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Author SHA1 Message Date
Greg Hogan
61e413eb7e
gnu: python-louvain-igraph: Update to 0.8.2. 
* gnu/packages/graph.scm (python-louvain-igraph): Update to 0.8.2.

Change-Id: Ifa755464fb88e0af6829d6f2569b900a80949e76
 2025-05-13 16:35:42 +00:00
Greg Hogan
782d431cca
gnu: python-vtraag-louvain: Deprecate. 
* gnu/packages/graph.scm (python-vtraag-louvain): Deprecate with
replacement python-louvain-igraph.

Change-Id: I4e8b938a0a7ffb1932209bfff97a84b075aabb0e
 2025-05-13 16:35:42 +00:00
Greg Hogan
73eb9b8d24
gnu: python-igraph: Update to 0.11.8. 
* gnu/packages/graph.scm (python-igraph): Update to 0.11.8.

Change-Id: I6493392a700ea64bb0bf3c300a39a323e9eebf36
 2025-05-13 16:35:41 +00:00
Greg Hogan
365d1ed908
gnu: igraph: Update to 0.10.15. 
* gnu/packages/graph.scm (igraph): Update to 0.10.15.
[source]: Remove patches.
* gnu/packages/patches/igraph-fix-varargs-integer-size.patch: Delete.
* gnu/local.mk (dist_patch_DATA): Update accordingly.

Change-Id: Iffbfdc83b347f9abf82891f5b97954903d3df3dd
 2025-05-13 16:35:40 +00:00
Greg Hogan
c6aaffba1c
gnu: Add %suitesparse-package-versions. 
* gnu/packages/maths.scm (%suitesparse-package-versions): New variable.
(suitesparse-version): Update to 7.10.2.
(suitesparse-source)[origin]: Update deletion list.
(suitesparse-amd, suitesparse-btf, suitesparse-camd, suitesparse-colamd,
suitesparse-ccolamd, suitesparse-cholmod, suitesparse-cxsparse,
suitesparse-klu, suitesparse-ldl, suitesparse-rbio,
suitesparse-mongoose, suitesparse-spex, suitesparse-spqr,
suitesparse-umfpack)[version]: Use %suitesparse-package-versions.
[arguments]<#:configure-flags>: Preserve include path.
(suitesparse-cholmod)[arguments]<#:phases>('install-license-files):
Update paths.
(suitesparse-cholmod)[arguments]<#:phases>('build-doc): Update paths.
(suitesparse-spex)[native-inputs]: Add texlive-fncychap.
(suitesparse-spqr)[native-inputs]: Add texlive-etoolbox.
* gnu/packages/patches/gklib-suitesparse.patch: Update version.

Change-Id: I14a9bfeddb37330c88a2e94b0992c2f1afbc5310
 2025-05-13 16:35:40 +00:00
Greg Hogan
9a41a54da2
gnu: diff-so-fancy: Update to 1.4.4. 
* gnu/packages/version-control.scm (diff-so-fancy): Update to 1.4.4.

Change-Id: If00c2b2cf653cb58bf92c05074d838a9c73a6cf0
 2025-05-13 16:35:39 +00:00
Greg Hogan
56f940e72f
gnu: Rename valgrind-next to valgrind. 
* gnu/packages/valgrind.scm (valgrind/pinned): Make public.
(valgrind): Delete.
(valgrind-next): Rename to valgrind.
(valgrind/interactive): Inherit from valgrind.
* gnu/packages/audio.scm (codec2),
* gnu/packages/bootloaders.scm (dtc),
* gnu/packages/chromium.scm (ungoogled-chromium),
* gnu/packages/crates-io.scm (rust-crabgrind-0.1),
* gnu/packages/crates-tls.scm (rust-rustls-pki-types-1),
* gnu/packages/file-systems.scm (bindfs),
* gnu/packages/gnome.scm (libratbag, gnome-software),
* gnu/packages/high-availability.scm (pacemaker),
* gnu/packages/linux.scm (multipath-tools),
* gnu/packages/machine-learning.scm (python-pytorch),
* gnu/packages/mpi.scm (openmpi-4),
* gnu/packages/music.scm (stargate),
* gnu/packages/perl-check.scm (perl-test-runvalgrind),
* gnu/packages/prolog.scm (trealla),
* gnu/packages/qt.scm (qtwebengine-5, qt-creator),
* gnu/packages/robotics.scm (aseba),
* gnu/packages/ruby.scm (ruby-ruby-memcheck),
* gnu/packages/spreadsheet.scm (sc-im),
* gnu/packages/web.scm (jq): Rename valgrind to valgrind/pinned.

