9b557b121e
gnu: r-paws-common: Update to 0.6.4.
...
* gnu/packages/cran.scm (r-paws-common): Update to 0.6.4.
Change-Id: If1f80809d172f00e80f638cb600948d44c7f5a84
2023-11-15 15:55:22 +01:00
cc93193655
gnu: r-clustree: Update to 0.5.1.
...
* gnu/packages/cran.scm (r-clustree): Update to 0.5.1.
Change-Id: If2d5a6cf33eab9f820c7a4fccd26aa1763f96e28
2023-11-15 15:55:22 +01:00
5fc4cb0d85
gnu: r-bbotk: Update to 0.7.3.
...
* gnu/packages/cran.scm (r-bbotk): Update to 0.7.3.
Change-Id: I5e50ff5b3ac039fbe47d8093088e3e59a2bd8803
2023-11-15 15:55:22 +01:00
b4cf3fde74
gnu: r-seurat: Update to 5.0.0.
...
* gnu/packages/cran.scm (r-seurat): Update to 5.0.0.
[propagated-inputs]: Add r-fastdummies, r-generics, r-lifecycle, r-rcpphnsw, and
r-rspectra.
Change-Id: If728a0340cdeec5c2d5671025711a2ed42ee265b
2023-11-15 15:55:22 +01:00
352ccf5122
gnu: r-warp: Update to 0.2.1.
...
* gnu/packages/cran.scm (r-warp): Update to 0.2.1.
Change-Id: Iee92904e0341b7a4cfe4947e33b2d5b6c76dcab2
2023-11-15 15:55:21 +01:00
a472decb25
gnu: r-rfast: Update to 2.1.0.
...
* gnu/packages/cran.scm (r-rfast): Update to 2.1.0.
Change-Id: Ifd1d7459d2293bd2ab26054c469c739025cb7f7a
2023-11-15 15:55:21 +01:00
64ab52eb4f
gnu: r-qgraph: Update to 1.9.8.
...
* gnu/packages/cran.scm (r-qgraph): Update to 1.9.8.
Change-Id: Ibfefb7aed42bd935806dc2f40d2b131cdf97eb3c
2023-11-15 15:55:21 +01:00
ec5a1c42ca
gnu: r-openmx: Update to 2.21.10.
...
* gnu/packages/cran.scm (r-openmx): Update to 2.21.10.
Change-Id: I7d4216b5e0394cd89e1d6aaf602e601c224d125d
2023-11-15 15:55:21 +01:00
a18e274401
gnu: r-actuar: Update to 3.3-4.
...
* gnu/packages/cran.scm (r-actuar): Update to 3.3-4.
Change-Id: I5ffe7de887122cd4aeb6fd7027d4c94ae1b9867e
2023-11-15 15:55:21 +01:00
1223000d14
gnu: r-actcd: Update to 1.3-0.
...
* gnu/packages/cran.scm (r-actcd): Update to 1.3-0.
Change-Id: Ie8befdde95bef6fc1b9be8c7d55a1720f74ed678
2023-11-15 15:55:21 +01:00
3dab9524e1
gnu: r-pracma: Update to 2.4.4.
...
* gnu/packages/cran.scm (r-pracma): Update to 2.4.4.
Change-Id: I079366cc3ab7923a80033de4e9fe3642bd272523
2023-11-15 15:55:21 +01:00
8e197faab1
gnu: r-lifecycle: Update to 1.0.4.
...
* gnu/packages/cran.scm (r-lifecycle): Update to 1.0.4.
Change-Id: I0b3a51251fa42a0a58b0c0a4e92b4103f48aae12
2023-11-15 15:55:21 +01:00
3b11a7f4a3
gnu: r-parameters: Update to 0.21.3.
...
* gnu/packages/cran.scm (r-parameters): Update to 0.21.3.
Change-Id: Ied9207097f2a8c6581fd54cf44299e6d596ce636
2023-11-15 15:55:21 +01:00
29c2ab6063
gnu: r-graphlayouts: Update to 1.0.2.
...
* gnu/packages/cran.scm (r-graphlayouts): Update to 1.0.2.
Change-Id: I74f68183e2d52676c3f90474bfb140ef57b70af6
2023-11-15 15:55:21 +01:00
a21cdec24d
gnu: r-covr: Update to 3.6.4.
...
* gnu/packages/cran.scm (r-covr): Update to 3.6.4.
Change-Id: I5797214f14f11cd6f7eea166210dd7534b5163bc
2023-11-15 15:55:21 +01:00
d889bccd9d
gnu: r-lintr: Update to 3.1.1.
...
* gnu/packages/cran.scm (r-lintr): Update to 3.1.1.
Change-Id: I92d7969babf3e5cfc3a950054b2457c6ae11ece2
2023-11-15 15:55:21 +01:00
fe4e56eb5d
gnu: r-text2vec: Update to 0.6.4.
...
* gnu/packages/cran.scm (r-text2vec): Update to 0.6.4.
Change-Id: I8dbeb739b9a37be325109b0e5ca04478439b84c2
2023-11-15 15:55:21 +01:00
e5d80567fe
gnu: r-lemon: Update to 0.4.7.
...
* gnu/packages/cran.scm (r-lemon): Update to 0.4.7.
Change-Id: I9b7e0965200d8c79ec3d7242d249a1c6c363ba9a
2023-11-15 15:55:21 +01:00
d8943a3ddd
gnu: r-nor1mix: Update to 1.3-2.
...
* gnu/packages/cran.scm (r-nor1mix): Update to 1.3-2.
