hash.scm +++ b/tests/hash.scm @@ -40,6 +40,14 @@ (test-begin "hash") +(test-equal "sha1, empty" + (base16-string->bytevector "da39a3ee5e6b4b0d3255bfef95601890afd80709") + (sha1 #vu8())) + +(test-equal "sha1, hello" + (base16-string->bytevector "2aae6c35c94fcfb415dbe95f408b9ce91ee846ed") + (sha1 (string->utf8 "hello world"))) + (test-equal "sha256, empty" %empty-sha256 (sha256 #vu8())) -- cgit 1.4.1 From dffc5ab5e47e45b94188828205c8d567994926ad Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Thu, 8 Mar 2018 11:55:06 +0100 Subject: vm: Use 9p mount tags below 32 chars. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fixes . Reported by Björn Höfling . * gnu/system/vm.scm (file-system->mount-tag): Use 'sha1' to compute the tag. --- gnu/system/vm.scm | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm index 91ff32ce9a..ae8780d2e1 100644 --- a/gnu/system/vm.scm +++ b/gnu/system/vm.scm @@ -30,6 +30,8 @@ #:use-module (guix records) #:use-module (guix modules) #:use-module (guix utils) + #:use-module (guix hash) + #:use-module (guix base32) #:use-module ((gnu build vm) #:select (qemu-command)) @@ -544,13 +546,13 @@ of the GNU system as described by OS." (define (file-system->mount-tag fs) "Return a 9p mount tag for host file system FS." - ;; QEMU mount tags cannot contain slashes and cannot start with '_'. - ;; Compute an identifier that corresponds to the rules. + ;; QEMU mount tags must be ASCII, at most 31-byte long, cannot contain + ;; slashes, and cannot start with '_'. Compute an identifier that + ;; corresponds to the rules. (string-append "TAG" - (string-map (match-lambda - (#\/ #\_) - (chr chr)) - fs))) + (string-drop (bytevector->base32-string + (sha1 (string->utf8 fs))) + 4))) (define (mapping->file-system mapping) "Return a 9p file system that realizes MAPPING." -- cgit 1.4.1 From 770986d5410c2f915c295c873cc8b0dec888d20d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 8 Mar 2018 12:25:05 +0100 Subject: gnu: feh: Update to 2.25.1. * gnu/packages/image-viewers.scm (feh): Update to 2.25.1. --- gnu/packages/image-viewers.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm index 7a33f6c871..cf612666f1 100644 --- a/gnu/packages/image-viewers.scm +++ b/gnu/packages/image-viewers.scm @@ -59,7 +59,7 @@ (define-public feh (package (name "feh") - (version "2.25") + (version "2.25.1") (home-page "https://feh.finalrewind.org/") (source (origin (method url-fetch) @@ -67,7 +67,7 @@ name "-" version ".tar.bz2")) (sha256 (base32 - "102rwi30n09l8rih6kv6bb7lhv3djklgzill4p2zag0h700yqfq6")))) + "197sm78bm33dvahr5nxqkbmpmdn4b13ahc9mrgn1l7n104bg4phc")))) (build-system gnu-build-system) (arguments '(#:phases (modify-phases %standard-phases (delete 'configure)) -- cgit 1.4.1 From c32e3ddedd103318ca3f0a4bf0c91c91e2517806 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 8 Mar 2018 09:50:07 +0100 Subject: services: agetty: Call default-serial-port only when starting. * gnu/services/base.scm (agetty-shepherd-service): Call default-serial-port only when starting. --- gnu/services/base.scm | 221 +++++++++++++++++++++++++------------------------- 1 file changed, 112 insertions(+), 109 deletions(-) diff --git a/gnu/services/base.scm b/gnu/services/base.scm index be30f2d9c3..343123a377 100644 --- a/gnu/services/base.scm +++ b/gnu/services/base.scm @@ -937,119 +937,122 @@ to use as the tty. This is primarily useful for headless systems." ;; mingetty-shepherd-service). (requirement '(user-processes host-name udev)) - (start #~(let ((tty #$(default-serial-port))) - (if tty - (make-forkexec-constructor - (list #$(file-append util-linux "/sbin/agetty") - #$@extra-options - #$@(if eight-bits? - #~("--8bits") - #~()) - #$@(if no-reset? - #~("--noreset") - #~()) - #$@(if remote? - #~("--remote") - #~()) - #$@(if flow-control? - #~("--flow-control") - #~()) - #$@(if host - #~("--host" #$host) - #~()) - #$@(if no-issue? - #~("--noissue") - #~()) - #$@(if init-string - #~("--init-string" #$init-string) - #~()) - #$@(if no-clear? - #~("--noclear") - #~()) + (start #~(lambda args + (let ((defaulted-tty #$(or tty (default-serial-port)))) + (apply + (if defaulted-tty + (make-forkexec-constructor + (list #$(file-append util-linux "/sbin/agetty") + #$@extra-options + #$@(if eight-bits? + #~("--8bits") + #~()) + #$@(if no-reset? + #~("--noreset") + #~()) + #$@(if remote? + #~("--remote") + #~()) + #$@(if flow-control? + #~("--flow-control") + #~()) + #$@(if host + #~("--host" #$host) + #~()) + #$@(if no-issue? + #~("--noissue") + #~()) + #$@(if init-string + #~("--init-string" #$init-string) + #~()) + #$@(if no-clear? + #~("--noclear") + #~()) ;;; FIXME This doesn't work as expected. According to agetty(8), if this option ;;; is not passed, then the default is 'auto'. However, in my tests, when that ;;; option is selected, agetty never presents the login prompt, and the ;;; term-ttyS0 service respawns every few seconds. - #$@(if local-line - #~(#$(match local-line - ('auto "--local-line=auto") - ('always "--local-line=always") - ('never "-local-line=never"))) - #~()) - #$@(if tty - #~() - #~("--keep-baud")) - #$@(if extract-baud? - #~("--extract-baud") - #~()) - #$@(if skip-login? - #~("--skip-login") - #~()) - #$@(if no-newline? - #~("--nonewline") - #~()) - #$@(if login-options - #~("--login-options" #$login-options) - #~()) - #$@(if chroot - #~("--chroot" #$chroot) - #~()) - #$@(if hangup? - #~("--hangup") - #~()) - #$@(if keep-baud? - #~("--keep-baud") - #~()) - #$@(if timeout - #~("--timeout" #$(number->string timeout)) - #~()) - #$@(if detect-case? - #~("--detect-case") - #~()) - #$@(if wait-cr? - #~("--wait-cr") - #~()) - #$@(if no-hints? - #~("--nohints?") - #~()) - #$@(if no-hostname? - #~("--nohostname") - #~()) - #$@(if long-hostname? - #~("--long-hostname") - #~()) - #$@(if erase-characters - #~("--erase-chars" #$erase-characters) - #~()) - #$@(if kill-characters - #~("--kill-chars" #$kill-characters) - #~()) - #$@(if chdir - #~("--chdir" #$chdir) - #~()) - #$@(if delay - #~("--delay" #$(number->string delay)) - #~()) - #$@(if nice - #~("--nice" #$(number->string nice)) - #~()) - #$@(if auto-login - (list "--autologin" auto-login) - '()) - #$@(if login-program - #~("--login-program" #$login-program) - #~()) - #$@(if login-pause? - #~("--login-pause") - #~()) - #$(or tty (default-serial-port)) - #$@(if baud-rate - #~(#$baud-rate) - #~()) - #$@(if term - #~(#$term) - #~())))) - (const #f))) ; never start. + #$@(if local-line + #~(#$(match local-line + ('auto "--local-line=auto") + ('always "--local-line=always") + ('never "-local-line=never"))) + #~()) + #$@(if tty + #~() + #~("--keep-baud")) + #$@(if extract-baud? + #~("--extract-baud") + #~()) + #$@(if skip-login? + #~("--skip-login") + #~()) + #$@(if no-newline? + #~("--nonewline") + #~()) + #$@(if login-options + #~("--login-options" #$login-options) + #~()) + #$@(if chroot + #~("--chroot" #$chroot) + #~()) + #$@(if hangup? + #~("--hangup") + #~()) + #$@(if keep-baud? + #~("--keep-baud") + #~()) + #$@(if timeout + #~("--timeout" #$(number->string timeout)) + #~()) + #$@(if detect-case? + #~("--detect-case") + #~()) + #$@(if wait-cr? + #~("--wait-cr") + #~()) + #$@(if no-hints? + #~("--nohints?") + #~()) + #$@(if no-hostname? + #~("--nohostname") + #~()) + #$@(if long-hostname? + #~("--long-hostname") + #~()) + #$@(if erase-characters + #~("--erase-chars" #$erase-characters) + #~()) + #$@(if kill-characters + #~("--kill-chars" #$kill-characters) + #~()) + #$@(if chdir + #~("--chdir" #$chdir) + #~()) + #$@(if delay + #~("--delay" #$(number->string delay)) + #~()) + #$@(if nice + #~("--nice" #$(number->string nice)) + #~()) + #$@(if auto-login + (list "--autologin" auto-login) + '()) + #$@(if login-program + #~("--login-program" #$login-program) + #~()) + #$@(if login-pause? + #~("--login-pause") + #~()) + defaulted-tty + #$@(if baud-rate + #~(#$baud-rate) + #~()) + #$@(if term + #~(#$term) + #~()))) + (const #f)) ; never start. + args)))) (stop #~(make-kill-destructor))))))) (define agetty-service-type -- cgit 1.4.1 From 875fe4b6b625fe4626403b42da72d5c20265d41f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 8 Mar 2018 12:40:22 +0100 Subject: gnu: nghttp2: Use a fixed variant of tzdata for tests. * gnu/packages/web.scm (nghttp2)[native-inputs]: Replace TZDATA with TZDATA-FOR-TESTS. --- gnu/packages/web.