bdbcdacfbd
gnu: Remove r-qs.
...
This package fails to build with R 4.6.0 as it depends on internal symbols
that have since been removed from R. r-qs has been abandoned in favor of
r-qs2, which is not a drop-in replacement.
See https://github.com/qsbase/qs/issues/103
* gnu/packages/cran.scm (r-qs): Delete variable.
Change-Id: Ia1b0268cb8f6b74e3c2ab6446cd956aaffa7291e
2026-05-28 12:13:47 +02:00
1240dc7006
gnu: Remove r-seurat-utils.
...
This package depends on r-qs, which fails to build with R 4.6.0. r-qs has
been abandoned in favor of r-qs2, which is not a drop-in replacement.
* gnu/packages/bioinformatics.scm (r-seurat-utils): Delete variable.
Change-Id: I2b62a766e4784e25599329c86c49a1e059dd909f
2026-05-28 12:13:47 +02:00
bcbee6077b
gnu: Remove r-seqbias.
...
This package was removed with Bioconductor 3.19 release. It depends on R
internal symbols, which have been removed.
* gnu/packages/bioconductor.scm (r-seqbias): Delete variable.
Change-Id: Ib8a834c1d69f329281904e739c429448474d511b
2026-05-28 12:13:47 +02:00
0d5d4cf8c7
gnu: Remove r-reqon.
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This package was removed with Bioconductor 3.20 release. It depends on
r-seqbias, which fails to build.
* gnu/packages/bioconductor.scm (r-reqon): Delete variable.
Change-Id: I7c9e731ebde3d2991b30140c7f2c26868e29664c
2026-05-28 12:13:47 +02:00
0b0c6d9850
gnu: r-misha: Update to 5.6.23.
...
* gnu/packages/bioinformatics.scm (r-misha): Update to 5.6.23.
[source]: Remove obsolete snippet.
[arguments]: Remove phase 'do-not-use-bundled-bigWigToWig.
[inputs]: Remove kentutils.
[propagated-inputs]: Add r-curl, r-digest, r-magrittr, r-ps, and r-yaml.
[native-inputs]: Add r-knitr and r-testthat.
Change-Id: Ia3bf627976d5963757b7ac0cede1cd43cff7da3b
2026-05-28 12:13:47 +02:00
48f4dbec9a
gnu: r-muscat: Add missing test inputs.
...
* gnu/packages/bioconductor.scm (r-muscat)[native-inputs]: Add r-deseq2 and
r-sctransform.
Change-Id: Ib4d4829a0fdfb59243a4960ba98686af4817b4c5
2026-05-28 12:13:47 +02:00
8dbddf3832
gnu: r-mvabund: Add missing input.
...
* gnu/packages/cran.scm (r-mvabund)[inputs]: Add gsl.
[properties]: Record updater-extra-inputs.
Change-Id: I19b1b683117b507843e615a32cdbb82c46dfceaa
2026-05-28 12:13:46 +02:00
e410f2b30a
gnu: r-rcppziggurat: Add missing input.
...
* gnu/packages/cran.scm (r-rcppziggurat)[inputs]: Add gsl.
[properties]: Record updater-extra-inputs.
Change-Id: Ice7fe6bc3611cc45d14ef7c0475523a431be9a45
2026-05-28 12:13:46 +02:00
df6e13facc
gnu: r-sf: Update to 1.1-1.
...
* gnu/packages/cran.scm (r-sf): Update to 1.1-1.
[propagated-inputs]: Remove r-magrittr.
Change-Id: If3dd9fb392a9b51179b1c0b4ca9bf7c756d6dcda
2026-05-28 12:13:46 +02:00
b97598040c
gnu: r-data-table: Update to 1.18.4.
...
* gnu/packages/cran.scm (r-data-table): Update to 1.18.4.
Change-Id: I23c4df82d0380337af8acbbd9da34c435308e18d
2026-05-28 12:13:46 +02:00
3f13c49e01
gnu: r-mgsub: Update to 2.0.0.
...
* gnu/packages/cran.scm (r-mgsub): Update to 2.0.0.
Change-Id: Ia967d86670673423df178ebb8a88d85f00a02284
2026-05-28 12:13:46 +02:00
f0e627fd0a
gnu: r-cpp11: Update to 0.5.5.