Change-Id: I64511ea1988a3ee7e3616a4bcd1f01347e151ba7
2023-11-15 15:55:21 +01:00
572457e4d7
gnu: r-mosaic: Update to 1.9.0.
...
* gnu/packages/cran.scm (r-mosaic): Update to 1.9.0.
[propagated-inputs]: Add r-tibble.
Change-Id: I15aa0fde963bca54680f3155312c14d6a4b54c63
2023-11-15 15:55:21 +01:00
9e866685ae
gnu: r-mosaicdata: Update to 0.20.4.
...
* gnu/packages/cran.scm (r-mosaicdata): Update to 0.20.4.
Change-Id: I3f421cdae96b3fca614a59836aa54e8c56a082df
2023-11-15 15:55:21 +01:00
33cc9d235e
gnu: r-ggformula: Update to 0.12.0.
...
* gnu/packages/cran.scm (r-ggformula): Update to 0.12.0.
[propagated-inputs]: Remove r-ggforce, r-ggstance, and r-magrittr.
Change-Id: Id40e2857d46d3f99393f0bd86179d612c2a01a75
2023-11-15 15:55:21 +01:00
5abfb1d49f
gnu: r-mosaiccore: Update to 0.9.4.0.
...
* gnu/packages/cran.scm (r-mosaiccore): Update to 0.9.4.0.
Change-Id: Ie6eea8c3d856fdeefc3361b5e64a438fe1970288
2023-11-15 15:55:21 +01:00
0a083112f0
gnu: r-proc: Update to 1.18.5.
...
* gnu/packages/cran.scm (r-proc): Update to 1.18.5.
Change-Id: I36ab2e49345241895ed6fb1fd88929dff28056cf
2023-11-15 15:55:21 +01:00
0de7e4d5fd
gnu: r-doby: Update to 4.6.20.
...
* gnu/packages/cran.scm (r-doby): Update to 4.6.20.
Change-Id: Id0a565f254065b55a9e947a174b60fafad2b5581
2023-11-15 15:55:21 +01:00
c65da604a2
gnu: r-rdpack: Update to 2.6.
...
* gnu/packages/cran.scm (r-rdpack): Update to 2.6.
Change-Id: I1d96901fa85f8c8d64c47bbbd8a84ac9883f3c97
2023-11-15 15:55:21 +01:00
c101519061
gnu: r-rastervis: Update to 0.51.6.
...
* gnu/packages/cran.scm (r-rastervis): Update to 0.51.6.
Change-Id: I7015583574faaf42cbe7df83dda7d05aaed4c475
2023-11-15 15:55:21 +01:00
c26dea6c49
gnu: r-collapsibletree: Update to 0.1.8.
...
* gnu/packages/cran.scm (r-collapsibletree): Update to 0.1.8.
Change-Id: Ibdf0f7b190d231f73f1817bcebd0523852385cde
2023-11-15 15:55:21 +01:00
dcb989dea8
gnu: r-data-tree: Update to 1.1.0.
...
* gnu/packages/cran.scm (r-data-tree): Update to 1.1.0.
[native-inputs]: Add r-rmarkdown.
Change-Id: Id29f4f08cf988d8699e61479a262dff07a630572
2023-11-15 15:55:21 +01:00
9e32016c9e
gnu: r-fbasics: Update to 4032.96.
...
* gnu/packages/cran.scm (r-fbasics): Update to 4032.96.
Change-Id: I1cbba3ad08a4f18618ad6e00b36c0e04ab67f0ae
2023-11-15 15:55:21 +01:00
37b665b714
gnu: r-leaflet: Update to 2.2.1.
...
* gnu/packages/cran.scm (r-leaflet): Update to 2.2.1.
Change-Id: I150f958f68c13284d29394f2fb66ed7b0efb6c10
2023-11-15 15:55:21 +01:00
fa8e97c557
gnu: r-xfun: Update to 0.41.
...
* gnu/packages/cran.scm (r-xfun): Update to 0.41.
Change-Id: I1836a13e924ba3af8a5977f54b1f85d7a4c9d4d5
2023-11-15 15:55:20 +01:00
e710d290f3
gnu: r-lava: Update to 1.7.3.
...
* gnu/packages/cran.scm (r-lava): Update to 1.7.3.
Change-Id: I9f2f75685f8ef058b505e9c29c9a23d31b9a7a46
2023-11-15 15:55:20 +01:00
116bfb3cd0
gnu: r-rmumps: Update to 5.2.1-25.
...
* gnu/packages/cran.scm (r-rmumps): Update to 5.2.1-25.
Change-Id: Id30606861beacd93a263fcaf33ef6beb73402463
2023-11-15 15:55:20 +01:00
60953d62c0
gnu: r-rgooglemaps: Update to 1.5.1.
...
* gnu/packages/cran.scm (r-rgooglemaps): Update to 1.5.1.
[propagated-inputs]: Remove r-sp.
Change-Id: Ib2f5762ddfb998f7aaf2640807c005782b890d27
2023-11-15 15:55:20 +01:00
e3fe8eed8f
gnu: r-maps: Update to 3.4.1.1.
...
* gnu/packages/cran.scm (r-maps): Update to 3.4.1.1.
Change-Id: I562ba446b9edcece65ec9078bd6d45949d0d82f1
2023-11-15 15:55:20 +01:00
76b34f7130
gnu: r-wesanderson: Update to 0.3.7.
...
* gnu/packages/cran.scm (r-wesanderson): Update to 0.3.7.
Change-Id: I8df7f543eb82dc45da68ba5a3b116006a8463973
2023-11-15 15:55:20 +01:00
4f68d59d5c
gnu: r-htmltools: Update to 0.5.7.
...