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index cfae9f9253..f5e004eda5 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -6368,7 +6368,7 @@ derivation by David Revoy from the original MonsterID by Andreas Gohr.") ;; Required by tests. ("cunit" ,cunit) - ("tzdata" ,tzdata))) + ("tzdata" ,tzdata-for-tests))) (inputs ;; Required to build the tools (i.e. without ‘--enable-lib-only’). `(("c-ares" ,c-ares) -- cgit 1.4.1 From 3e25d2b22e6c37ca948b67be0a5f2fc09ea50e61 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 8 Mar 2018 12:44:41 +0100 Subject: gnu: python-msgpack-transitional: Use a distinct name. * gnu/packages/python.scm (python-msgpack-transitional)[name]: New field. --- gnu/packages/python.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index eb25e893ff..73b0e91327 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5875,6 +5875,7 @@ reading and writing MessagePack data.") (define-public python-msgpack-transitional (package (inherit python-msgpack) + (name "python-msgpack-transitional") (arguments (substitute-keyword-arguments (package-arguments python-msgpack) ((#:phases phases) -- cgit 1.4.1 From 7f2f834550a2b81bcd7d1713b3b170f981554380 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Sun, 18 Feb 2018 14:46:26 -0500 Subject: gnu: milkytracker: Actually link with the JACK library. * gnu/packages/music.scm (milkytracker)[arguments]: Add appropriate configure flag. --- gnu/packages/music.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 65dfa92896..f47749b380 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2609,7 +2609,9 @@ of tools for manipulating and accessing your music.") (("add_subdirectory\\(resources/music\\)") "")))))) (build-system cmake-build-system) (arguments - '(#:tests? #f)) ; no check target + '(#:tests? #f ; no check target + ;; This flag ensures that MilkyTracker links with the JACK library. + #:configure-flags '("-DCMAKE_CXX_FLAGS=-ljack"))) (inputs `(("alsa-lib" ,alsa-lib) ("jack" ,jack-1) -- cgit 1.4.1 From 84c195e505ce581227099e861172f5e65f3d66d7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Mar 2018 18:51:32 +0100 Subject: gnu: r-dropbead: Update to 0-2.d746c6f. * gnu/packages/bioinformatics.scm (r-dropbead): Update to 0-2.d746c6f. --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d6c7c05dd5..73765dafe7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10880,8 +10880,8 @@ memory usage and processing time is minimized.") (license license:expat))) (define-public r-dropbead - (let ((commit "cf0be5ae5302684bd03e78ab65b142900bbbb840") - (revision "1")) + (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") + (revision "2")) (package (name "r-dropbead") (version (string-append "0-" revision "." (string-take commit 7))) @@ -10894,7 +10894,7 @@ memory usage and processing time is minimized.") (file-name (git-file-name name version)) (sha256 (base32 - "1b2lphsc236s1rdzlijxg8yl1jnqpwcvj4x938r89rqpj93jb780")))) + "0sbzma49aiiyw8b0jpr7fnhzys9nsqmp4hy4hdz1gzyg1lhnca26")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) -- cgit 1.4.1 From fee7f8a94ec64943109ba9c37f75c28749fb18bd Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 8 Mar 2018 20:29:13 +0200 Subject: gnu: nano: Update to 2.9.4. * gnu/packages/nano.scm (nano): Update to 2.9.4. --- gnu/packages/nano.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/nano.scm b/gnu/packages/nano.scm index d6bef33695..07c7ed36cb 100644 --- a/gnu/packages/nano.scm +++ b/gnu/packages/nano.scm @@ -30,7 +30,7 @@ (define-public nano (package (name "nano") - (version "2.9.3") + (version "2.9.4") (source (origin (method url-fetch) @@ -38,7 +38,7 @@ version ".tar.xz")) (sha256 (base32 - "04j05nbnp8vjjwja90d83p4s6ywyl6qhggflcjzw0p9d9gyvr0vp")))) + "0nm3zy4azr5rkxjq7jfybbj3cnddmvxc49rxyqm9cp2zfdp75y9c")))) (build-system gnu-build-system) (inputs `(("gettext" ,gettext-minimal) -- cgit 1.4.1