TakeV/guix
1
0
Fork 0
Code Issues Pull requests Packages Projects Releases Wiki Activity
125338 commits 102 branches 35 tags 561 MiB
Commit graph

125338 commits

This branch
This branch
All branches
Author SHA1 Message Date
Ricardo Wurmus 1fc6c1d2ab
gnu: r-gensa: Update to 1.1.10.1. 
* gnu/packages/cran.scm (r-gensa): Update to 1.1.10.1.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus 5cac6f401c
gnu: r-d3r: Update to 1.1.0. 
* gnu/packages/cran.scm (r-d3r): Update to 1.1.0.
[propagated-inputs]: Remove r-rlang.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus cb8c68da4b
gnu: r-jqr: Update to 1.3.0. 
* gnu/packages/cran.scm (r-jqr): Update to 1.3.0.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus 92fce36949
gnu: r-curl: Update to 5.1.0. 
* gnu/packages/cran.scm (r-curl): Update to 5.1.0.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus 4d9908cd61
gnu: r-jade: Update to 2.0-4. 
* gnu/packages/cran.scm (r-jade): Update to 2.0-4.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus 6d2df3bd9e
gnu: r-gunifrac: Update to 1.8. 
* gnu/packages/cran.scm (r-gunifrac): Update to 1.8.
[propagated-inputs]: Add r-inline.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus fa97d8c2d0
gnu: r-ggstatsplot: Update to 0.12.1. 
* gnu/packages/cran.scm (r-ggstatsplot): Update to 0.12.1.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus b253dbe7a0
gnu: r-datawizard: Update to 0.9.0. 
* gnu/packages/cran.scm (r-datawizard): Update to 0.9.0.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus c64777cfe0
gnu: r-activepathways: Update to 2.0.2. 
* gnu/packages/bioconductor.scm (r-activepathways): Update to 2.0.2.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus f1259b80be
gnu: r-valr: Update to 0.7.0. 
* gnu/packages/bioconductor.scm (r-valr): Update to 0.7.0.
[propagated-inputs]: Add r-lifecycle.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus 8c22cc96f0
gnu: r-biomartr: Update to 1.0.5. 
* gnu/packages/bioconductor.scm (r-biomartr): Update to 1.0.5.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus 3fba8cd274
refresh: Fix sorting of updates by file and line number. 
* guix/scripts/refresh.scm (guix-refresh): Add cascade-sort procedure and use
it to sort specs by package location.
 2023-10-05 15:16:26 +02:00
Ekaitz Zarraga 044a76c280
doc: contributing: Add alternative setups section. 
Start with Guile Studio and Vim/NeoVim.

* doc/contributing.texi (Alternative Setups): Add section explaining
other setups that are similar to the one in The Perfect Setup.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-10-05 15:05:41 +03:00
Andrew Tropin eeb7132ec3
gnu: emacs-telega: Update to 0.8.03-1.17bfa50. 
* gnu/packages/emacs-xyz.scm (emacs-telega-server): Update to
0.8.03-1.17bfa50.
 2023-10-05 14:16:39 +04:00
Andrew Tropin 9e963c9d75
gnu: tdlib: Update to 1.8.16-0.4d1d22d. 
* gnu/packages/messaging.scm (tdlib): Update to 1.8.16-0.4d1d22d.
 2023-10-05 14:16:38 +04:00
Ricardo Wurmus 276b9287c1
gnu: r-aplot: Update to 0.2.1. 
* gnu/packages/cran.scm (r-aplot): Update to 0.2.1.
 2023-10-05 10:31:09 +02:00
Ricardo Wurmus d841c23dc5
gnu: r-tximeta: Update to 1.18.3. 
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.18.3.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus b53f7a87b2
gnu: r-biodb: Update to 1.8.1. 
* gnu/packages/bioconductor.scm (r-biodb): Update to 1.8.1.
[propagated-inputs]: Add r-git2r.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus bf7c049147
gnu: r-gviz: Update to 1.44.2. 
* gnu/packages/bioconductor.scm (r-gviz): Update to 1.44.2.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus 9220702479
gnu: r-s4vectors: Update to 0.38.2. 
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.38.2.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus 6492c6496b
gnu: r-biocstyle: Update to 2.28.1. 
* gnu/packages/bioconductor.scm (r-biocstyle): Update to 2.28.1.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus 27fd2d2c2a
gnu: r-yapsa: Update to 1.26.8. 
* gnu/packages/bioconductor.scm (r-yapsa): Update to 1.26.8.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus 6a1b46e7ab
gnu: r-enrichplot: Update to 1.20.3. 
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.20.3.
[propagated-inputs]: Add r-ggfun.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus 3f3c986001
gnu: r-spectra: Update to 1.10.3. 
* gnu/packages/bioconductor.scm (r-spectra): Update to 1.10.3.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus b82dc9b724
gnu: r-keggrest: Update to 1.40.1. 
* gnu/packages/bioconductor.scm (r-keggrest): Update to 1.40.1.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus b56dabc7a3
gnu: r-genomeinfodb: Update to 1.36.4. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.36.4.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus 28b2b7c367
gnu: r-ensembldb: Update to 2.24.1. 
* gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.24.1.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus fefad76048
gnu: r-ancombc: Update to 2.2.2. 
* gnu/packages/bioconductor.scm (r-ancombc): Update to 2.2.2.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus caf9f847ef
gnu: r-omnipathr: Update to 3.8.2. 
* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.8.2.
 2023-10-05 10:23:27 +02:00
Liliana Marie Prikler 759b55712e
gnu: curl: Update to 8.3.0. 
According to upstream, the current version has 19 security issues.
See also <https://curl.se/docs/vuln-7.85.0.html>.

