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2019-03-06gnu: bismark: Update to 0.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bismark): Update to 0.20.1. [source]: Remove obsolete snippet. [arguments]: Add build phase "replace-plotly.js" and add requried modules; adjust "install" phase. [inputs]: Add perl-carp and perl-getopt-long. [native-inputs]: Add plotly.js and uglify-js.
2019-03-06gnu: Add fuseiso.Pierre Neidhardt
* gnu/packages/linux.scm (fuseiso): New variable.
2019-03-06gnu: Add r-scde.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scde): New variable.
2019-03-06gnu: Add bowtie1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bowtie1): New variable.
2019-03-06gnu: octave, octave-cli: Update to 5.1.0.Kei Kebreau
* gnu/packages/maths.scm (octave, octave-cli): Update to 5.1.0.
2019-03-06gnu: crawl, crawl-tiles: Update to 0.23.1.Kei Kebreau
* gnu/packages/games.scm (crawl, crawl-tiles): Update to 0.23.1. [native-inputs]: Add python and python-pyyaml. [arguments]: Add 'patch-python' phase, modify the 'check' phase and move the 'check' phase back after the 'build' phase.
2019-03-06gnu: perl-czplib: Fix installation directory.Ricardo Wurmus
* gnu/packages/perl.scm (perl-czplib)[arguments]: Fix installation directory.
2019-03-06gnu: Add guile-studio.Ricardo Wurmus
* gnu/packages/guile-xyz.scm (guile-studio): New variable.
2019-03-06gnu: Add genrich.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (genrich): New variable.
2019-03-06gnu: r-dnacopy: Remove duplicate definition.Ricardo Wurmus
Reported by Christopher Baines <mail@cbaines.net>. * gnu/packages/bioinformatics.scm (r-dnacopy): Remove variable.
2019-03-06gnu: Add r-org-dr-eg-db.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-org-dr-eg-db): New variable.
2019-03-06gnu: java-eclipse-jdt-core: Update to 3.16.0.Ricardo Wurmus
* gnu/packages/java.scm (java-eclipse-jdt-core): Update to 3.16.0.
2019-03-06gnu: java-eclipse-core-resources: Update to 3.13.200.Ricardo Wurmus
* gnu/packages/java.scm (java-eclipse-core-resources): Update to 3.13.200.
2019-03-06gnu: java-eclipse-core-runtime: Update to 3.15.100.Ricardo Wurmus
* gnu/packages/java.scm (java-eclipse-core-runtime): Update to 3.15.100.
2019-03-06gnu: java-eclipse-equinox-common: Update to 3.10.200.Ricardo Wurmus
* gnu/packages/java.scm (java-eclipse-equinox-common): Update to 3.10.200.
2019-03-06gnu: shaderc: Update to 2018.0.Rutger Helling
* gnu/packages/vulkan.scm (shaderc): Update to 2018.0.
2019-03-06gnu: spirv-tools: Update to 2019.1.Rutger Helling
* gnu/packages/vulkan.scm (spirv-tools): Update to 2019.1. [arguments]: Add 'fixgcc7 phase. [native-inputs]: Add gcc-7.
2019-03-06gnu: spirv-headers: Update to commit 8bea0a2.Rutger Helling
* gnu/packages/vulkan.scm (spirv-headers): Update to commit 8bea0a2.
2019-03-06gnu: glslang: Update to 7.11.3113.Rutger Helling
* gnu/packages/vulkan.scm (glslang): Update to 7.11.3113.
2019-03-05gnu: MPD: Update to 0.21.5.Leo Famulari
* gnu/packages/mpd.scm (mpd): Update to 0.21.5.
2019-03-05gnu: FFmpeg: Build with AV1 support.Arne Babenhauserheide
* gnu/packages/video.scm (ffmpeg)[inputs]: Add libaom. [arguments]: Pass '--enable-libaom' to #:configure-flags. (ffmpeg-3.4)[inputs, arguments]: Filter out libaom.
2019-03-05gnu: Add libaom.Arne Babenhauserheide
* gnu/packages/video.scm (libaom): New variable. Co-authored-by: Leo Famulari <leo@famulari.name>
2019-03-06gnu: you-get: Update to 0.4.1256.Tobias Geerinckx-Rice
* gnu/packages/video.scm (you-get): Update to 0.4.1256.
2019-03-06gnu: youtube-dl: Update to 2019.03.01.Tobias Geerinckx-Rice
* gnu/packages/video.scm (youtube-dl): Update to 2019.03.01.
2019-03-06gnu: plantuml: Update to 1.2019.2.Tobias Geerinckx-Rice
* gnu/packages/uml.scm (plantuml): Update to 1.2019.2.
2019-03-06gnu: xinit: Update to 1.4.1.Tobias Geerinckx-Rice
* gnu/packages/xorg.scm (xinit): Update to 1.4.1.