* gnu/packages/cran.scm (r-htmltools): Update to 0.5.7.
Change-Id: I065ece3404d36b1a860ed141c4d6631779ea4c05
2023-11-15 15:55:20 +01:00
e47637b8df
gnu: r-httr2: Update to 1.0.0.
...
* gnu/packages/cran.scm (r-httr2): Update to 1.0.0.
[propagated-inputs]: Add r-lifecycle and r-vctrs.
Change-Id: Ie52627aa382f59b6251953620ac1a38576f92a5d
2023-11-15 15:55:20 +01:00
a3341b68d4
gnu: r-ggpp: Update to 0.5.5.
...
* gnu/packages/cran.scm (r-ggpp): Update to 0.5.5.
Change-Id: Ifaff1e48d8fd7f166d8ae9f70bdd0cfc099de3ca
2023-11-15 15:55:20 +01:00
3b34ecaef9
gnu: r-waldo: Update to 0.5.2.
...
* gnu/packages/cran.scm (r-waldo): Update to 0.5.2.
Change-Id: I1273af36bcd2b9223acb071db3703d2fa3827e61
2023-11-15 15:55:20 +01:00
d64662b6f9
gnu: r-collapse: Update to 2.0.6.
...
* gnu/packages/cran.scm (r-collapse): Update to 2.0.6.
Change-Id: Id3522ad2adc4d50d1ce4eeb3406c1bdb7177bbfd
2023-11-15 15:55:20 +01:00
34a5f9adb9
gnu: r-afpt: Update to 1.1.0.4.
...
* gnu/packages/cran.scm (r-afpt): Update to 1.1.0.4.
Change-Id: Ia4922ee208924a77cc2725a0d00e7d8a82f77c26
2023-11-15 15:55:20 +01:00
9b270ccefa
gnu: r-abn: Update to 3.0.3.
...
* gnu/packages/bioconductor.scm (r-abn): Update to 3.0.3.
Change-Id: Id94ec47d805af9da63dbf43a9edbd5e7c3a5a62a
2023-11-15 15:55:20 +01:00
fefc250c60
gnu: r-activepathways: Update to 2.0.3.
...
* gnu/packages/bioconductor.scm (r-activepathways): Update to 2.0.3.
Change-Id: I4199c307d48583c0894a39af78f6a4027cb0cf54
2023-11-15 15:55:20 +01:00
285dd08443
gnu: r-ggpicrust2: Update to 1.7.3.
...
* gnu/packages/bioconductor.scm (r-ggpicrust2): Update to 1.7.3.
Change-Id: I18ab123d640ceec9315a21dff48ed2f1ea4ddff5
2023-11-15 15:55:20 +01:00
8eed542ddd
gnu: nyxt: Update to 3.9.2.
...
* gnu/packages/web-browsers.scm (nyxt): Update to 3.9.2.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2023-11-15 15:17:04 +01:00
0d55b7b06e
gnu: cl-slime-swank: Update to 2.28-1.735258a.
...
* gnu/packages/lisp-xyz.scm (sbcl-slime-swank): Update to 2.28-1.735258a.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
Change-Id: I109d71f8184ec1b1a3f8ad30b11e57f4280ae916
2023-11-15 15:17:04 +01:00
e6a9b48877
gnu: emacs-slime: Update to 2.28-1.735258a.
...
* gnu/packages/emacs-xyz.scm (emacs-slime): Update to 2.28-1.735258a.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2023-11-15 15:17:04 +01:00
7dd3a3240b
gnu: emacs-flycheck-grammalecte: Add missing propagated input.
...
* gnu/packages/emacs-xyz.scm (emacs-flycheck-grammalecte)[propagated-inputs]:
Add EMACS-PKG-INFO.
Change-Id: Ic54be88146277a6838eb9b55eeab8c190d2a0c01
2023-11-15 14:18:16 +01:00
f87c955725
gnu: spindle: Update to 0.13; remove input labels.
...
* gnu/packages/admin.scm (spindle): Update to 0.13.
[inputs]: Remove labels.
Change-Id: I2ccaaf2385797d81de2b1ffe28452281b4e5ae90
2023-11-15 11:36:21 +01:00
006f9f0f21
gnu: spindle: Fix compilation with GCC 11.
...
* gnu/packages/admin.scm (spindle)[arguments]: Add CXXFLAGS
to #:configure-flags.
Change-Id: I660228b8839a524791273f3fc7b6935d704b6715
2023-11-15 11:36:21 +01:00
aaee0e4af3
gnu: launchmon: Fix compilation with GCC 11.
...
* gnu/packages/admin.scm (launchmon)[arguments]: New field.
Change-Id: I30665896ef90e74b91055c85bcfe991af24f3a38
2023-11-15 11:36:20 +01:00
f8cad88615
gnu: intel-mpi-benchmarks: Update to 2021.3.
...
* gnu/packages/benchmark.scm (intel-mpi-benchmarks/openmpi): Update to
2021.3.
2023-11-15 11:36:20 +01:00
ad2fcbfca4
gnu: openmpi: Update to 4.1.6.
...
* gnu/packages/mpi.scm (openmpi): Update to 4.1.6.
2023-11-15 11:36:20 +01:00
59d29ebbb2
gnu: psm2: Update to 12.0.
...
* gnu/packages/linux.scm (psm2): Update to 12.0.
2023-11-15 11:36:20 +01:00
8c1c045a87
gnu: libfabric: Update to 1.19.0.
...
* gnu/packages/linux.scm (libfabric): Update to 1.19.0.
2023-11-15 11:36:20 +01:00
3f7eeaa57c
gnu: rdma-core: Update to 48.0.
