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130256 Commits (1348be9115d15f8066d3d194d2c8d38ffa61fbae)

Author SHA1 Message Date
Ricardo Wurmus 2d83a25450
import/cran: Generate rudimentary ARGUMENTS field. 
* guix/import/cran.scm (phases-for-inputs, maybe-arguments): New procedures.
(description->package): Splice in result of MAYBE-ARGUMENTS.

Change-Id: I578e1903f37c91bf865f0be49b04187ec372ed05
 2024-01-21 11:08:13 +01:00
Ricardo Wurmus 1d00a9edff
gnu: Add r-protgear. 
* gnu/packages/bioconductor.scm (r-protgear): New variable.

Change-Id: Ic6d5cae65d4f76df4488ee2462071ba68b50c184
 2024-01-21 11:08:13 +01:00
Liliana Marie Prikler 0afe456973
Revert "gnu: emacs-minimal: Update to 29.2." 
This reverts commit b9bc400d85.

Fixes: Too many rebuilds <http://logs.guix.gnu.org/guix/2024-01-21.log#095235>
Reported-by: Efraim Flashner <efraim@flashner.co.il>
 2024-01-21 10:09:55 +01:00
Liliana Marie Prikler ed3aa00249
gnu: gnome-shell-extension-paperwm: Use new package style. 
* gnu/packages/gnome-xyz.scm (gnome-shell-extension-paperwm)[arguments]:
Convert to list of G-Expressions.
[native-inputs]: Drop labels.

Co-authored-by: Justin Veilleux <terramorpha@cock.li>
Co-authored-by: Vivien Kraus <vivien@planete-kraus.eu>
 2024-01-21 09:48:21 +01:00
terramorpha 5fa60c3e81
gnu: gnome-shell-extension-paperwm: Update to 44.17.0. 
* gnu/packages/gnome-xyz.scm (gnome-shell-extension-paperwm): Update to 44.17.0.

Change-Id: I3d9923ccfdb35b9952c24d8dd3d064c3cba7b8c2
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2024-01-21 09:32:29 +01:00
Vagrant Cascadian ccbbe3bd57
gnu: vcmi: Update to 1.4.2. 
* gnu/packages/games.scm (vcmi): Update to 1.4.2.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2024-01-21 09:32:29 +01:00
Liliana Marie Prikler b9bc400d85
gnu: emacs-minimal: Update to 29.2. 
* gnu/packages/emacs.scm (emacs-minimal): Update to 29.2.
 2024-01-21 09:32:29 +01:00
Liliana Marie Prikler c7f937cfdd
gnu: emacs-minimal: Set upstream-name to “emacs”. 
* gnu/packages/emacs.scm (emacs-minimal)[properties]: Add ‘upstream-name’.
 2024-01-21 09:32:28 +01:00
Ricardo Wurmus 0facea431a
gnu: Add r-netgsa. 
* gnu/packages/bioconductor.scm (r-netgsa): New variable.

Change-Id: I79b842854db80bbacdb8ff4c9fccfabdfc04d779
 2024-01-21 08:33:56 +01:00
Ricardo Wurmus 815e378dee
gnu: Add r-glassofast. 
* gnu/packages/cran.scm (r-glassofast): New variable.

Change-Id: I6ec7a1f8d4391d7d93f23789f448476b866e4687
 2024-01-21 08:33:51 +01:00
Ricardo Wurmus 6648e34342
gnu: Add r-rcy3. 
* gnu/packages/bioconductor.scm (r-rcy3): New variable.

Change-Id: Ia295e8a174f65c8378ae83bdc1dde2877a48ff45
 2024-01-21 08:30:40 +01:00
Clément Lassieur 0ef8afe1e1
gnu: torbrowser: Add support for language localisation. 
* gnu/packages/gnuzilla.scm (all-mozilla-locales): Export it.
* gnu/packages/tor.scm (%torbrowser-locales, translation-base-browser,
translation-tor-browser): New variables.
(torbrowser)[arguments]: In ‘setenv’ phase, set MOZ_CHROME_MULTILOCALE.  Add
‘copy-firefox-locales’, ‘copy-basebrowser-locales’, ‘copy-torbrowser-locales’
and ‘build-locales’ phases.

Change-Id: Ia5b28fa5d885f24140893dc270e57e83b0250c67
 2024-01-21 01:17:51 +01:00
Ricardo Wurmus 8ca35ca44f
gnu: r-cytolib: Update to 2.14.1. 
* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.14.1.
[source]: Do not unbundle included boost.
[arguments]: Remove.
[inputs]: Remove boost.