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* gnu/packages/cran.scm (r-cpp11): Update to 0.5.5.
Change-Id: I1857e893276bdb90c16ded39a3ac479d31634dbe
2026-05-28 12:13:46 +02:00
59d56d830d
gnu: r-exactextractr: Disable two tests.
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* gnu/packages/cran.scm (r-exactextractr)[arguments]: Disable two tests.
Change-Id: I19933ae758c913e707b25e8e89c4132e5339b060
2026-05-28 12:13:46 +02:00
f94b2fa8b3
gnu: r-spectre: Update to 1.3.0.
...
* gnu/packages/bioinformatics.scm (r-spectre): Update to 1.3.0.
[propagated-inputs]: Replace r-qs with r-qs2.
Change-Id: Ia55fed95e05ab7acf5e43d4ff32569156f6e4e93
2026-05-28 12:13:45 +02:00
41cefea1e0
gnu: r-terra: Update to 1.9-25.
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* gnu/packages/cran.scm (r-terra): Update to 1.9-25.
[input]: Replace proj-9.3 with proj.
Change-Id: I6e9e07658fc8e3e92f638bcf632910e37f8340d7
2026-05-28 12:13:45 +02:00
3ba4f6de9a
gnu: r-pizzarr: Update to 0.2.0.
...
* gnu/packages/bioinformatics.scm (r-pizzarr): Update to 0.2.0.
[build-system]: Use cargo-build-system.
[arguments]: Add phases from the r-build-system; enable most tests.
[inputs]: Add openssl, zlib, and zstd:lib; add cargo inputs.
[native-inputs]: Add pkg-config and r-minimal.
[propagated-inputs]: Remove r-qs; add r-qs2.
* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Add entries for extendr
and r-pizzarr.
* gnu/packages/rust-sources.scm (rust-extendr-0.8.1.93d7244): New variable.
Change-Id: Ibce9ce84bedac56978729513756b8476769126bb
2026-05-28 12:13:45 +02:00
6c23765499
gnu: r-rstpm2: Add missing test input.
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* gnu/packages/cran.scm (r-rstpm2)[native-inputs]: Add r-eha.
Change-Id: I8df4e0c06f4dcc147f4eb3a3b3f70840f1279ef2
2026-05-28 12:13:45 +02:00
d91ec342c6
gnu: Add r-eha.
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* gnu/packages/cran.scm (r-eha): New variable.
Change-Id: I8cfe81ec60f57c10c17ddaede5f0f1369516bf80
2026-05-28 12:13:45 +02:00
341381466f
gnu: r-universalmotif: Update to 1.30.1.
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* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.30.1.
Change-Id: I7e7cfe559bfdee2da0d2eb060021b765f71e1683
2026-05-28 12:13:44 +02:00
b0accc4fa4
gnu: r-scrapper: Update to 1.6.2.
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* gnu/packages/bioconductor.scm (r-scrapper): Update to 1.6.2.
Change-Id: Ib93e9f1751db7fc9440486bf299362fb13ecee88
2026-05-28 12:13:44 +02:00
edb8d97aef
gnu: r-scrnaseq: Update to 2.26.0.
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* gnu/packages/bioconductor.scm (r-scrnaseq): Update to 2.26.0.
Change-Id: I9ddf947f97c5e5e41a3ab7b34fbe7619b92425c5
2026-05-28 12:13:44 +02:00
0c676c2ca2
gnu: r-limma: Update to 3.68.1.
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* gnu/packages/bioconductor.scm (r-limma): Update to 3.68.1.
Change-Id: Id51bfc31a6f3424677f86baf6cfd3cfb99f0a4df
2026-05-28 12:13:44 +02:00
ac6e193694
gnu: r-dmrcate: Update to 3.8.0.
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* gnu/packages/bioconductor.scm (r-dmrcate): Update to 3.8.0.
Change-Id: I2dbc7ef5e40948a6c3d48c793acf026d1fd27e82
2026-05-28 12:13:44 +02:00
e0ffc36c4b
gnu: r-zebrafishrnaseq: Update to 1.32.0.
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* gnu/packages/bioconductor.scm (r-zebrafishrnaseq): Update to 1.32.0.
