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Author SHA1 Message Date
Ricardo Wurmus
f34bcc5c6b
gnu: r-copywriter: Update to 2.26.0. 
* gnu/packages/bioconductor.scm (r-copywriter): Update to 2.26.0.
 2021-11-07 22:34:37 +00:00
Ricardo Wurmus
e5d90645ea
gnu: r-complexheatmap: Update to 2.10.0. 
* gnu/packages/bioconductor.scm (r-complexheatmap): Update to 2.10.0.
[propagated-inputs]: Remove r-cairo.
 2021-11-07 22:34:37 +00:00
Ricardo Wurmus
126a4b6c9d
gnu: r-chipseq: Update to 1.44.0. 
* gnu/packages/bioconductor.scm (r-chipseq): Update to 1.44.0.
 2021-11-07 22:34:37 +00:00
Ricardo Wurmus
cd7c1e2c3e
gnu: r-chipseeker: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.30.0.
 2021-11-07 22:34:37 +00:00
Ricardo Wurmus
395e9ab420
gnu: r-category: Update to 2.60.0. 
* gnu/packages/bioconductor.scm (r-category): Update to 2.60.0.
 2021-11-07 22:34:37 +00:00
Ricardo Wurmus
a6b83bd30d
gnu: r-bsgenome: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-bsgenome): Update to 1.62.0.
 2021-11-07 22:34:37 +00:00
Ricardo Wurmus
eea602cdbb
gnu: r-biovizbase: Update to 1.42.0. 
* gnu/packages/bioconductor.scm (r-biovizbase): Update to 1.42.0.
 2021-11-07 22:34:37 +00:00
Ricardo Wurmus
7851f7f2c6
gnu: r-biostrings: Update to 2.62.0. 
* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.62.0.
 2021-11-07 22:34:37 +00:00
Ricardo Wurmus
d0ceaf62fc
gnu: r-biomart: Update to 2.50.0. 
* gnu/packages/bioconductor.scm (r-biomart): Update to 2.50.0.
 2021-11-07 22:34:37 +00:00
Ricardo Wurmus
918c08e20d
gnu: r-biobase: Update to 2.54.0. 
* gnu/packages/bioconductor.scm (r-biobase): Update to 2.54.0.
 2021-11-07 22:34:37 +00:00
Ricardo Wurmus
e606add2e4
gnu: r-bamsignals: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-bamsignals): Update to 1.26.0.
 2021-11-07 22:34:37 +00:00
Ricardo Wurmus
9efb70c077
gnu: r-aroma-light: Update to 3.24.0. 
* gnu/packages/bioconductor.scm (r-aroma-light): Update to 3.24.0.
 2021-11-07 22:34:37 +00:00
Ricardo Wurmus
7f291d0965
gnu: r-annotationhub: Update to 3.2.0. 
* gnu/packages/bioconductor.scm (r-annotationhub): Update to 3.2.0.
 2021-11-07 22:34:37 +00:00
Ricardo Wurmus
c46f294350
gnu: r-annotationforge: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.36.0.
 2021-11-07 22:34:37 +00:00
Ricardo Wurmus
0e31c0034a
gnu: r-annotationfilter: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-annotationfilter): Update to 1.18.0.
 2021-11-07 22:34:36 +00:00
Ricardo Wurmus
eccd328684
gnu: r-annotationdbi: Update to 1.56.1. 
* gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.56.1.
 2021-11-07 22:34:36 +00:00
Ricardo Wurmus
eee1bc786a
gnu: r-annotate: Update to 1.72.0. 
* gnu/packages/bioconductor.scm (r-annotate): Update to 1.72.0.
 2021-11-07 22:34:36 +00:00
Ricardo Wurmus
5b63db8f83
gnu: r-affxparser: Update to 1.66.0. 
* gnu/packages/bioconductor.scm (r-affxparser): Update to 1.66.0.
 2021-11-07 22:34:36 +00:00
Ricardo Wurmus
5de927226c
gnu: r-affyio: Update to 1.64.0. 
* gnu/packages/bioconductor.scm (r-affyio): Update to 1.64.0.
 2021-11-07 22:34:36 +00:00
Ricardo Wurmus
5ab6e9e100
gnu: r-affycoretools: Update to 1.66.0. 
* gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.66.0.
 2021-11-07 22:34:36 +00:00
Ricardo Wurmus
21b5db3f1e
gnu: r-affycontam: Update to 1.52.0. 
* gnu/packages/bioconductor.scm (r-affycontam): Update to 1.52.0.
 2021-11-07 22:34:36 +00:00
Ricardo Wurmus
71f58a16ae
gnu: r-affycompatible: Update to 1.54.0. 
* gnu/packages/bioconductor.scm (r-affycompatible): Update to 1.54.0.
 2021-11-07 22:34:36 +00:00
Ricardo Wurmus
a610856e88
gnu: r-affycomp: Update to 1.70.0. 
* gnu/packages/bioconductor.scm (r-affycomp): Update to 1.70.0.
 2021-11-07 22:34:36 +00:00
Ricardo Wurmus
1a4e10d555
gnu: r-affy: Update to 1.72.0. 
* gnu/packages/bioconductor.scm (r-affy): Update to 1.72.0.
 2021-11-07 22:34:36 +00:00
Ricardo Wurmus
a85e744c3d
gnu: r-iranges: Update to 2.28.0. 
* gnu/packages/bioconductor.scm (r-iranges): Update to 2.28.0.
 2021-11-07 22:34:36 +00:00
Ricardo Wurmus
1acf3f1821
gnu: r-ideoviz: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-ideoviz): Update to 1.30.0.
 2021-11-07 22:34:36 +00:00
Ricardo Wurmus
b0a2fc9253
gnu: r-bluster: Update to 1.4.0. 
* gnu/packages/bioconductor.scm (r-bluster): Update to 1.4.0.
 2021-11-07 22:34:36 +00:00
Ricardo Wurmus
35ccf99fff
gnu: r-delayedarray: Update to 0.20.0. 
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.20.0.
 2021-11-07 22:34:35 +00:00
Ricardo Wurmus
7cc053eaca
gnu: r-deepsnv: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-deepsnv): Update to 1.40.0.
 2021-11-07 22:34:35 +00:00
Ricardo Wurmus
628a8f8c78
gnu: r-decipher: Update to 2.22.0. 
* gnu/packages/bioconductor.scm (r-decipher): Update to 2.22.0.
 2021-11-07 22:34:35 +00:00
Ricardo Wurmus
07b14e81f9
gnu: r-cummerbund: Update to 2.36.0. 
* gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.36.0.
 2021-11-07 22:34:35 +00:00
Ricardo Wurmus
9d51c1f423
gnu: r-coverageview: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-coverageview): Update to 1.32.0.
 2021-11-07 22:34:35 +00:00
Ricardo Wurmus
3622390699
gnu: r-biocgenerics: Update to 0.40.0. 
* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.40.0.
 2021-11-07 22:34:35 +00:00
Ricardo Wurmus
6ed26516bf
gnu: r-biocversion: Update to 3.14.0. 
* gnu/packages/bioconductor.scm (r-biocversion): Update to 3.14.0.
 2021-11-07 22:34:35 +00:00
Ricardo Wurmus
fc0fa7a431
gnu: r-aneufinder: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-aneufinder): Update to 1.22.0.
 2021-11-07 22:34:35 +00:00
Ricardo Wurmus
d1c79f5a2c
gnu: r-biocparallel: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.28.0.
[arguments]: Adjust build phase to patch renamed file.
 2021-11-07 22:34:35 +00:00
Ricardo Wurmus
4a92ab58f6
gnu: Add r-msfeatures. 
* gnu/packages/bioconductor.scm (r-msfeatures): New variable.
 2021-11-07 22:34:34 +00:00
Ricardo Wurmus
22b568de43
guix: Upgrade to Bioconductor 3.14. 
* guix/build-system/r.scm (bioconductor-uri): Bump Bioconductor version to
3.14.
* guix/import/cran.scm (%bioconductor-version): Same.
 2021-11-07 22:34:34 +00:00
Ricardo Wurmus
92b85194cd
gnu: r-with-tests: Update patch to DESCRIPTION file. 
* gnu/packages/statistics.scm (r-with-tests)[arguments]: Patch line breaks and
spaces in DESCRIPTION file to ensure reproducible build.
 2021-11-07 22:34:34 +00:00
Ricardo Wurmus
108111114d
gnu: r-with-tests: Remove trailing #T. 
* gnu/packages/statistics.scm (r-with-tests)[arguments]: Remove trailing #T
from build phases.
 2021-11-07 22:34:34 +00:00
Ricardo Wurmus
17d0bbef88
gnu: r-with-tests: Update to 4.1.2. 
* gnu/packages/statistics.scm (r-with-tests): Update to 4.1.2.
 2021-11-07 22:34:29 +00:00
Thorsten Wilms
bd41e590dd
gnu: ardour: Update to 6.9. 
* gnu/packages/audio.scm (ardour): Update to 6.9.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-11-07 23:10:41 +01:00
Ludovic Courtès
859122e5ab
shell: Actually clean up the profile cache. 
Previously, most actions would leave the cache as-is because
'guix-environment*' would indirectly call 'exit', and thus its
continuation was never reached.