Change-Id: Ibe26b9df3f73e67fb9f53676a2c27a5aed714895
 2024-01-21 00:17:45 +01:00
Troy Figiel e1d3be4113
gnu: python-pandera: Fix build. 
* gnu/packages/python-science.scm (python-pandera): Fix build.
[source]: Delete tests/modin directory.
[native-inputs]: Remove python-modin.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-20 22:03:03 +00:00
Troy Figiel 7c540ed106
gnu: python-pandas-stubs: Update to 1.5.3.230321. 
* gnu/packages/python-science.scm (python-pandas-stubs): Update to
1.5.3.230321.
[arguments]<#:test-flags>: Ignore tests that require a version of
python-pyarrow with ORC integration.
[native-inputs]: Add python-odfpy.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-20 22:02:49 +00:00
Kaelyn Takata c79ffe25e9
gnu: xorg-server-xwayland: Update to 23.2.4 [security fixes]. 
Fixes CVE-2023-6816, CVE-2024-0229, CVE-2024-21885, CVE-2024-21886,
CVE-2024-0409, and CVE-2024-0408.  See the X.Org security advisory
<https://lists.x.org/archives/xorg/2024-January/061525.html> for more
information.

* gnu/packages/xorg.scm (xorg-server-xwayland): Update to 23.2.4.

Change-Id: Ie6343d34652ba0caf00940775b5b227dd9bc05bc
Signed-off-by: John Kehayias <john.kehayias@protonmail.com>
 2024-01-20 16:52:09 -05:00
Kaelyn Takata ed6ff0ec7b
gnu: xorg-server: Update to 21.1.11 [security fixes]. 
Fixes CVE-2023-6816, CVE-2024-0229, CVE-2024-21885, CVE-2024-21886,
CVE-2024-0409, and CVE-2024-0408.  See the X.Org security advisory
<https://lists.x.org/archives/xorg/2024-January/061525.html> for more
information.

Copyright line updated as followup to commits
3080abba40 and
158502e40d.

* gnu/packages/xorg.scm (xorg-server): Update to 21.1.11.

Change-Id: I07cb273e2a504f94f8f26624d26ad79c6e92f109
Signed-off-by: John Kehayias <john.kehayias@protonmail.com>
 2024-01-20 16:52:08 -05:00
Jack Hill 856b4a603a
gnu: gnutls: Update to 3.8.3 [security-fixes]. 
Fixes CVE-2024-0553 and CVE-2024-0567.

gnu/packages/tls.scm (gnutls-3.8.2): Rename to ...
(gnutls/fixed): ... this.  Update to 3.8.3.
(gnutls): Rename replacement to gnutls/fixed.

Change-Id: Ic44b3b0481ffd51cdc42a2d71a598f001b43c6f7
Signed-off-by: John Kehayias <john.kehayias@protonmail.com>
Co-authored-by: John Kehayias <john.kehayias@protonmail.com>
 2024-01-20 16:52:05 -05:00
Wamm K. D 782d69fb7f
gnu: Add python-manimpango. 
* gnu/packages/python-xyz.scm (python-manimpango): New variable.

Co-authored-by: Troy Figiel <troy@troyfigiel.com>
Change-Id: I80effb2412e7c35ddf69c0d3ff6e2f052f282840
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-20 21:35:29 +00:00
Ricardo Wurmus 9072f27f5d
gnu: r-org-hs-eg-db: Update to 3.18.0. 
* gnu/packages/bioconductor.scm (r-org-hs-eg-db): Update to 3.18.0.

Change-Id: Iaba83a413858a95e81b6488a2f8cde648f0bdeed
 2024-01-20 19:52:40 +01:00
Ricardo Wurmus d441454ba8
gnu: Add r-methylclockdata. 
* gnu/packages/bioconductor.scm (r-methylclockdata): New variable.

Change-Id: Id76373a9aec8276dcfd1ec3428d2ce9c81cc51d2
 2024-01-20 19:52:24 +01:00
Ricardo Wurmus 2b3a21c55f
gnu: Add r-experimenthubdata. 
* gnu/packages/bioconductor.scm (r-experimenthubdata): New variable.

Change-Id: I5faf26f483898b162bc1f863a4aceb6f46c52c18
 2024-01-20 19:52:05 +01:00
Ricardo Wurmus c4838027b4
gnu: Add r-jaspar2016. 
* gnu/packages/bioconductor.scm (r-jaspar2016): New variable.

Change-Id: Ib2970791207b426c39bd0226e01107a35fec0bb2
 2024-01-20 19:50:13 +01:00
Ricardo Wurmus 6f93502ced
gnu: Add r-genomicstate. 
* gnu/packages/bioconductor.scm (r-genomicstate): New variable.

