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Author SHA1 Message Date
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
Mădălin Ionel Patrașcu
4221c3d4da
gnu: Add r-parody. 
* gnu/packages/bioconductor.scm (r-parody): New variable.
 2023-10-04 11:03:23 +02:00
Mădălin Ionel Patrașcu
b84f6c2c0e
gnu: Add r-mdqc. 
* gnu/packages/bioconductor.scm (r-mdqc): New variable.
 2023-10-04 11:03:23 +02:00
Mădălin Ionel Patrașcu
9f08080b38
gnu: Add r-apcomplex. 
* gnu/packages/bioconductor.scm (r-apcomplex): New variable.
 2023-10-04 11:03:23 +02:00
Mădălin Ionel Patrașcu
e65ba1ccee
gnu: Add r-org-sc-sgd-db. 
* gnu/packages/bioconductor.scm (r-org-sc-sgd-db): New variable.
 2023-10-04 11:03:23 +02:00
Mădălin Ionel Patrașcu
1025316d80
gnu: Add r-hybridmtest. 
* gnu/packages/bioconductor.scm (r-hybridmtest): New variable.
 2023-10-04 11:03:23 +02:00
Mădălin Ionel Patrașcu
f989150083
gnu: Add r-repmis. 
* gnu/packages/cran.scm (r-repmis): New variable.
 2023-10-04 11:03:23 +02:00
Mădălin Ionel Patrașcu
58a3333f58
gnu: Add r-anota2seq. 
* gnu/packages/bioconductor.scm (r-anota2seq): New variable.
 2023-10-04 11:03:23 +02:00
Nicolas Goaziou
d0aaa5aacf
gnu: emacs-yeetube: Update to 2.0.5. 
* gnu/packages/emacs-xyz.scm (emacs-yeetube): Update to 2.0.5.
[arguments]<#:phases>: Update variable names holding executable locations.
 2023-10-04 10:58:33 +02:00
Nicolas Goaziou
d3021c4538
gnu: emacs-yaml-mode: Update to 0.0.16. 
* gnu/packages/emacs-xyz.scm (emacs-yaml-mode): Update to 0.0.16.
 2023-10-04 10:58:33 +02:00
Nicolas Goaziou
b346b93d41
gnu: emacs-org-dynamic-agenda: Update to 0.3.1. 
* gnu/packages/emacs-xyz.scm (emacs-org-dynamic-agenda): Update to 0.3.1.
 2023-10-04 10:58:33 +02:00
Nicolas Goaziou
e576f2ac3b
gnu: emacs-irony-mode: Update to 1.6.0. 
* gnu/packages/emacs-xyz.scm (emacs-irony-mode): Update to 1.6.0.
 2023-10-04 10:58:32 +02:00
Nicolas Goaziou
43741bca58
gnu: emacs-eldoc-box: Update to 1.11.1. 
* gnu/packages/emacs-xyz.scm (emacs-eldoc-box): Update to 1.11.1.
 2023-10-04 10:58:32 +02:00
Nicolas Goaziou
27e27cb3b6
gnu: emacs-corfu-terminal: Update to 0.7. 
* gnu/packages/emacs-xyz.scm (emacs-corfu-terminal): Update to 0.7.
 2023-10-04 10:58:32 +02:00
Nicolas Goaziou
71b5fdea89
gnu: emacs-clj-refactor: Update to 3.9.4. 
* gnu/packages/emacs-xyz.scm (emacs-clj-refactor): Update to 3.9.4.
 2023-10-04 10:58:32 +02:00
Charles
24fc0370d0
gnu: Add cl-ini. 
* gnu/packages/lisp-xyz.scm (sbcl-cl-ini, ecl-cl-ini, cl-ini): New variables.
 2023-10-03 20:54:40 -05:00
fanquake
0c6198319a
gnu: Add python-altgraph. 
* gnu/packages/python-xyz.scm (python-altgraph): New variable.

Co-authored-by: jgart <jgart@dismail.de>
 2023-10-03 20:46:05 -05:00
Nicolas Goaziou
8e6022732a
gnu: emacs-yeetube: Improve package style. 
* gnu/packages/emacs-xyz.scm (emacs-yeetube): Fix indentation.
[synopsis, description]: Use Texinfo markup.  Add proper capitalization.
 2023-10-03 22:09:33 +02:00
Nicolas Goaziou
761cc5ae23
gnu: emacs-yeetube: Use executables from inputs. 
* gnu/packages/emacs-xyz.scm (emacs-yeetube)[arguments]: Set locations for
"mpv" and "yt-dlp" executables from the store instead of relying on `executable-find'.
 2023-10-03 22:09:33 +02:00