...
* gnu/packages/linux.scm (rdma-core): Update to 48.0.
2023-11-15 11:36:20 +01:00
975350fab7
gnu: ucx: Update to 1.15.0.
...
* gnu/packages/fabric-management.scm (ucx): Update to 1.15.0.
* gnu/packages/patches/ucx-tcp-iface-ioctl.patch: Update for 1.15.0.
2023-11-15 11:36:20 +01:00
d117c6b422
gnu: opensm: Update to 3.3.24.
...
* gnu/packages/fabric-management.scm (opensm): Update to 3.3.24.
2023-11-15 11:36:20 +01:00
f1f8d56b75
gnu: hwloc: Update to 2.9.3.
...
* gnu/packages/mpi.scm (hwloc-2): Update to 2.9.3.
2023-11-15 11:36:19 +01:00
96753702a0
gnu: slurm: Add 23.02.6.
...
* gnu/packages/parallel.scm (slurm): Update to 23.02.6.
(slurm-22.05): New variable.
2023-11-15 11:36:19 +01:00
d67fa732f7
gnu: opensm: Use gexps.
...
* gnu/packages/fabric-management.scm (opensm)[arguments]: Use gexps.
2023-11-15 11:36:19 +01:00
ab6f63f3cb
gnu: opensm: Use the right version string for the doc directory.
...
Previously, when built with ‘--with-latest=opensm’, the package would
install its documentation under a directory with the wrong version
string.
* gnu/packages/fabric-management.scm (opensm)[arguments]: Use the name
and version of THIS-PACKAGE.
2023-11-15 11:36:19 +01:00
b712e563cf
gnu: soci: Add PIE flag.
...
* gnu/packages/databases.scm (soci)[arguments]: Set CMAKE_CXX_FLAGS to add
-fPIE.
Change-Id: I79527759d0d35833168f5106a9d6f372375a8ebe
2023-11-14 23:46:08 +01:00
bd0f217321
gnu: agda-1lab: Update to 549fdb1c948a975e90e70f871993a4a4239aa280.
...
* gnu/packages/agda.scm (agda-1lab): Update to
549fdb1c948a975e90e70f871993a4a4239aa280.
Change-Id: Iad77350fea5a6378e836cbd18c1f4a51bd5a5f0e
2023-11-14 13:47:53 +01:00
c5c2a82082
gnu: agda-cubical: Update to 0.6.
...
* gnu/packages/agda.scm (agda-cubical): Update to 0.6.
Change-Id: I1d6edc44755260e505985fb974c632ec6fff2b49
2023-11-14 13:47:53 +01:00
5f4b3ccf50
gnu: agda-categories: Adapt to agda-stdlib 1.7.3.
...
* gnu/packages/patches/agda-categories-use-stdlib-1.7.3.patch: New patch.
* gnu/packages/agda.scm (agda-categories)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Register it.
Change-Id: I25f16d55f14465a1dae882fd8ec47a95f8598e5c
2023-11-14 13:47:10 +01:00
7374e14f51
gnu: agda-stdlib: Update to 1.7.3.
...
* gnu/packages/agda.scm (agda-stdlib): Update to 1.7.3.
Change-Id: Ic941073814a6a2150d470fc05218dc8d19954445
2023-11-14 13:30:49 +01:00
a521757306
gnu: agda: Update to 2.6.4.
...
* gnu/packages/agda.scm (agda): Update to 2.6.4. Also build with
optimizations and cluster counting support.
* gnu/packages/patches/agda-use-sphinx-5.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
Change-Id: I98a66678ec401b9201d9fd3a0f606fff9767b4bc
2023-11-14 13:30:48 +01:00
5cb2574243
gnu: Add ghc-text-icu.
...
* gnu/packages/haskell-xyz.scm (ghc-text-icu): New variable.
Change-Id: I553f1fef4e76aeea6d09901917fd5d6032c23d46
2023-11-14 13:30:45 +01:00
b25954181c
gnu: emacs-denote: Update to 2.1.0.
...
* gnu/packages/emacs-xyz.scm (emacs-denote): Update to 2.1.0.
Change-Id: I4d0f585604ef049480842b4c052edd1aef300e15
2023-11-14 13:21:41 +01:00
cb399d96fb
gnu: emacs-org: Update to 9.6.12.
...
* gnu/packages/emacs-xyz.scm (emacs-org): Update to 9.6.12.
Change-Id: I0d2b063526f24b7104fcbab972f212e279060f27
2023-11-14 13:21:41 +01:00
3254429a41
gnu: emacs-package-lint: Update to 0.21.
...
* gnu/packages/emacs-xyz.scm (emacs-package-lint): Update to 0.21.
Change-Id: I82e28b8e1c211389e99f1947c5c7ddfcba893612
2023-11-14 13:21:41 +01:00
21822095e8
gnu: emacs-compat: Update to 29.1.4.4.
...
* gnu/packages/emacs-xyz.scm (emacs-compat): Update to 29.1.4.4.
Change-Id: I11705cb0c2b50bb445711bfdfdb142557aa58b04
2023-11-14 13:21:40 +01:00
b5d419b4ab
gnu: emacs-flycheck-grammalecte: Improve package style.
...
* gnu/packages/emacs-xyz.scm (emacs-flycheck-grammalecte)[arguments]Use
G-expressions.
<#:exclude>: Remove non-existing excluded file.
<#:emacs>: Use EMACS-NO-X.
<#:phases>: Use G-expressions.
Change-Id: Ic5a3c5e3f5271e75cd369cdd40ce210d7c2b859b
2023-11-14 13:21:40 +01:00
a572e55ea5
gnu: emacs-flycheck-grammalecte: Update to 2.4.