2019-03-06gnu: lxc: Fix documentation directory.Tobias Geerinckx-Rice
* gnu/packages/virtualization.scm (lxc)[arguments]: Set ‘--docdir’ in #:configure-flags.
2019-03-06gnu: lxc: Update to 3.1.0.Tobias Geerinckx-Rice
* gnu/packages/virtualization.scm (lxc): Update to 3.1.0.
2019-03-05gnu: dav1d: Update to 0.2.0.Leo Famulari
* gnu/packages/video.scm (dav1d): Update to 0.2.0. [source]: Add alternate URL.
2019-03-05gnu: singularity: Leave PATH unchanged.Ludovic Courtès
Previously 'singularity help' & co. would all fail on Guix System because Coreutils, grep, etc. were not found in $PATH. * gnu/packages/linux.scm (singularity)[source](snippet): Remove "PATH" setting from 'bin/singularity.in'.
2019-03-05gnu: singularity: Patch 'Makefile.in' in a snippet.Ludovic Courtès
* gnu/packages/linux.scm (singularity)[source](snippet, modules): New fields. [arguments]: Remove 'disable-install-hook' phase.
2019-03-05gnu: wpa-supplicant: Add 'cpe-name' property.Ludovic Courtès
* gnu/packages/admin.scm (wpa-supplicant-minimal)[properties]: New field.
2019-03-05gnu: Syncthing: Update to 1.1.0.Leo Famulari
* gnu/packages/syncthing.scm (syncthing): Update to 1.1.0.
2019-03-05gnu: emacs-no-x-toolkit: Fix configure flags.Efraim Flashner
* gnu/packages/emacs.scm (emacs-no-x-toolkit)[arguments]: Don't lose custom configure flags.
2019-03-05gnu: emacs-disk-usage: Update to 1.3.0.Pierre Neidhardt
* gnu/packages/emacs-xyz.scm (emacs-disk-usage): Update to 1.3.0.
2019-03-05gnu: thinkfan: Let the build system handle rcscripts/.Tobias Geerinckx-Rice
This moves them from /share/thinkfan to their conventional locations in /etc and /lib; the former was an arbitrary Guixism anyway. * gnu/packages/linux.scm (thinkfan)[arguments]: Re-write 'install-rc-scripts' as 'create-init-scripts' and move it after the 'unpack' phase.
2019-03-05gnu: thinkfan: Update to 1.0.2.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (thinkfan): Update to 1.0.2. [arguments]: Adjust source directory.
2019-03-05gnu: iucode-tool: Update to 2.3.1.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (iucode-tool): Update to 2.3.1.
2019-03-05gnu: f2fs-tools: Update to 1.12.0.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (f2fs-tools): Update to 1.12.0.
2019-03-05gnu: f2fs-tools: Don't use NAME in source URI.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (f2fs-tools-1.7, f2fs-tools)[source]: Hard-code NAME.
2019-03-05gnu: xfsprogs: Update to 4.20.0.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (xfsprogs): Update to 4.20.0.
2019-03-05gnu: libnftnl: Update to 1.1.2.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (libnftnl): Update to 1.1.2.
2019-03-05gnu: genext2fs: Update to 1.4.1-4.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (genext2fs): Update to 1.4.1-4. [arguments]: Add 'apply-debian-patches' phase. [native-inputs]: Add autoconf and automake.
2019-03-05gnu: wget2: Update to 1.99.1.Efraim Flashner
This fixes https://issues.guix.info/issue/34718. * gnu/packages/wget.scm (wget2): Update to 1.99.1. [arguments]: Add phase to skip network tests. Update custom 'bootstrap phase to not require unnecessary binaries. [inputs]: Remove doxygen, python. Move autoconf, automake, flex, gettext-minimal, libtool ... [native-inputs]: ... to here. Add python-2.
2019-03-05gnu: rust: Update to 1.31.1.Ivan Petkov
* gnu/patches/rust-1.30-gdb-llvm.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/rust.scm (rust): Rename to... (rust-1.29): ...this. (rust-1.30): New variable. (rust): New variable. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
2019-03-05gnu: scdoc: Update to 1.9.4.Rutger Helling
* gnu/packages/man.scm (scdoc): Update to 1.9.4.
2019-03-05gnu: Add mailcatcher.Pierre Neidhardt
* gnu/packages/ruby.scm (mailcatcher): New variable.
2019-03-05gnu: Add ruby-skinny.Pierre Neidhardt
* gnu/packages/ruby.scm (ruby-skinny): New variable.
2019-03-05gnu: Add ruby-thin.Pierre Neidhardt
* gnu/packages/ruby.scm (ruby-thin): New variable.
2019-03-05gnu: Add ruby-sinatra.Pierre Neidhardt
* gnu/packages/ruby.scm (ruby-sinatra): New variable.
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