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2021-11-07gnu: r-dexseq: Update to 1.40.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dexseq): Update to 1.40.0.
2021-11-07gnu: r-deseq2: Update to 1.34.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.34.0.
2021-11-07gnu: r-copywriter: Update to 2.26.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-copywriter): Update to 2.26.0.
2021-11-07gnu: r-complexheatmap: Update to 2.10.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-complexheatmap): Update to 2.10.0. [propagated-inputs]: Remove r-cairo.
2021-11-07gnu: r-chipseq: Update to 1.44.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chipseq): Update to 1.44.0.
2021-11-07gnu: r-chipseeker: Update to 1.30.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.30.0.
2021-11-07gnu: r-category: Update to 2.60.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-category): Update to 2.60.0.
2021-11-07gnu: r-bsgenome: Update to 1.62.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bsgenome): Update to 1.62.0.
2021-11-07gnu: r-biovizbase: Update to 1.42.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biovizbase): Update to 1.42.0.
2021-11-07gnu: r-biostrings: Update to 2.62.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.62.0.
2021-11-07gnu: r-biomart: Update to 2.50.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biomart): Update to 2.50.0.
2021-11-07gnu: r-biobase: Update to 2.54.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biobase): Update to 2.54.0.
2021-11-07gnu: r-bamsignals: Update to 1.26.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bamsignals): Update to 1.26.0.
2021-11-07gnu: r-aroma-light: Update to 3.24.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-aroma-light): Update to 3.24.0.
2021-11-07gnu: r-annotationhub: Update to 3.2.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotationhub): Update to 3.2.0.
2021-11-07gnu: r-annotationforge: Update to 1.36.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.36.0.
2021-11-07gnu: r-annotationfilter: Update to 1.18.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotationfilter): Update to 1.18.0.
2021-11-07gnu: r-annotationdbi: Update to 1.56.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.56.1.
2021-11-07gnu: r-annotate: Update to 1.72.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotate): Update to 1.72.0.
2021-11-07gnu: r-affxparser: Update to 1.66.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affxparser): Update to 1.66.0.
2021-11-07gnu: r-affyio: Update to 1.64.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affyio): Update to 1.64.0.
2021-11-07gnu: r-affycoretools: Update to 1.66.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.66.0.
2021-11-07gnu: r-affycontam: Update to 1.52.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affycontam): Update to 1.52.0.
2021-11-07gnu: r-affycompatible: Update to 1.54.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affycompatible): Update to 1.54.0.
2021-11-07gnu: r-affycomp: Update to 1.70.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affycomp): Update to 1.70.0.
2021-11-07gnu: r-affy: Update to 1.72.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affy): Update to 1.72.0.
2021-11-07gnu: r-iranges: Update to 2.28.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-iranges): Update to 2.28.0.
2021-11-07gnu: r-ideoviz: Update to 1.30.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ideoviz): Update to 1.30.0.
2021-11-07gnu: r-bluster: Update to 1.4.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bluster): Update to 1.4.0.
2021-11-07gnu: r-delayedarray: Update to 0.20.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.20.0.
2021-11-07gnu: r-deepsnv: Update to 1.40.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-deepsnv): Update to 1.40.0.
2021-11-07gnu: r-decipher: Update to 2.22.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-decipher): Update to 2.22.0.
2021-11-07gnu: r-cummerbund: Update to 2.36.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.36.0.
2021-11-07gnu: r-coverageview: Update to 1.32.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-coverageview): Update to 1.32.0.
2021-11-07gnu: r-biocgenerics: Update to 0.40.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.40.0.
2021-11-07gnu: r-biocversion: Update to 3.14.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocversion): Update to 3.14.0.
2021-11-07gnu: r-aneufinder: Update to 1.22.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-aneufinder): Update to 1.22.0.
2021-11-07gnu: r-biocparallel: Update to 1.28.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.28.0. [arguments]: Adjust build phase to patch renamed file.
2021-11-07gnu: Add r-msfeatures.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-msfeatures): New variable.
2021-11-07gnu: r-with-tests: Update patch to DESCRIPTION file.Ricardo Wurmus
* gnu/packages/statistics.scm (r-with-tests)[arguments]: Patch line breaks and spaces in DESCRIPTION file to ensure reproducible build.
2021-11-07gnu: r-with-tests: Remove trailing #T.Ricardo Wurmus
* gnu/packages/statistics.scm (r-with-tests)[arguments]: Remove trailing #T from build phases.
2021-11-07gnu: r-with-tests: Update to 4.1.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-with-tests): Update to 4.1.2.
2021-11-07gnu: ardour: Update to 6.9.Thorsten Wilms
* gnu/packages/audio.scm (ardour): Update to 6.9. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-11-07doc: Improve documentation of the Bash home serviceXinglu Chen
* doc/guix.texi (Shells Home Services): Document ‘home-bash-extension’ configuration record. * gnu/home/services/shells.scm (generate-home-bash-documentation): Extract docstrings from ‘home-bash-extension’. (home-bash-configuration): Expound on docstrings. (home-bash-extension): Likewise. Fixes: <https://issues.guix.gnu.org/50991> Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-11-07home: services: bash: Add ‘aliases’ field.Xinglu Chen
* doc/guix.texi (Shells Home Services): Document it. * gnu/home/services/shells.scm (bash-serialize-aliases): New procedure. (home-bash-configuration, home-bash-extension): Add ‘aliases’ field. (home-bash-extensions): Adjust accordingly. * guix/scripts/home/import.scm (generate-bash-configuration+modules): Populate the ‘alias’ field. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-11-07file-systems: Validate the 'flags' field.Ludovic Courtès
Fixes <https://issues.guix.gnu.org/51425>. Reported by Jonathan Brielmaier <jonathan.brielmaier@web.de>. * gnu/system/file-systems.scm (invalid-file-system-flags) (%validate-file-system-flags): New procedures. (validate-file-system-flags): New macro. (<file-system>)[flags]: Add 'sanitize' property.
2021-11-07gnu: 0ad: Update to 0.0.25b-alpha.Brendan Tildesley
* gnu/packages/games.scm (0ad-data): Update to 0.0.25b-alpha. Unpack .zip files without need for a snippet. (0ad): Update to 0.0.25b-alpha. [arguments]<#:phases>: Properly unbundle cxxtest. Respect #:tests?. Install Freedesktop mimeinfo. Install icon to hicolor theme instead of share/pixmaps, which I don't think is used. <#:tests> Disable tests for now since they don't run. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-11-07gnu: ansible-core: Update to 2.11.6.Tobias Geerinckx-Rice
* gnu/packages/admin.scm (ansible-core): Update to 2.11.6.
2021-11-07gnu: xfstests: Update to 1.1.0-1.bae1d15.Tobias Geerinckx-Rice
* gnu/packages/file-systems.scm (xfstests): Update to 1.1.0-1.bae1d15.
2021-11-07gnu: lv2: Update to 1.18.2.Tobias Geerinckx-Rice
* gnu/packages/audio.scm (lv2): Update to 1.18.2.
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