Change-Id: I94a96f87d8a9d672b673fcab16aea45e23de9636
2026-05-28 12:13:44 +02:00
cab200653a
gnu: r-tximportdata: Update to 1.40.0.
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* gnu/packages/bioconductor.scm (r-tximportdata): Update to 1.40.0.
Change-Id: I0e7142e2a6653de73e3d47d47fee7cbe294333bf
2026-05-28 12:13:44 +02:00
801bb92a9a
gnu: r-tcgabiolinksgui-data: Update to 1.32.0.
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* gnu/packages/bioconductor.scm (r-tcgabiolinksgui-data): Update to 1.32.0.
Change-Id: I41f6e1a4ed50ea069939ba641dc6797eecb7cf7e
2026-05-28 12:13:43 +02:00
ea8503d0cd
gnu: r-systempiperdata: Update to 2.16.0.
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* gnu/packages/bioconductor.scm (r-systempiperdata): Update to 2.16.0.
Change-Id: Ie85d08f8923ac5381d25ed66da8f826cafbeabf4
2026-05-28 12:13:43 +02:00
73d1f7ae6b
gnu: r-sesamedata: Update to 1.30.0.
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* gnu/packages/bioconductor.scm (r-sesamedata): Update to 1.30.0.
Change-Id: I9816045889e8bb115cc9726f7824989faedf4472
2026-05-28 12:13:43 +02:00
e06b634441
gnu: r-scpdata: Update to 1.20.0.
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* gnu/packages/bioconductor.scm (r-scpdata): Update to 1.20.0.
Change-Id: If2ebd4ef53e99298329cfe49f1f55969133f281e
2026-05-28 12:13:43 +02:00
46b795c279
gnu: r-rtcga-rnaseq: Update to 20151101.42.0.
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* gnu/packages/bioconductor.scm (r-rtcga-rnaseq): Update to 20151101.42.0.
Change-Id: Ia84b23833e92749eb9892545be039a6cd6772016
2026-05-28 12:13:43 +02:00
84dbefed24
gnu: r-rnbeads-hg19: Update to 1.44.0.
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* gnu/packages/bioconductor.scm (r-rnbeads-hg19): Update to 1.44.0.
Change-Id: I44714670aa905ac0b0af539cdb7decb1362d1c5f
2026-05-28 12:13:43 +02:00
8820c9f777
gnu: r-rnaseqdata-hnrnpc-bam-chr14: Update to 0.50.0.
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* gnu/packages/bioconductor.scm (r-rnaseqdata-hnrnpc-bam-chr14): Update to 0.50.0.
Change-Id: I888b3ad8df394c819d923b690b9d4559320abfea
2026-05-28 12:13:43 +02:00
b0d3cd3089
gnu: r-rcistarget-hg19-motifdbs-cisbponly-500bp: Update to 1.32.0.
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* gnu/packages/bioconductor.scm (r-rcistarget-hg19-motifdbs-cisbponly-500bp): Update to 1.32.0.
Change-Id: I3d7892df42c6e7541cfa11208114bd1dcf49ef19
2026-05-28 12:13:43 +02:00
aa5d03153e
gnu: r-curatedtcgadata: Update to 1.34.0.
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* gnu/packages/bioconductor.scm (r-curatedtcgadata): Update to 1.34.0.
Change-Id: I2938cb9e94d494b332480282b863cb32ddb2d91d
2026-05-28 12:13:42 +02:00
5ae59b07a7
gnu: r-gagedata: Update to 2.50.0.
...
* gnu/packages/bioconductor.scm (r-gagedata): Update to 2.50.0.
Change-Id: I7d2878e3139ad9c773548230dbec1b70aebedcd1
2026-05-28 12:13:42 +02:00
73cc9ab759
gnu: r-affydata: Update to 1.60.0.
...
* gnu/packages/bioconductor.scm (r-affydata): Update to 1.60.0.
[native-inputs]: Add r-biobase.
Change-Id: I4c0d4b588c5ea1b0c53b2424cc9a3b9b9d57da52
2026-05-28 12:13:42 +02:00
f03931b143
gnu: r-all: Update to 1.54.0.
...
* gnu/packages/bioconductor.scm (r-all): Update to 1.54.0.