Change-Id: I1b86c8e849af7b69b5fa9ea2a0e43b4e3e1850b2
 2024-01-20 19:45:26 +01:00
Ricardo Wurmus 4e706e6b18
gnu: Add r-shinymeta. 
* gnu/packages/cran.scm (r-shinymeta): New variable.

Change-Id: I35e1c032283cdc010e4551c0d33f9d4202d9deee
 2024-01-20 19:45:26 +01:00
Ricardo Wurmus c410d4e268
gnu: Add r-ensdb-hsapiens-v79. 
* gnu/packages/bioconductor.scm (r-ensdb-hsapiens-v79): New variable.

Change-Id: I773615df66194ddb195f013f7000d175ac07d095
 2024-01-20 19:45:26 +01:00
Maxim Cournoyer 9c367ee196
gnu: Add rust-rustc-demangle-capi-0.1. 
* gnu/packages/crates-io.scm (rust-rustc-demangle-capi-0.1): New variable.

Change-Id: I98afb19ed4bdbcb9107a1ab30af49b055802b8b0

Reviewed-by: Efraim Flashner <efraim@flashner.co.il>
Change-Id: Ifeaefa5a377600320c3fd2a637aefaf29707e3b7
 2024-01-19 22:57:27 -05:00
Maxim Cournoyer b509dedf83
gnu: guile-hall: Update to 0.4.1-1.7558ba9. 
* gnu/packages/guile-xyz.scm (guile-hall): Update to 0.4.1-1.7558ba9.
[arguments] <modules>: Remove (ice-9 match) and (ice-9 ftw) modules.
Add (guix build guile-build-system).
<phases>: Use gexps.  Streamline hall-wrap-binaries phase.
[native-inputs]: Add guile-3.0 and gettext-minimal.
[propagated-inputs]: Delete field, moving guile-config to...
[inputs]: ... here.  Add bash-minimal and guile-lib.

Change-Id: Idef796dc3ba9ca3fa4df8114efe91af7c5cf7be0
 2024-01-19 22:57:15 -05:00
Maxim Cournoyer c66a1a0f0f
gnu: reuse: Update to 3.0.1. 
* gnu/packages/license.scm (reuse): Update to 3.0.1.
[arguments]: New field.

Change-Id: Ibbc5ae8cfa0e0e62b6c64bd90387022e88f9c933
 2024-01-19 22:50:24 -05:00
Vinicius Monego dae418afd7
gnu: symengine: Update to 0.11.2. 
* gnu/packages/algebra.scm (symengine): Update to 0.11.2.

Change-Id: I34c24dd8591e306a7740f0a3d51077aceec67fab
 2024-01-19 22:01:31 -03:00
Vinicius Monego a185dd97e4
gnu: python-metpy: Update to 1.6.1. 
* gnu/packages/geo.scm (python-metpy): Update to 1.6.1.

Change-Id: Id8d8d6db3e31307242e56c494b6dee7c2ffab8f1
 2024-01-19 22:01:31 -03:00
Vinicius Monego a6b249bd67
gnu: python-deepxde: Update to 1.10.1. 
* gnu/packages/machine-learning.scm (python-deepxde): Update to 1.10.1.

Change-Id: If3515735d4adee8a2f1e9460d6ccb72c6ce26321
 2024-01-19 22:01:31 -03:00
Vinicius Monego 826b4331d3
gnu: python-mapie: Update to 0.8.2. 
* gnu/packages/statistics.scm (python-mapie): Update to 0.8.2.

Change-Id: I82098caa8ed5d3bf68eec9f374f600d203d6b178
 2024-01-19 22:01:31 -03:00
Vinicius Monego b482a6c768
gnu: libngspice: Update to 42. 
* gnu/packages/engineering.scm (libngspice, ngspice): Update to 42.

Change-Id: Ib7b72724f8f46ce376bd6517cb2652c870edcb0d
 2024-01-19 22:01:31 -03:00
Vinicius Monego 9c67673d7b
gnu: darktable: Update to 4.6.0. 
* gnu/packages/photo.scm (darktable): Update to 4.6.0.

Change-Id: Ic64b02e8d191ba91fde1b95b9bcb4321a471dcba
 2024-01-19 22:01:31 -03:00
Vinicius Monego 946cd84d57
gnu: darktable: Enable more optional features. 
* gnu/packages/photo.scm (darktable)[inputs]: Add libjxl, portmidi.

Change-Id: I7747dfc2e88379a13182590f87514951bdd70e0c
 2024-01-19 22:01:30 -03:00
Vinicius Monego e7d14578ad
gnu: darktable: Build with GCC. 
* gnu/packages/photo.scm (darktable)[arguments][#:phases]: Delete the
'prepare-build-environment phase.
[native-inputs]: Remove clang. Add gcc-13.

