TakeV/guix
1
0
Fork 0
Code Issues Pull requests Packages Projects Releases Wiki Activity
62160 commits 102 branches 35 tags 561 MiB
Commit graph

62160 commits

This branch
This branch
All branches
Author SHA1 Message Date
Ricardo Wurmus f189f536be
gnu: r-s4vectors: Update to 0.26.1. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.26.1.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 1a9de6cfe8
gnu: r-bioccheck: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.24.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 9f416be83d
gnu: r-biocstyle: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 1ca88fb8e9
gnu: r-biocviews: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 5de96ae98b
gnu: r-grohmm: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.22.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus bb18d11d85
gnu: r-systempiper: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.22.0.
[propagated-inputs]: Add r-assertthat, r-magrittr, r-rsvg, r-dot, and
r-stringr; remove r-biocgenerics.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 681cca95b3
gnu: r-shortread: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.46.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 3d2899dab5
gnu: r-gostats: Update to 2.54.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.54.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus be414286bc
gnu: r-category: Update to 2.54.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.54.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus a8613ff861
gnu: r-gseabase: Update to 1.50.1. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.50.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 7d8b96e24b
gnu: r-rbgl: Update to 1.64.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.64.0.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 397568dbca
gnu: r-annotationforge: Update to 1.30.1. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.30.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus db5addba2c
gnu: r-dexseq: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.34.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 3d7de4ed82
gnu: r-deseq2: Update to 1.28.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.28.1.
[propagated-inputs]: Remove r-hmisc.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 5fdea056c9
gnu: r-genefilter: Update to 1.70.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.70.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus c85e5ac0df
gnu: r-rgraphviz: Update to 2.32.0. 
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.32.0.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 2226a2a8de
gnu: r-preprocesscore: Update to 1.50.0. 
* gnu/packages/statistics.scm (r-preprocesscore): Update to 1.50.0.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 67a289e5bd
gnu: Add r-dot. 
* gnu/packages/cran.scm (r-dot): New variable.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 06ceac32e6
gnu: Add r-v8. 
* gnu/packages/cran.scm (r-v8): New variable.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus e6aacef67e
gnu: Add r-scatterpie. 
* gnu/packages/cran.scm (r-scatterpie): New variable.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 45f54b418b
gnu: Add r-gprofiler2. 
* gnu/packages/cran.scm (r-gprofiler2): New variable.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus f9311eaa7c
gnu: node: Build shared library. 
* gnu/packages/node.scm (node)[arguments]: Build shared library.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 8e518d4802
guix: Update to Bioconductor 3.11. 
* guix/build-system/r.scm (bioconductor-uri): Use new URL.
* guix/import/cran.scm (%bioconductor-version): Update to 3.11.
 2020-06-13 01:19:38 +02:00
Ricardo Wurmus a620d22ea8
gnu: r-gprofiler: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-gprofiler): Move this variable from here...
* gnu/packages/cran.scm (r-gprofiler): ...to here.
 2020-06-13 01:19:38 +02:00
Christopher Baines db6290af7c
lint: check-patch-file-names: Use origin-actual-file-name. 
This avoids crashes for the patch-file-names checker where a <origin> is used
for a patch, but without a value for the file-name field. This is currently
the case with the bash package.

* guix/lint.scm (check-patch-file-names): Change origin-file-name to
origin-actual-file-name.
 2020-06-12 22:26:47 +01:00
Ludovic Courtès 29e4d3ea06
gnu: guile-sqlite3: Update to 0.1.1. 
* gnu/packages/guile.scm (guile-sqlite3): Update to 0.1.1.
[source]: Remove 'patches', 'modules', and 'snippet'.
* gnu/packages/patches/guile-sqlite3-fix-cross-compilation.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
 2020-06-12 18:56:11 +02:00
Ludovic Courtès 52c529ff20
git-authenticate: Disallow SHA1 (and MD5) signatures. 
* guix/git-authenticate.scm (commit-signing-key): Add
 #:disallowed-hash-algorithms and honor it.
(authenticate-commit)[recent-commit?]: New variable.
Pass #:disallowed-hash-algorithms to 'commit-signing-key'.
* tests/git-authenticate.scm ("signed commits, SHA1 signature"): New test.
 2020-06-12 18:56:11 +02:00
Katherine Cox-Buday 7def5056b6
gnu: Add liblogging. 
* gnu/packages/c.scm (liblogging): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-12 18:56:11 +02:00
Katherine Cox-Buday 0aee6e51b4
gnu: Add libfastjson. 
* gnu/packages/c.scm (libfastjson): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-12 18:56:10 +02:00
Katherine Cox-Buday 70a49ef76b
gnu: Add libestr. 
* gnu/packages/c.scm (libestr): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-12 18:56:10 +02:00
Ryan Desfosses 3bec7a356a
gnu: Add emacs-shell-pop. 
* gnu/packages/emacs-xyz.scm (emacs-shell-pop): New variable

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-12 18:56:10 +02:00
Efraim Flashner 205a0ecd5b
download: Add more apache mirrors. 
* guix/download.scm (%mirrors): Add more apache mirrors.
 2020-06-12 18:28:51 +03:00
Efraim Flashner 9a01efa262
gnu: Fix apache mirror URIs. 
* gnu/packages/web.scm (serf)[source]: Remove redundant part of URI.
* gnu/packages/java.scm (ant-bootstrap, java-commons-httpclient,
java-jakarta-oro)[source]: Same.
* gnu/packages/maven.scm (maven-shared-utils, maven-plugin-annotations,
maven-wagon-provider-api, maven-artifact)[source]: Same.
 2020-06-12 18:23:27 +03:00
Mathieu Othacehe fd1e885236
system: image: Do not produce an HFS tree when building an ISO. 
Use "mbr_only" mode to make sure that no HFS+ tree are generated.

