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2019-03-06gnu: r-bsgenome-dmelanogaster-ucsc-dm3: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-dmelanogaster-ucsc-dm3): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3): ...to here.
2019-03-06gnu: r-bsgenome-celegans-ucsc-ce10: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce10): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce10): ...to here.
2019-03-06gnu: r-bsgenome-celegans-ucsc-ce6: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce6): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce6): ...to here.
2019-03-06gnu: r-bsgenome-mmusculus-ucsc-mm10: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm10): ...to here.
2019-03-06gnu: r-bsgenome-mmusculus-ucsc-mm9: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm9): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9): ...to here.
2019-03-06gnu: r-bsgenome-hsapiens-ucsc-hg19: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19): ...to here.
2019-03-06gnu: r-bsgenome-hsapiens-1000genomes-hs37d5: Move to (gnu packages ↵Ricardo Wurmus
bioconductor). * gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-1000genomes-hs37d5): ...to here.
2019-03-06gnu: r-txdb-hsapiens-ucsc-hg19-knowngene: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): Move from here... * gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): ...to here.
2019-03-06gnu: r-geneplotter: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-geneplotter): Move from here... * gnu/packages/bioconductor.scm (r-geneplotter): ...to here.
2019-03-06gnu: Add guile-stis-parser.Ricardo Wurmus
* gnu/packages/guile-xyz.scm (guile-stis-parser): New variable.
2019-03-06gnu: r-copynumber: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-copynumber): Move from here... * gnu/packages/bioconductor.scm (r-copynumber): ...to here.
2019-03-06gnu: Update copyright headers.Ricardo Wurmus
This is a follow-up to commit 1fe9a36173335b559c695357bc8d884f1d4b144a. * gnu/packages/bioconductor.scm: Update copyright header to account for moved package.
2019-03-06gnu: font-gnu-unifont: Update to 12.0.01.Efraim Flashner
* gnu/packages/fonts.scm (font-gnu-unifont): Update to 12.0.01.
2019-03-06gnu: cabextract: Don't use NAME in source URI.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (cabextract)[source]: Hard-code NAME.
2019-03-06gnu: cabextract: Update to 1.9.1.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (cabextract): Update to 1.9.1.
2019-03-06gnu: lcov: Update to 1.14.Tobias Geerinckx-Rice
* gnu/packages/code.scm (lcov): Update to 1.14.
2019-03-06gnu: python-mako: Update home page.Marius Bakke
* gnu/packages/python-xyz.scm (python-mako)[home-page]: Use HTTPS.
2019-03-06gnu: fuseiso: Fix typo.Marius Bakke
* gnu/packages/linux.scm (fuseiso)[synopsis]: s/imsages/images.
2019-03-06gnu: valgrind: Add download mirror.Marius Bakke
* gnu/packages/valgrind.scm (valgrind)[source](uri): Add mirror.
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.
2019-03-05artwork: Update snapshot to b975164.Ludovic Courtès
* gnu/artwork.scm (%artwork-repository): Update to b975164.
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'.
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