Change-Id: Ia0dc1c6a717ccd00cd31d378aa51ce63fbf1806a
 2024-01-19 22:01:30 -03:00
Vinicius Monego 5073187524
gnu: gmic: Update to 3.3.3. 
gmic was integrated into Krita 5+.

* gnu/packages/image-processing.scm (gmic, gmic-qt): Update to 3.3.3.
(gmic-qt-krita): Delete variable.

Change-Id: I44e33b570bcf3e1df3eba5eb9ede1f333f8a177a
 2024-01-19 22:01:30 -03:00
Vinicius Monego 53096bb5a0
gnu: labplot: Update to 2.10.1. 
* gnu/packages/kde.scm (labplot): Update to 2.10.1.
[source]<origin>: Update URI.

Change-Id: I03d24410304fb14daa20f7a75f6947caed63ab84
 2024-01-19 22:01:22 -03:00
Vinicius Monego 9f918e9c48
gnu: python-symengine: Update to 0.11.0. 
* gnu/packages/python-xyz.scm (python-symengine): Update to 0.11.0.
[native-inputs]: Replace python-cython with python-cython-3.

Change-Id: Ieab464491e3df6e2bdb5b552cbf48ebf67ff81e4
 2024-01-19 21:56:37 -03:00
Ricardo Wurmus eb1d80ac77
gnu: Add r-trnadbimport. 
* gnu/packages/bioconductor.scm (r-trnadbimport): New variable.

Change-Id: I5a232b50c08ef999f691566ccf5c0fbaf0eb21ea
 2024-01-19 23:55:43 +01:00
Ricardo Wurmus 74ce9d7e3b
gnu: Add r-trna. 
* gnu/packages/bioconductor.scm (r-trna): New variable.

Change-Id: Ifce902910fa75ddc471d8a25cc974307c19fd1d0
 2024-01-19 23:55:43 +01:00
Ricardo Wurmus 1d56a24509
gnu: Add r-modstrings. 
* gnu/packages/bioconductor.scm (r-modstrings): New variable.

Change-Id: Ia61816213a7d128ab50a9ae2b2c8879e6ac00499
 2024-01-19 23:55:43 +01:00
Ricardo Wurmus 5c10649a50
gnu: Add r-structstrings. 
* gnu/packages/bioconductor.scm (r-structstrings): New variable.

Change-Id: I9759520a03ee8178432591c48bf56fb25a379f27
 2024-01-19 23:55:43 +01:00
Ricardo Wurmus d084e9d036
gnu: Add python-mediapy. 
* gnu/packages/python-xyz.scm (python-mediapy): New variable.

Change-Id: I2e55c018670053c662ae2d896feefab3b505b139
 2024-01-19 23:55:43 +01:00
Ricardo Wurmus d8c718d44c
gnu: Add r-flames. 
* gnu/packages/bioconductor.scm (r-flames): New variable.

Change-Id: I551a8f9d7de16e2281898b9541572dd244aadc36
 2024-01-19 23:55:43 +01:00
Artyom V. Poptsov f7c0ccb186
gnu: kubo: Update to 0.16.0. 
* gnu/packages/ipfs.scm (kubo): Update to 0.16.0.
  [arguments]: Use go-1.18.
  [home-page]: Set to "https://ipfs.tech".

Change-Id: I06239354b0c9c23294d5aeac6d01f67636d5d3a5
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-19 21:51:35 +00:00
Maxim Cournoyer c0f423bf1a
gnu: emacs-evil-quickscope: Skip failing test. 
* gnu/packages/emacs-xyz.scm (emacs-evil-quickscope)
[arguments]: Use gexps.  Add disable-failing-tests phase.

Change-Id: If372531778eab6e3fc164a2f63b98d6775193114
 2024-01-19 15:05:53 -05:00
Maxim Cournoyer d6170e03e3
gnu: emacs-shx: Fix test failure. 
* gnu/packages/patches/emacs-shx-byte-compilation-test.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/emacs-xyz.scm (emacs-shx): Apply it.

Change-Id: I6d8edd3b50f99f1c4cd495216caf9648dfee4ea3
 2024-01-19 15:05:53 -05:00
Maxim Cournoyer 33f12b7dcd
gnu/local.mk: Sort Emacs patches and fix 2044 year in copyright notice. 
* gnu/local.mk: Correct 2044 copyright year.
(dist_patch_DATA): Sort emacs patches.

Change-Id: Ib9669bb1d7fb2556d6d809d62624981fa66d27f3
 2024-01-19 15:05:53 -05:00