* gnu/packages/curl.scm (curl/fixed): New variable.
(curl): Use it as replacement.
 2023-10-05 09:41:31 +02:00
Efraim Flashner a31725ff90
gnu: openjdk-10: Fix building on aarch64-linux. 
* gnu/packages/java.scm (openjdk-10)[arguments]: Replace inherited
'patch-for-aarch64 phase for changes in source code layout.

Co-authored-by: Christopher Baines <mail@cbaines.net>
Co-authored-by: Tim Johann <t1m@phrogstar.de>
 2023-10-05 09:54:04 +03:00
Efraim Flashner 6f8f98f334
gnu: universal-ctags: Update to 6.0.20231001.0. 
* gnu/packages/code.scm (universal-ctags): Update to 6.0.20231001.0.
 2023-10-05 09:54:04 +03:00
Kjartan Oli Agustsson c3f47bb2ee
gnu: tree-sitter-java: Update to 0.20.1. 
* gnu/packages/tree-sitter.scm (tree-sitter-java): Update to 0.20.1.

Signed-off-by: Andrew Tropin <andrew@trop.in>
 2023-10-05 09:54:23 +04:00
Maxim Cournoyer ecb1b335d4
gnu: emacs-elpy: Update to 1.35.0-2.7ff8ffa. 
* gnu/packages/emacs-xyz.scm (emacs-elpy): Update to 1.35.0-2.7ff8ffa.
[origin]: Apply patch.
[arguments]: Disable a new test in the disable-broken-tests phase.
* gnu/packages/patches/emacs-elpy-dup-test-name.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2023-10-05 01:34:21 -04:00
Maxim Cournoyer 22d2f94eb2
gnu: phoronix-test-suite: Do not propagate gcc-toolchain. 
* gnu/packages/benchmark.scm (gcc-toolchain*): Replace gcc-toolchain-12
reference with gcc-toolchain.
* gnu/packages/benchmark.scm (phoronix-test-suite): Augment wrap-binary phase
with GCC variables.
[propagated-inputs]: Delete field, moving gcc-toolchain to...
[inputs]: ... here.
[search-paths]: New field.
 2023-10-04 23:30:42 -04:00
Maxim Cournoyer 2d8aa104aa
search-paths: Add GCC search paths. 
* guix/search-paths.scm ($C_INCLUDE_PATH, $CPLUS_INCLUDE_PATH)
($LIBRARY_PATH, %gcc-search-paths): New variables.
 2023-10-04 23:30:41 -04:00
John Kehayias 20df2ee697
gnu: libxpm: Graft with 3.5.17 [security fixes]. 
Fixes CVE-2023-43788 and CVE-2023-43789.  See the X.Org security advisory
<https://lists.x.org/archives/xorg/2023-October/061506.html> for more
information.

* gnu/packages/xorg.scm (libxpm)[replacement]: New field, set to ...
(libxpm/fixed): ... this new variable.
 2023-10-04 18:46:22 -04:00
John Kehayias b317eb8a9e
gnu: libx11: Update replacement to 1.8.7 [security fixes]. 
Fixes CVE-2023-43785, CVE-2023-43786, and CVE-2023-43787.  See the X.Org
security advisory <https://lists.x.org/archives/xorg/2023-October/061506.html>
for more information.