[native-inputs]: Add r-rpart.
Change-Id: Ia95ed032df922768e631e8130e5b81f9e3043774
2026-05-28 12:13:42 +02:00
2f7c9cb009
gnu: r-hsmmsinglecell: Update to 1.32.0.
...
* gnu/packages/bioconductor.scm (r-hsmmsinglecell): Update to 1.32.0.
Change-Id: If94fe35b407d636feecd2c6170895fbf2f750326
2026-05-28 12:13:42 +02:00
d871f2a06d
gnu: r-prolocdata: Update to 1.50.0.
...
* gnu/packages/bioconductor.scm (r-prolocdata): Update to 1.50.0.
Change-Id: Ia6da02c40713ba068dcc5ab01b76f021e1f7a74a
2026-05-28 12:13:42 +02:00
16c6c347f9
gnu: r-pasillabamsubset: Update to 0.50.0.
...
* gnu/packages/bioconductor.scm (r-pasillabamsubset): Update to 0.50.0.
Change-Id: I4aaf16a429c42fe87b4bbce76aa5d4af57cf0fa6
2026-05-28 12:13:42 +02:00
7a4575a86c
gnu: r-pasilla: Update to 1.40.0.
...
* gnu/packages/bioconductor.scm (r-pasilla): Update to 1.40.0.
Change-Id: I00a64ea1e76718e4f9bf6107894adf6280850dd6
2026-05-28 12:13:42 +02:00
1c3c21134b
gnu: r-msigdb: Update to 1.20.0.
...
* gnu/packages/bioconductor.scm (r-msigdb): Update to 1.20.0.
Change-Id: I144589804554930825a5a99a40ca8726c8e399dc
2026-05-28 12:13:41 +02:00
e4d202a332
gnu: r-msdata: Update to 0.52.0.
...
* gnu/packages/bioconductor.scm (r-msdata): Update to 0.52.0.
Change-Id: Ia24c626f9fe2e70c0f55ca70c866824df683e7ba
2026-05-28 12:13:41 +02:00
c986978dcc
gnu: r-minionsummarydata: Update to 1.42.0.
...
* gnu/packages/bioconductor.scm (r-minionsummarydata): Update to 1.42.0.
Change-Id: Ic9ecb643982b30312642971ee96eaa60541fa34c
2026-05-28 12:13:41 +02:00
d48200b857
gnu: r-minfidataepic: Update to 1.38.0.
...
* gnu/packages/bioconductor.scm (r-minfidataepic): Update to 1.38.0.
Change-Id: I3f83498562edb9010d4627ac934d89f85e483048
2026-05-28 12:13:41 +02:00
c2181a6895
gnu: r-minfidata: Update to 0.58.0.
...
* gnu/packages/bioconductor.scm (r-minfidata): Update to 0.58.0.
Change-Id: If375e3486dfb1ac821a24784791607d94407c4d2
2026-05-28 12:13:41 +02:00
cbb3a1e21e
gnu: r-mousegastrulationdata: Update to 1.26.0.
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* gnu/packages/bioconductor.scm (r-mousegastrulationdata): Update to 1.26.0.
Change-Id: Ie7046d19a1ce3448bceeacb38447e96e1289775e
2026-05-28 12:13:41 +02:00
9772ecc3fa
gnu: r-methylclockdata: Update to 1.20.0.
...
* gnu/packages/bioconductor.scm (r-methylclockdata): Update to 1.20.0.
Change-Id: Id3fa6b8e36cf85ddadbb5a3b0de9a05ac21420ba
2026-05-28 12:13:41 +02:00
bfc17619b3
gnu: r-methylaiddata: Update to 1.44.0.
...
* gnu/packages/bioconductor.scm (r-methylaiddata): Update to 1.44.0.
Change-Id: I9962b7337510d27b978c923b85597b7d8bda9155
2026-05-28 12:13:41 +02:00
86214dd9aa
gnu: r-macrophage: Update to 1.28.0.
...
* gnu/packages/bioconductor.scm (r-macrophage): Update to 1.28.0.
Change-Id: I4d343235bb9413310fc12cbba4d6186cd3a5b88f
2026-05-28 12:13:41 +02:00
Ricardo Wurmus