* guix/scripts/shell.scm (guix-shell): Move call to
'maybe-remove-expired-cache-entries' to EXIT-HOOK.
 2021-11-07 23:10:41 +01:00
Xinglu Chen
b999c80c2e
import: egg: Allow imports of a specific version. 
* guix/import/egg.scm (eggs-repository): Change URL.
(egg-metadata): Accept optional #:version keyword argument.
(egg->guix-package): Accept ‘version’ argument.
(egg-recursive-import): Add ‘version’ argument and honor it.
* guix/scripts/import/egg.scm (guix-import-egg): Parse a specification instead
of just a package name.
* doc/guix.texi (Invoking guix import): Document it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-11-07 23:10:41 +01:00
Xinglu Chen
2f665d4309
doc: Improve documentation of the Bash home service 
* 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>
 2021-11-07 23:10:41 +01:00
Xinglu Chen
4b96998292
home: services: bash: Add ‘aliases’ field. 
* 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>
 2021-11-07 23:10:41 +01:00
Ludovic Courtès
5eb5c0789f
file-systems: Validate the 'flags' field. 
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.
 2021-11-07 23:10:41 +01:00
Ludovic Courtès
4d59596a1c
ui: 'load*' correctly reports 'read-error' in all cases. 
Previously, 'read-error' exceptions other than "missing closing paren"
would not be reported; instead, we'd directly call (exit 1) without
printing anything.

Fixes <https://issues.guix.gnu.org/51463>.
Reported by Alice BRENON <alice.brenon@ens-lyon.fr>.

* guix/ui.scm (report-load-error): Report the error without re-throwing
upon 'read-error'.
* tests/guix-build.sh: Add test.
 2021-11-07 23:10:41 +01:00
Brendan Tildesley
dab2ac2ed5
gnu: 0ad: Update to 0.0.25b-alpha. 
* 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>
 2021-11-07 22:57:05 +01:00
Tobias Geerinckx-Rice
90cd653abe
gnu: ansible-core: Update to 2.11.6. 
* gnu/packages/admin.scm (ansible-core): Update to 2.11.6.
 2021-11-07 22:52:43 +01:00