* gnu/packages/xorg.scm (libx11-fixed): Update to 1.8.7.
 2023-10-04 17:57:13 -04:00
Maxim Cournoyer de8fc548c6
gnu: emacs-debbugs: Preserve subject when replying to patch threads. 
* gnu/packages/patches/emacs-debbugs-keep-patch-subject.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/emacs-xyz.scm (emacs-debbugs) [origin]: Use it.
 2023-10-04 16:32:45 -04:00
David Elsing e718647930
gnu: Remove suitesparse-3. 
* gnu/packages/maths.scm (suitesparse-3): Delete variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-10-04 17:59:03 +03:00
David Elsing 151687a7a2
gnu: scilab: Update to 2023.1.0. 
* gnu/packages/maths.scm (scilab): Update to 2023.1.0.
[source] Use git-fetch.
<modules>: Add (guix build utils) and (ice-9 ftw).
<patches>: Add patch for hdf5 >= 1.10.
<snippet>: Move contents of the "scilab" directory to its parents. Remove
the other files and autogenerated files.
[native-inputs]: Add autoconf, autoconf-archive, automake, bison, eigen, flex,
libtool, ocaml and ocaml-findlib.
[inputs]: Add ocaml-num, replace hdf5-1.8 by hdf5-1.14 and suitesparse-3 by
suitesparse.
[arguments]: Remove quasiquote. Add --enable-build-parser,
--with-eigen-include=..., OCAMLC=... and OCAMLOPT=... to #:configure-flags.
<#:phases>: Add fix-ocaml-num, remove-desktop-files,
bootstrap-dynamic_link-scripts and build-parsers phases. Remove fixes for
compilation and linker errors from the pre-build phase.
[home-page]: Update URL.
[description]: Add two spaces between sentences.
[license]: Update to gpl2 and bsd-3.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-10-04 17:58:22 +03:00
Andy Tai 37d0befca0
gnu: parallel: Update to 20230922. 
* gnu/packages/parallel.scm (parallel): Update to 20230922.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-10-04 17:25:46 +03:00
Timotej Lazar 264baefa88
gnu: freerdp: Update to 2.11.2. 
* gnu/packages/rdesktop.scm (freerdp): Update to 2.11.2.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2023-10-04 15:09:26 +02:00
Ekaitz Zarraga c1af4060e9
gnu: guile-mastodon: Update to 0.0.1-0a94ae6b 
Message-ID: <0064c4ff9262c4906131909ae1276667033f8811.1696343806.git.ekaitz@elenq.tech>
From: Ekaitz Zarraga <ekaitz@elenq.tech>
Date: Tue, 3 Oct 2023 16:28:58 +0200
Subject: [PATCH] gnu: guile-mastodon: Update to 0.0.1-0a94ae6b

* gnu/packages/guile-xyz.scm (guile-mastodon): Update to 0.0.1-0a94ae6b

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2023-10-04 15:05:24 +02:00
Peter Polidoro 06e53c577e
gnu: kicad: Update to 7.0.8. 
* gnu/packages/engineering.scm (kicad): Update to 7.0.8.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2023-10-04 15:03:00 +02:00
Jean-Pierre De Jesus DIAZ 3ba8f3f0d8
guix: meson-configuration: Fix boolean assigment. 
* guix/build/meson-configuration.scm (write-assigment): Print true for
  #t and false for #f.  Previously it was inverting the values.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2023-10-04 14:58:42 +02:00
Jonathan Brielmaier 4a99dd7322
gnu: ultrastar-deluxe: Update to 2023.9.0. 
* gnu/packages/games.scm (ultrastar-deluxe): Update to 2023.9.0.
[source]: Use tagged version again.

Tested-by: Jonathan Brielmaier <jonathan.brielmaier@web.de>
 2023-10-04 13:45:55 +02:00
Mădălin Ionel Patrașcu 5f2704517c
gnu: r-dofuture: Add r-markdown. 
* gnu/packages/cran.scm (r-dofuture)[native-inputs]: Add r-markdown.
 2023-10-04 11:21:52 +02:00
Mădălin Ionel Patrașcu 273ee56bc2
gnu: Add r-arrayquality. 
* gnu/packages/bioconductor.scm (r-arrayquality): New variable.
 2023-10-04 11:03:23 +02:00
Mădălin Ionel Patrașcu 4edacf416b
gnu: Add r-arraymvout. 
* gnu/packages/bioconductor.scm (r-arraymvout): New variable.
 2023-10-04 11:03:23 +02:00