...
* gnu/packages/emacs-xyz.scm (emacs-flycheck-grammalecte): Update to 2.4.
Change-Id: I372e3e55534606dba6fed2c2d2f00dc27dc76c0e
2023-11-14 13:21:40 +01:00
3d15e9e5bc
gnu: insight-toolkit-4.12: Fix building.
...
* gnu/packages/image-processing.scm (insight-toolkit-4.12)[arguments]:
Add a configure-flag to build with c++14.
Change-Id: I5e7a0a3ed47e4e3f25611147f8e66c58a1bf8a8c
2023-11-14 08:57:48 +02:00
f9f36b08e5
gnu: ffmpeg-2.8: Update to 2.8.22.
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* gnu/packages/video.scm (ffmpeg-2.8): Update to 2.8.22.
Change-Id: I4ab83a07f60692aa43d04a81dd227b56a95a1d74
2023-11-14 08:16:52 +02:00
b3f110184f
gnu: ffmpeg-3.4: Update to 3.4.13.
...
* gnu/packages/video.scm (ffmpeg-3.4): Update to 3.4.13.
Change-Id: I9ef7b61dcdeab96d4021150fb57b3739a61376d0
2023-11-14 08:16:51 +02:00
b8dac014b1
gnu: ffmpeg-5: Update to 5.1.4.
...
* gnu/packages/video.scm (ffmpeg-5): Update to 5.1.4.
Change-Id: I4ea8faa3bcee2e34287af4461d078850de17154f
2023-11-14 08:16:45 +02:00
4963d4c6bb
gnu: appstream: Update to 0.16.4.
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* gnu/packages/freedesktop.scm (appstream): Update to 0.16.4.
[arguments]<#:configure-flags>: Add “-Dsystemd=false”.
<#:phases>: Adjust accordingly.
Change-Id: I9c22cbd10681666c20e848dbc1e52ca08431d984
2023-11-11 01:38:07 +01:00
02555467ce
gnu: libxmlb: Update to 0.3.14.
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* gnu/packages/xml.scm (libxmlb): Update to 0.3.14.
Change-Id: I8571b3f46a5528d04cc2ea013ff2ab0ef4ba19da
2023-11-11 01:37:59 +01:00
a7e831a556
gnu: gtk: Update to 4.12.3.
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* gnu/packages/gtk.scm (gtk): Update to 4.12.3.
[source]: Remove snippet.
[arguments]<#:configure-flags>: Add “--no-suite=headless”.
<#:phases>: Also patch text-color tests in gsk/nodeparser.
Change-Id: Iedabfd12ae4f60f02ea21f427b85aeb6b17d03d6
2023-11-11 01:19:20 +01:00
72e886328c
Merge branch 'master' into gnome-team
...
Change-Id: I88d3789460d1a89917451d80405d89a2824006ac
2023-11-04 07:43:44 +01:00
f54f36b363
gnu: passff-host: Add explicit references to inputs and remove some.
...
This removes ‘coreutils’, ‘grep’, ‘sed’, ‘which’, ‘bash-minimal’ and
‘gnu-make’ inputs, which were only used by the Makefile and
install_host_app.sh. Instead of running install_host_app.sh (through
‘make’) which does a few text substitutions, do the text substitutions with
Scheme code. This simplifies things and avoids unnecessary native inputs.
* gnu/packages/browser-extensions.scm (passff-host)[build-system]: Change to
copy-build-system.
[arguments]: Copy passff.json and passff.py. Do text substitutions on
them rather than running make. Refer to ‘password-store’ and ‘python’ through
inputs rather than directly.
[inputs]: Add PASSWORD-STORE and PYTHON.
Change-Id: I8fdb757516a7c30eae36b15f2a8d91e1445b19a5
2023-11-04 00:52:39 +01:00
625cfb4c4c
gnu: password-store: Add missing ‘tail’ input.
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* gnu/packages/password-utils.scm (password-store)[arguments]: Add “tail” to
the list of requisites.
[inputs]: Add COREUTILS.
Change-Id: I7f59e6c0abfb5396b9548edaec08d3b0a7c0eb23
2023-11-04 00:52:38 +01:00
10d728139d
gnu: Add r-ggbreak.
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* gnu/packages/cran.scm (r-ggbreak): New variable.
Change-Id: I27d62d0110fb56e77dc8cf82581adb6259317c2d
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-03 23:39:57 +01:00
479fdc8451
gnu: python-pymc: Update to 5.9.1.
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* gnu/packages/statistics.scm (python-pymc): Update to 5.9.1.
Change-Id: I3d7927e7173f36ba4edeab06bd930c285432c29f
2023-11-03 19:25:36 -03:00
43d9fa0802
gnu: python-pytensor: Update to 2.17.3.
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* gnu/packages/python-science.scm (python-pytensor): Update to 2.17.3.
Change-Id: I2843aca1df4d43883bf643e6e363bd3700202c45
2023-11-03 19:25:36 -03:00
1879bfd88f
gnu: python-deepxde: Update to 1.10.0.
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* gnu/packages/machine-learning.scm (python-deepxde): Update to 1.10.0.
Change-Id: Ibc37f9e7df45c49f590beb1dda87236e853b88c1
2023-11-03 19:25:36 -03:00
96e8502faa
gnu: Add python-emcee.
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* gnu/packages/statistics.scm (python-emcee): New variable.
2023-11-03 19:25:35 -03:00
a7d56852e3
gnu: Add python-salib.
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* gnu/packages/python-science.scm (python-salib): New variable.