Change-Id: I9dec25abce643ef6d815a2cc50414c4f65f1e8d3
 2025-05-13 16:35:39 +00:00
Greg Hogan
8e0bab93e5
gnu: fmt: Update to 11.2.0. 
* gnu/packages/pretty-print.scm (fmt): Update to 11.2.0.

Change-Id: Ifde5f94dc58dfc2617e2c5d731e8a97d4ca4705f
 2025-05-13 16:35:37 +00:00
Greg Hogan
2bb9ba3350
gnu: imhex-pattern-language: Downgrade dependency. 
* gnu/packages/hexedit.scm (imhex-pattern-language)
[native-inputs]: Replace fmt-11 with fmt-10.

Change-Id: I8e9c51c3f5f2127bd4c663227dd0b4145e2d2c4f
 2025-05-13 16:35:37 +00:00
Sergey Trofimov
4e43c0dd21
gnu: Remove quazip-0. 
Packages depending on quazip@0.9.1 have been migrated to quazip@1.4.

* gnu/packages/compression.scm (quazip-0): Delete variable.

Change-Id: Ia952c3758fd39ce0f9c04b7a89bd9b8365af6974
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-05-13 17:25:27 +02:00
Sergey Trofimov
95bc29934e
gnu: nomacs: Update to 3.21.1. 
* gnu/packages/image-viewers.scm (nomacs): Update to 3.21.1.
[arguments]<#:configure-flags>: Enable quazip.
[inputs], [native-inputs]: Switch to Qt6.
[inputs]<plugins>: Fetch from a fork that is updated to support Qt6.

Change-Id: I957054430043b72e6f50c4849fbce92f12b51adc
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-05-13 17:25:19 +02:00
Ricardo Wurmus
8b2426a1a1
gnu: Add r-anglemania. 
* gnu/packages/bioinformatics.scm (r-anglemania): New variable.

Change-Id: I14e8df223af809cb2a0bb2e569c9a6976de35e6b
 2025-05-13 17:01:01 +02:00
Ricardo Wurmus
ee4f2236e0
gnu: Add r-bigstatsr. 
* gnu/packages/cran.scm (r-bigstatsr): New variable.

Change-Id: I5e4bc7f9f6567c7cf93cc12bb3d33b46c00646aa
 2025-05-13 17:01:01 +02:00
Ricardo Wurmus
9e948013cd
gnu: Add r-bigparallelr. 
* gnu/packages/cran.scm (r-bigparallelr): New variable.

Change-Id: I3667c9ae8dce38b8501e8427da96091be0ce7162
 2025-05-13 17:01:01 +02:00
Ricardo Wurmus
c43835f485
gnu: Add r-bigreadr. 
* gnu/packages/cran.scm (r-bigreadr): New variable.

Change-Id: Ie59f4a1fbc469febedcd584cacac3ddd8d094c26
 2025-05-13 17:01:01 +02:00
Ricardo Wurmus
5fde1bc527
gnu: Add r-psychometric. 
* gnu/packages/cran.scm (r-psychometric): New variable.

Change-Id: Ifcca90bd90a4f7b8207692e01b535621e548a87e
 2025-05-13 17:01:01 +02:00
Ricardo Wurmus
6e8b3fd238
gnu: Add r-multilevel. 
* gnu/packages/cran.scm (r-multilevel): New variable.

Change-Id: I28a9ac6ae1498ea703eff45ae56855cab7de9bb6
 2025-05-13 17:01:01 +02:00
Ricardo Wurmus
e2b41eb747
gnu: Add r-rmio. 
* gnu/packages/cran.scm (r-rmio): New variable.

Change-Id: I6d43d59449d2d483d13fed0cdd14df2effb5e46d
 2025-05-13 17:01:01 +02:00
Ricardo Wurmus
1e2eecfa4b
gnu: Add r-bigassertr. 
* gnu/packages/cran.scm (r-bigassertr): New variable.

Change-Id: I07b591f4025da1233a915f747054943188a2158c
 2025-05-13 17:01:01 +02:00
Leo Famulari
171e4e66c7
gnu: linux-libre 5.15: Update to 5.15.182. 
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.182.
(linux-libre-5.15-pristine-source, deblob-scripts-5.15): Update hashes.

Change-Id: Ie29d4aef9fd1377a622f5796384b80d737272f6a
 2025-05-13 10:49:49 -04:00
Leo Famulari
1279f4b392
gnu: linux-libre 6.1: Update to 6.1.138. 
* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.138.
(linux-libre-6.1-pristine-source, deblob-scripts-6.1): Update hashes.

Change-Id: Ie1a51704c15e449a7f6bcdb17a7744b5be578d6e
 2025-05-13 10:49:48 -04:00
Leo Famulari
52bb4645d3
gnu: linux-libre 6.6: Update to 6.6.90. 
* gnu/packages/linux.scm (linux-libre-6.6-version): Update to 6.6.90.
(linux-libre-6.6-pristine-source): Update hash.

