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
3080abba40158502e40d
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
Maxim Cournoyer
ec24673bf9
gnu: emacs-org-journal: Disable failing tests.
...
* gnu/packages/emacs-xyz.scm (emacs-org-journal)
[arguments]: Add disable-failing-tests phase.
Change-Id: I466cb46613a7048ccbda66cd7855001a04871891
2024-01-19 15:05:52 -05:00
Maxim Cournoyer
72f31a9be6
gnu: emacs-ess: Disable flaky "command-without-trailing-newline-test" test.
...
* gnu/packages/statistics.scm [arguments]: Add new disable-etests syntax in
'skip-failing-tests phase, and use it to disable the
'command-without-trailing-newline-test' test.
Change-Id: I99f52685691d86dc633fe6061f9ef3332159eb4e
2024-01-19 15:05:52 -05:00
Arun Isaac
4987618368
gnu: wfmash: Update to 0.12.5.
...
* gnu/packages/bioinformatics.scm (wfmash): Update to 0.12.5.
(source): Use git-fetch. Update git repository URL.
(arguments): In check phase, symlink to "../source/data" and change wfmash
invocation arguments.
(home-page): Update URL.
Change-Id: I78f228f06a6a12e6904a58a12fd4201743e84d72
2024-01-19 18:04:39 +00:00
Greg Hogan
15efd5a7f4
gnu: python-graph-tool: Update to 2.59.
...
* gnu/packages/graph.scm (python-graph-tool): Update to 2.59.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: I08ecb5fe76183fa980fedf2408fc1df93ebbc63d
2024-01-19 17:20:04 +00:00
Christopher Baines
4d91ddf5bc
gnu: guix-build-coordinator: Update to 0-95.dc04b74.
...
* gnu/packages/package-management.scm (guix-build-coordinator): Update to
0-95.dc04b74.
Change-Id: I89d968e72188428d40906a7d55533dfd25c7ec25
2024-01-19 16:45:38 +00:00
Christopher Baines
6fb4cb7ca3
gnu: bffe: Update to 0-3.1c12da4.
...
* gnu/packages/package-management.scm (bffe): Update to 0-3.1c12da4.
Change-Id: I90a4231961aed434c2b4ffa07189b85e108b5c46
2024-01-19 16:45:38 +00:00
Sharlatan Hellseher
65e7828a95
gnu: nsq: Fix build on i686-linux.
...
As seen in https://ci.guix.gnu.org/build/3329277/details
* gnu/packages/high-availability.scm (nsq)[arguments]<#:phases>{check}:
Skip '-race' option during tests on i686-linux.
Change-Id: I952d7187443835d5fbcb74f0ae09b923bd6bdb29
2024-01-19 13:57:54 +00:00
Cayetano Santos
0eadd48648
gnu: Add emacs-vhdl-mode.
...
* gnu/packages/emacs-xyz.scm (emacs-vhdl-mode): New variable.
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Modified-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Change-Id: I7e261fc25ae011c20f22e1078ae40bacff3a6947
2024-01-18 22:42:42 -05:00
Maxim Cournoyer
05be458f02
gnu: Add emacs-pde.
...
* gnu/packages/emacs-xyz.scm (emacs-pde): New variable.
Change-Id: Icab5d8acf9d441bb4a832a82e75432d64cc77ba7
2024-01-18 22:41:02 -05:00
Maxim Cournoyer
33783e3695
gnu: perl-b-keywords: Update to 1.26.
...
* gnu/packages/perl.scm (perl-b-keywords): Update to 1.26.
Change-Id: I3fdb9acf9f257ff9583179e29b2e6a26104b7e0d
2024-01-18 22:10:58 -05:00
Maxim Cournoyer
2d40e6f7ab
build: perl: Accept Gexps for #:module-build-flags.
...
* guix/build-system/perl.scm (perl-build) [module-build-flags]: Accept gexps.
Change-Id: If1daa4d9a8cf97824b75f2113f4d7d83256463ce
2024-01-18 22:10:58 -05:00
Maxim Cournoyer
90b1fe57d0
gnu: emacs: Patch awk, find, sed and sh commands.
...
Before this change, using Emacs in a pure environment, e.g. 'guix shell --pure
emacs', would cause problems such as:
jka-compr-insert-file-contents: Uncompression program ‘sh’ not found
And other problems were found requiring the other tools.
* gnu/packages/emacs.scm (emacs-minimal) [arguments]: Extend the
patch-program-file-names phase.
[inputs]: Add findutils, gawk and sed.
Series-changes: 2
- Patch references in place instead of wrapping via PATH
Change-Id: Ifb4fe2fc12ddc9eae387adb3da3f7821fab78e65
2024-01-18 22:10:58 -05:00