2023-11-03 19:25:35 -03:00
9642b1c7af
gnu: python-openturns: Update to 1.21.1.
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* gnu/packages/statistics.scm (python-openturns): Update to 1.21.1.
2023-11-03 19:25:35 -03:00
a55c3110be
gnu: python-opentsne: Update to 1.0.0.
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* gnu/packages/machine-learning.scm (python-opentsne): Update to 1.0.0.
2023-11-03 19:25:35 -03:00
ef473d3422
gnu: symengine: Update to 0.11.1.
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* gnu/packages/algebra.scm (symengine): Update to 0.11.1.
2023-11-03 19:25:31 -03:00
eb93ab2d14
gnu: r-gdata: Remove Excel from description.
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gdata 3.0.0 has removed support for reading Excel files.
* gnu/packages/statistics.scm (r-gdata)[description]: Update it.
Change-Id: Ic4090bc765d330d38136bf1b1dbbb6bb136edd39
2023-11-03 22:49:28 +01:00
8be2f44765
gnu: Remove r-sigpathway.
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This package has been removed with the release of Bioconductor 3.18.
* gnu/packages/bioconductor.scm (r-sigpathway): Remove variable.
Change-Id: I5cb9d938f370aa28b196f9cea95fb6024c2e6e37
2023-11-03 22:49:28 +01:00
38b5777ec8
gnu: r-rhdf5filters: Simplify.
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* gnu/packages/bioconductor.scm (r-rhdf5filters)[arguments]: Remove
'use-system-libraries phase and pass configure flags to disable bundled
libraries.
Change-Id: I2fb115e7b3df00cccb3f8d6659d465075d21f19b
2023-11-03 22:49:28 +01:00
78641cf9da
gnu: r-spams: Build with C++11.
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* gnu/packages/statistics.scm (r-spams)[arguments]: Add phase 'use-c++11.
Change-Id: Ie477af6afe8993919090f6c81e071cee542e69bc
2023-11-03 22:49:28 +01:00
142313cf0c
gnu: Remove r-genomegraphs.
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This package had been removed from Bioconductor with release 3.11.
* gnu/packages/bioconductor.scm (r-genomegraphs): Remove variable.
Change-Id: I73cc8cc8546089d91212176939b8c0c0a7afc309
2023-11-03 22:49:28 +01:00
0150529188
gnu: Remove r-wavetiling.
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This package had been removed from Bioconductor since release 3.12.
* gnu/packages/bioconductor.scm (r-wavetiling): Remove variable.
Change-Id: I5eb624d975f0eb170b263266b144eacf11944580
2023-11-03 22:49:28 +01:00
abaca151b2
gnu: r-mpo-db: Include HPO sqlite database.
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* gnu/packages/bioconductor.scm (r-mpo-db)[arguments]: Bypass fetching of the
database from the internet when in build environment.
[native-inputs]: Add MPO.sqlite.
Change-Id: Ic7228322b89ce78a85a9bd5ffbd985ccd906d268
2023-11-03 22:49:28 +01:00
b30127052e
gnu: r-readwriter: Update to 0.3.2-1.12d32cb.
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* gnu/packages/bioinformatics.scm (r-readwriter): Update to 0.3.2-1.12d32cb.
Change-Id: I412190ce94bee4e7b5fce27db7ef8a72188e74f4
2023-11-03 22:49:28 +01:00
c66c66ee3f
gnu: r-hpo-db: Include HPO sqlite database.
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* gnu/packages/bioconductor.scm (r-hpo-db)[arguments]: Bypass fetching of the
database from the internet when in build environment.
[native-inputs]: Add HPO.sqlite.
Change-Id: Ie01605ef2531d992fb85c07bae5cfaabda626ea6
2023-11-03 22:49:28 +01:00
a938342899
gnu: r-rhdf5lib: Adjust modifications to Makevars.
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* gnu/packages/bioconductor.scm (r-rhdf5lib)[arguments]: Adjust patch.
Change-Id: Iaef3d2d80c22de1c2a0b64e7c13f5fa3b8e5719d
2023-11-03 22:49:28 +01:00
c82c9c8090
gnu: r-phyloseq: Update to 1.46.0.
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* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.46.0.
Change-Id: Id11b5e913529ac8efce0d046168f4a9dbe0dbabd
2023-11-03 22:49:28 +01:00
1c3e8ab395
gnu: r-tximeta: Update to 1.20.0.
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* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.20.0.
Change-Id: I8d9c5d01efc8f6c64290cdfdd193d95cd1da9152
2023-11-03 22:49:28 +01:00
270d7e1079
gnu: r-tricycle: Update to 1.10.0.
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* gnu/packages/bioconductor.scm (r-tricycle): Update to 1.10.0.
Change-Id: I72a9e1140c17ce8605bfe6e83cc290eb1ae2fad2
2023-11-03 22:49:28 +01:00
9ee38f4ee6
gnu: r-tcgabiolinks: Update to 2.30.0.
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* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.30.0.
Change-Id: If7e571bfa6454bfa94dd395606575391dc506ecd
2023-11-03 22:49:28 +01:00
28480926a5
gnu: r-biscuiteer: Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-biscuiteer): Update to 1.16.0.
Change-Id: Ib6cffbbeedfe87932acfcbfb2b789b4c92a9bf81
2023-11-03 22:49:28 +01:00
53ebbff56c
gnu: r-omnipathr: Update to 3.10.1.
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* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.10.1.
[propagated-inputs]: Add r-lubridate and r-stringi.
Change-Id: Ia18b66848cd6996dfdc551bf4b182bb5ac3e17a8
2023-11-03 22:49:28 +01:00
41a4f01473
gnu: r-omicade4: Update to 1.42.0.