Change-Id: I0495bf7b49ba748bd51d13672e64884e937a7257
 2025-05-13 10:49:48 -04:00
Leo Famulari
dde13af78d
gnu: linux-libre 6.12: Update to 6.12.28. 
* gnu/packages/linux.scm (linux-libre-6.12-version): Update to 6.12.28.
(linux-libre-6.12-pristine-source): Update hash.

Change-Id: I9d6e99e2b5b1d6adfd2f63276ae21f3cc3df9b72
 2025-05-13 10:49:48 -04:00
Leo Famulari
8cdae66789
gnu: linux-libre: Update to 6.14.6. 
* gnu/packages/linux.scm (linux-libre-6.14-version): Update to 6.14.6.
(linux-libre-6.14-pristine-source): Update hash.

Change-Id: I7b4666ced0ca94b81eb1ff9786fc1caaa15f885b
 2025-05-13 10:49:48 -04:00
Ricardo Wurmus
04270c718f
gnu: r-mlr3misc: Update to 0.17.0. 
* gnu/packages/cran.scm (r-mlr3misc): Update to 0.17.0.
[propagated-inputs]: Add r-cli.

Change-Id: I38e2e8c7c4d3cd65b127c356f135dc1dad3fc1c9
 2025-05-13 14:50:17 +02:00
Ricardo Wurmus
7a067167cd
gnu: r-softimpute: Update to 1.4-3. 
* gnu/packages/cran.scm (r-softimpute): Update to 1.4-3.

Change-Id: I4b718844ffa382222f418696705ad316e09a8cb9
 2025-05-13 14:50:17 +02:00
Ricardo Wurmus
45beaab565
gnu: r-svglite: Update to 2.2.1. 
* gnu/packages/cran.scm (r-svglite): Update to 2.2.1.

Change-Id: I6c4f6cf94cefb0839aa97f401574cc71b156ea77
 2025-05-13 14:50:17 +02:00
Ricardo Wurmus
a43f5aac03
gnu: r-data-table: Update to 1.17.2. 
* gnu/packages/cran.scm (r-data-table): Update to 1.17.2.

Change-Id: I587b5fbbe6cc5e78711f6cc883cbec5b4b9054e8
 2025-05-13 14:50:16 +02:00
Ricardo Wurmus
6ecfb09fb7
gnu: r-bsseq: Update to 1.44.1. 
* gnu/packages/bioconductor.scm (r-bsseq): Update to 1.44.1.

Change-Id: I860ab39c7e188a381d2519c4399f7747e867c474
 2025-05-13 14:50:16 +02:00
Ricardo Wurmus
5d2845186d
gnu: r-biotmle: Update to 1.32.1. 
* gnu/packages/bioconductor.scm (r-biotmle): Update to 1.32.1.

Change-Id: I21be4c7ca5dbff137bce7a143c22eb9b8f417fe8
 2025-05-13 14:50:16 +02:00
Ricardo Wurmus
301621fa0b
gnu: r-erma: Update to 1.24.1. 
* gnu/packages/bioconductor.scm (r-erma): Update to 1.24.1.

Change-Id: I25e19882b92ec6008817e89e8e0aaaa4efe15764
 2025-05-13 14:50:16 +02:00
Ricardo Wurmus
857e115455
gnu: r-spatialexperiment: Update to 1.18.1. 
* gnu/packages/bioconductor.scm (r-spatialexperiment): Update to 1.18.1.

Change-Id: Ieca3d4685fd7ff56e027793813cd3fe4e034c91b
 2025-05-13 14:50:16 +02:00
Ricardo Wurmus
cc0c561b40
gnu: r-singlecellexperiment: Update to 1.30.1. 
* gnu/packages/bioconductor.scm (r-singlecellexperiment): Update to 1.30.1.

Change-Id: I0238fc7c9e7b798821e29570cf9d78261f2306f4
 2025-05-13 14:50:16 +02:00
Ricardo Wurmus
d55ee8edd0
gnu: r-chromvar: Update to 1.30.1. 
* gnu/packages/bioconductor.scm (r-chromvar): Update to 1.30.1.

Change-Id: Id9344c4f85834a8b050ff3c30c7a1128d3f36a61
 2025-05-13 14:50:16 +02:00
Ricardo Wurmus
ecbebc5ca9
gnu: r-circrnaprofiler: Update to 1.22.1. 
* gnu/packages/bioconductor.scm (r-circrnaprofiler): Update to 1.22.1.