* gnu/system/image.scm (system-image): Set MKRESCUE_SED_MODE to "mbr_only".
 2020-06-12 17:21:18 +02:00
Pierre Neidhardt cd0f1fbd1a
gnu: xf86-input-libinput: Reduce closure size. 
* gnu/packages/xorg.scm (xf86-input-libinput)[inputs]: Replace libinput by
libinput-minimal.
 2020-06-12 09:00:45 +02:00
Chris Marusich 21887021b9
guix: lint: Support origins in check-patch-file-names. 
* guix/lint.scm (check-patch-file-names)[starts-with-package-name?]: New
procedure, extracted from the existing logic.  Using it, add a clause to
the match-lambda to handle origin records.
 2020-06-11 22:30:14 -07:00
Ekaitz Zarraga 9c6ea3cb56
gnu: icecat: Fix WebGL support. 
* gnu/packages/gnuzilla.scm (icecat): Wrap mesa.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2020-06-12 01:29:54 +02:00
Ludovic Courtès 8a02e45d93
shepherd: 'read-pid-file/container' terminates the whole process group. 
This mirrors a change made in the Shepherd 0.8.0.  Previously, upon
startup failure, we could have left processes behind.

* gnu/build/shepherd.scm (read-pid-file/container): Kill (- PID) instead
of PID.
 2020-06-12 00:04:42 +02:00
Ludovic Courtès b6b95685d0
shepherd: Unblock signals in the child process. 
Fixes <https://bugs.gnu.org/41791>.
Reported by Tobias Geerinckx-Rice <me@tobias.gr>.

This change mirrors changes made in the Shepherd 0.8.1, where signals
are blocked in the shepherd process in support of 'signalfd'.  The
regression was introduced with the switch to 0.8.1 in
3f9c62d1a8b345909adaeb22f454ad22554c55a1: child processes would not
receive SIGTERM upon 'herd stop SERVICE'.

* gnu/build/shepherd.scm <top level>: Autoload (shepherd system).
(make-forkexec-constructor/container): Call call to 'sigaction' and
'unblock-signals'.
 2020-06-12 00:04:42 +02:00
Jakub Kądziołka 648ae62112
gnu: Add exercism and dependencies. 
* gnu/packages/education.scm (exercism): New variable.
* gnu/packages/patches/exercism-disable-self-update.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/golang.scm (go-github-com-spf13-afero)
  (go-github-com-spf13-cast)
  (go-github-com-spf13-cobra)
  (go-github-com-spf13-jwalterweatherman)
  (go-github-com-spf13-viper)
  (go-github-com-fsnotify-fsnotify)
  (go-github-com-magiconair-properties)
  (go-github-com-pelletier-go-toml)
  (go-github-com-subosito-gotenv)
  (go-gopkg-in-ini-v1)
  (go-github-com-mitchellh-mapstructure): New variables.
 2020-06-11 22:44:27 +02:00
Mark H Weaver 437e64b7d3
gnu: linux-libre: Update to 5.4.46. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.46.
(linux-libre-5.4-pristine-source): Update hash.
 2020-06-11 16:19:38 -04:00
Mark H Weaver 48f3631b0f
gnu: linux-libre@5.7: Update to 5.7.2. 
* gnu/packages/linux.scm (linux-libre-5.7-version): Update to 5.7.128.
(linux-libre-5.7-pristine-source): Update hash.
 2020-06-11 16:19:36 -04:00
Mark H Weaver 1c02643a06
gnu: linux-libre@5.6: Remove. 
Users of linux-libre-5.6 should migrate to version 5.7.

* gnu/packages/linux.scm (deblob-scripts-5.6, linux-libre-5.6-version)
(linux-libre-5.6-pristine-source, linux-libre-5.6-source)
(linux-libre-headers-5.6, linux-libre-arm-generic-5.6)
(linux-libre-arm64-generic-5.6): Remove variables.
 2020-06-11 16:19:34 -04:00
Mark H Weaver e37aff92e2
gnu: linux-libre@4.19: Update to 4.19.128. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.128.
(linux-libre-4.19-pristine-source): Update hash.
 2020-06-11 16:19:32 -04:00
Mark H Weaver e5630f5d3c
gnu: linux-libre@4.14: Update to 4.14.184. 
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.184.
(linux-libre-4.14-pristine-source): Update hash.
 2020-06-11 16:19:30 -04:00
Mark H Weaver 523d63638a
gnu: linux-libre@4.9: Update to 4.9.227. 
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.227.
(linux-libre-4.9-pristine-source): Update hash.
 2020-06-11 16:19:27 -04:00
Mark H Weaver 59feeb96e4
gnu: linux-libre@4.4: Update to 4.4.227. 
* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.227.
(linux-libre-4.4-pristine-source): Update hash.
 2020-06-11 16:19:25 -04:00
Efraim Flashner e73a016df2
gnu: adns: Update to 1.6.0. 
* gnu/packages/adns.scm (adns): Update to 1.6.0.
[source]: Use https.
[native-inputs]: Add m4.
 2020-06-11 23:13:40 +03:00
Efraim Flashner 4908ba058f
gnu: subversion: Update to 1.14.0. 
* gnu/packages/version-control.scm (subversion): Update to 1.14.0.
[source]: Update source URI.
 2020-06-11 22:41:02 +03:00
Ludovic Courtès ecf92194a5
gnu: nghttp2: Replace with version 1.41 [fixes CVE-2020-11080]. 
* gnu/packages/web.scm (nghttp2-1.41): New variable.
(nghttp2)[replacement]: New field.
 2020-06-11 19:05:05 +02:00