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* gnu/packages/bioconductor.scm (r-omicade4): Update to 1.42.0.
Change-Id: I4369e5721116bf73f096ee39a516ada94c348872
2023-11-03 22:49:28 +01:00
73efb254d8
gnu: r-dmrseq: Update to 1.22.0.
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* gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.22.0.
Change-Id: I738c2fb7e0fa3e816d3767f854b8f9ed77425591
2023-11-03 22:49:28 +01:00
f6e56299e7
gnu: r-dada2: Update to 1.30.0.
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* gnu/packages/bioconductor.scm (r-dada2): Update to 1.30.0.
Change-Id: I0955c3a61b4d81cd6809e2eb287d8acfcccfb789
2023-11-03 22:49:28 +01:00
407e9b2710
gnu: r-bsseq: Update to 1.38.0.
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* gnu/packages/bioconductor.scm (r-bsseq): Update to 1.38.0.
Change-Id: Ie31f0b5c726da98a0caa4c658a5c62c1a5f40eaa
2023-11-03 22:49:28 +01:00
69d7d7a6db
gnu: r-biotmle: Update to 1.26.0.
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* gnu/packages/bioconductor.scm (r-biotmle): Update to 1.26.0.
Change-Id: Ied1d1e649fba277aa724040af31334f664d2debd
2023-11-03 22:49:28 +01:00
9f2c8b711b
gnu: r-biotip: Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-biotip): Update to 1.16.0.
Change-Id: I73503554b0271e5fe950c6da367b4893972f27e9
2023-11-03 22:49:28 +01:00
a7d1b8832a
gnu: r-bioqc: Update to 1.30.0.
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* gnu/packages/bioconductor.scm (r-bioqc): Update to 1.30.0.
Change-Id: I0b5fd7cac1283a7f12a1221ad453eb56767e8b90
2023-11-03 22:49:28 +01:00
ee259a9ad9
gnu: r-bionetstat: Update to 1.22.0.
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* gnu/packages/bioconductor.scm (r-bionetstat): Update to 1.22.0.
Change-Id: I92f2ebef0b65b947a719bdd1008f07ce279263a4
2023-11-03 22:49:28 +01:00
b0190a7d5c
gnu: r-bionet: Update to 1.62.0.
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* gnu/packages/bioconductor.scm (r-bionet): Update to 1.62.0.
Change-Id: I0712a4ba67c27b32d6666e91d9515f0299e61848
2023-11-03 22:49:27 +01:00
63f3a845ea
gnu: r-bionero: Update to 1.10.0.
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* gnu/packages/bioconductor.scm (r-bionero): Update to 1.10.0.
Change-Id: I396a37dd28571a471b45d4d8aca6ce40a1cbd384
2023-11-03 22:49:27 +01:00
4ccceb31b9
gnu: r-biomvcclass: Update to 1.70.0.
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* gnu/packages/bioconductor.scm (r-biomvcclass): Update to 1.70.0.
Change-Id: I0c6214669ec284d314eb7dc90270558934070e4b
2023-11-03 22:49:27 +01:00
b4e803a8a9
gnu: r-mvcclass: Update to 1.76.0.
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* gnu/packages/bioconductor.scm (r-mvcclass): Update to 1.76.0.
Change-Id: I6e7fa851c804009ae41a955b117d95b33fd1b2f0
2023-11-03 22:49:27 +01:00
c91a1a8bc8
gnu: r-biomformat: Update to 1.30.0.
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* gnu/packages/bioconductor.scm (r-biomformat): Update to 1.30.0.
Change-Id: I661d11f81a0dedbc8381b5ba1806643b5ff52aa6
2023-11-03 22:49:27 +01:00
2b4dcd4a7b
gnu: r-biodb: Update to 1.10.0.
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* gnu/packages/bioconductor.scm (r-biodb): Update to 1.10.0.
Change-Id: If1d14855b2bf134741c54c0a51daefdf2b80a49f
2023-11-03 22:49:27 +01:00
9480ea5046
gnu: r-biocthis: Update to 1.12.0.
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* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.12.0.
Change-Id: I8400ebfd178f916488e022152e75db59f05994e6
2023-11-03 22:49:27 +01:00
327c9bd7c8
gnu: r-basilisk: Update to 1.14.0.
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* gnu/packages/bioconductor.scm (r-basilisk): Update to 1.14.0.
Change-Id: I86f5306de138eb1fedffbae65c14f9acd504c86c
2023-11-03 22:49:27 +01:00
b5527cc3c6
gnu: r-basilisk-utils: Update to 1.14.0.
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* gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.14.0.
Change-Id: I6113042a10770ee50e4ef997ee41fe109f917885
2023-11-03 22:49:27 +01:00
b2389dcfc1
gnu: r-dir-expiry: Update to 1.10.0.
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* gnu/packages/bioconductor.scm (r-dir-expiry): Update to 1.10.0.
Change-Id: I1081ec981a52a51a351d98e5079f8fd4bcc399d0
2023-11-03 22:49:27 +01:00
d5026a9e16
gnu: r-genetclassifier: Update to 1.42.0.
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* gnu/packages/bioconductor.scm (r-genetclassifier): Update to 1.42.0.
Change-Id: I323ca2d408c640b05c9d845570ee7af28616cce2
2023-11-03 22:49:27 +01:00
31fef7c331
gnu: r-minet: Update to 3.60.0.
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* gnu/packages/bioconductor.scm (r-minet): Update to 3.60.0.