Change-Id: I443629810f3ce69d1f5e80e72a6022a98bd8a002
 2025-05-13 14:50:15 +02:00
Ricardo Wurmus
1a2a984e4f
gnu: r-rcistarget: Update to 1.28.1. 
* gnu/packages/bioconductor.scm (r-rcistarget): Update to 1.28.1.

Change-Id: I1083e6d34e049079d0269b61882978fdee6db604
 2025-05-13 14:50:15 +02:00
Ricardo Wurmus
11ecd7aa64
gnu: r-sgseq: Update to 1.42.1. 
* gnu/packages/bioconductor.scm (r-sgseq): Update to 1.42.1.

Change-Id: I4b7d49f17579e8bb11fd35412e63b435be6f15b6
 2025-05-13 14:50:15 +02:00
Ricardo Wurmus
ac13c578f0
gnu: r-roar: Update to 1.44.1. 
* gnu/packages/bioconductor.scm (r-roar): Update to 1.44.1.

Change-Id: Ib66646c2eb6e3cb0f0906812a04ef08b666d52cb
 2025-05-13 14:50:15 +02:00
Ricardo Wurmus
7a0ed52e51
gnu: r-yamss: Update to 1.34.1. 
* gnu/packages/bioconductor.scm (r-yamss): Update to 1.34.1.

Change-Id: Ia41fad0a328e1ec1a761847fa79a9c16962cc400
 2025-05-13 14:50:15 +02:00
Ricardo Wurmus
0acf9956fc
gnu: r-aucell: Update to 1.30.1. 
* gnu/packages/bioconductor.scm (r-aucell): Update to 1.30.1.

Change-Id: I28263f9fc21ac8272f6a8ba61aa641cfb35302c4
 2025-05-13 14:50:15 +02:00
Ricardo Wurmus
c73edded1a
gnu: r-allelicimbalance: Update to 1.46.1. 
* gnu/packages/bioconductor.scm (r-allelicimbalance): Update to 1.46.1.

Change-Id: I4af917145424e03ca90831ba71e8f304b5dd49bb
 2025-05-13 14:50:15 +02:00
Ricardo Wurmus
c6a9b298bd
gnu: r-mlinterfaces: Update to 1.88.1. 
* gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.88.1.

Change-Id: I2a8f4a08b53fed8ee8f086c66b5ee58df4b22cf6
 2025-05-13 14:50:14 +02:00
Ricardo Wurmus
b2af3e05a0
gnu: r-clusterexperiment: Update to 2.28.1. 
* gnu/packages/bioconductor.scm (r-clusterexperiment): Update to 2.28.1.

Change-Id: Ic789105fd575a93da69d68eadf9091583018fd2c
 2025-05-13 14:50:14 +02:00
Ricardo Wurmus
bf22c1df8a
gnu: r-enrichplot: Update to 1.28.2. 
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.28.2.

Change-Id: Ib9712ce68e48f747fdd4b5b9a3ee4b4513af0604
 2025-05-13 14:50:14 +02:00
Ricardo Wurmus
95b930fc91
gnu: r-minfi: Update to 1.54.1. 
* gnu/packages/bioconductor.scm (r-minfi): Update to 1.54.1.

Change-Id: I997568d0f2cb70a42c72a98b60b74f34a0a97694
 2025-05-13 14:50:14 +02:00
Ricardo Wurmus
21d2e4a632
gnu: r-milor: Update to 2.4.1. 
* gnu/packages/bioconductor.scm (r-milor): Update to 2.4.1.

Change-Id: Ie58731e8bf176fde4e5e70e38504dc5b7ef57a45
 2025-05-13 14:50:14 +02:00
Ricardo Wurmus
38ba7b801f
gnu: r-scone: Update to 1.32.1. 
* gnu/packages/bioconductor.scm (r-scone): Update to 1.32.1.

Change-Id: I4087316689bb32f7b892b291122ae7a89ff9ace4
 2025-05-13 14:50:14 +02:00
Ricardo Wurmus
5984b9ddbb
gnu: r-treesummarizedexperiment: Update to 2.16.1. 
* gnu/packages/bioconductor.scm (r-treesummarizedexperiment): Update to 2.16.1.

Change-Id: I43666115877afe54857a9e93255e725eaaeb9237
 2025-05-13 14:50:14 +02:00
Ricardo Wurmus
fe8e769103
gnu: r-interactionset: Update to 1.36.1. 
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.36.1.

Change-Id: Ie5687ce5dc1de1d029f156950debbb0e520db17e
 2025-05-13 14:50:13 +02:00
Ricardo Wurmus
3e759802a9
gnu: r-variantannotation: Update to 1.54.1. 
* gnu/packages/bioconductor.scm (r-variantannotation): Update to 1.54.1.

Change-Id: I3607250b3db5e6fc99e95f8af79cce1bc24369d2
 2025-05-13 14:50:13 +02:00