Change-Id: I4944d2e34aacc6d3ba8c5a2d2176ecf7b33ca6b8
2023-11-03 22:49:27 +01:00
ae127ddf0d
gnu: r-biobtreer: Update to 1.14.0.
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* gnu/packages/bioconductor.scm (r-biobtreer): Update to 1.14.0.
Change-Id: Icf0458c6931237a405178361778a68c1a068337c
2023-11-03 22:49:27 +01:00
d40b4c5063
gnu: r-bgeedb: Update to 2.28.0.
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* gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.28.0.
Change-Id: I558f36065a9a751710843f21c6089231309705ca
2023-11-03 22:49:27 +01:00
38f88c84bf
gnu: r-bgeecall: Update to 1.18.1.
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* gnu/packages/bioconductor.scm (r-bgeecall): Update to 1.18.1.
Change-Id: I5db747786c63f248dec01879e41a9837c94d6d6c
2023-11-03 22:49:27 +01:00
58661d1d54
gnu: r-beclear: Update to 2.18.0.
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* gnu/packages/bioconductor.scm (r-beclear): Update to 2.18.0.
Change-Id: Ia52d2072c95c4ff68cabe22cd6f9da8f3f7833b3
2023-11-03 22:49:27 +01:00
6ddf9ed610
gnu: r-megadepth: Update to 1.12.0.
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* gnu/packages/bioconductor.scm (r-megadepth): Update to 1.12.0.
Change-Id: Ia8424334f3183442a8e7ffb21ba664b93f6342a3
2023-11-03 22:49:27 +01:00
9d0492c750
gnu: r-ballgown: Update to 2.34.0.
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* gnu/packages/bioconductor.scm (r-ballgown): Update to 2.34.0.
Change-Id: Ice69c2be8df89cb103e73de328ac6eb5919f0502
2023-11-03 22:49:27 +01:00
7e36e3ed55
gnu: r-guitar: Update to 2.18.0.
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* gnu/packages/bioconductor.scm (r-guitar): Update to 2.18.0.
Change-Id: I2cd39de6e1fedbc3ed9a137373d6836e930296f2
2023-11-03 22:49:27 +01:00
0c881be497
gnu: r-chromstar: Update to 1.28.0.
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* gnu/packages/bioconductor.scm (r-chromstar): Update to 1.28.0.
Change-Id: I48a305a00b1fe7c89ca4f9700ebe6f65a6265080
2023-11-03 22:49:27 +01:00
d775b141cf
gnu: r-snpstats: Update to 1.52.0.
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* gnu/packages/bioconductor.scm (r-snpstats): Update to 1.52.0.
Change-Id: Ia770e5b05a7998d552b8ccb5386ddc1ad6722217
2023-11-03 22:49:27 +01:00
3b0e948493
gnu: r-snprelate: Update to 1.36.0.
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* gnu/packages/bioconductor.scm (r-snprelate): Update to 1.36.0.
Change-Id: I79ab3d448ab4b10a97d9c9d36b3b849a7c491508
2023-11-03 22:49:27 +01:00
bbe5704c17
gnu: r-snapcgh: Update to 1.72.0.
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* gnu/packages/bioconductor.scm (r-snapcgh): Update to 1.72.0.
Change-Id: I7b2adbcb45461b5dc4f8248f92bfbda5f145d906
2023-11-03 22:49:27 +01:00
6b8c604e48
gnu: r-pathview: Update to 1.42.0.
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* gnu/packages/bioconductor.scm (r-pathview): Update to 1.42.0.
Change-Id: I56a1425210667cc9b1ee41d20b9a71a749f6ff91
2023-11-03 22:49:27 +01:00
740e7ff51b
gnu: r-parody: Update to 1.60.0.
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* gnu/packages/bioconductor.scm (r-parody): Update to 1.60.0.
Change-Id: I409588b32e582c0c6cd631d56a92ca430e2429d4
2023-11-03 22:49:27 +01:00
e9618ab210
gnu: r-ldblock: Update to 1.32.0.
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* gnu/packages/bioconductor.scm (r-ldblock): Update to 1.32.0.
Change-Id: I4183a3b48e050120ffb1e5cbba3894a5637ad1cc
2023-11-03 22:49:27 +01:00
9f139605ef
gnu: r-kegggraph: Update to 1.62.0.
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* gnu/packages/bioconductor.scm (r-kegggraph): Update to 1.62.0.
Change-Id: Iadaa3580a5755ca5e611d980241191c4ae8b9452
2023-11-03 22:49:27 +01:00
b6288f949f
gnu: r-gwastools: Update to 1.48.0.
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* gnu/packages/bioconductor.scm (r-gwastools): Update to 1.48.0.
[native-inputs]: Add r-knitr.
Change-Id: I0544357b6f954e4812d1cdb983e12ed34f83b0d1
2023-11-03 22:49:27 +01:00
11300bd9ee
gnu: r-gwascat: Update to 2.34.0.
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* gnu/packages/bioconductor.scm (r-gwascat): Update to 2.34.0.
Change-Id: I3ae4066f1e36e30cecdf15cb9a5bfb469f0d6b49
2023-11-03 22:49:27 +01:00
3e5e4bf311
gnu: r-gviz: Update to 1.46.0.
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* gnu/packages/bioconductor.scm (r-gviz): Update to 1.46.0.
Change-Id: Ib7b7f039dffd4f25731a4be3edfa6ecd293ceeff
2023-11-03 22:49:26 +01:00
Ricardo Wurmus
Andre A. Gomes
Nicolas Goaziou
Ludovic Courtès
Ludovic Courtès
Josselin Poiret
Efraim Flashner
Liliana Marie Prikler
Clément Lassieur
Afkhami, Navid
Vinicius Monego