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8737 Commits

Author SHA1 Message Date
Ludovic Courtès
1ae20f03f4 gnu: Reference the inherited inputs values. 
This commit was made by running this command:

  sed -e's/modify-inputs (package-\([a-z-]*\)inputs [a-zA-Z0-9-]\+)/modify-inputs \1inputs/g' -i gnu/packages/*.scm

… and then reverting individual hunks where the change would trigger unbound
variable warnings or other issues (such as ‘native-inputs’ is bound in the
body of the ‘inputs’ field, but it refers to the ‘native-inputs’ thunk defined
just above).

Change-Id: I6d94819f2809313fa1fbefc61897502ee7d66fab
 2026-03-20 13:27:16 +01:00
Ricardo Wurmus
93cf0c54e3 gnu: r-phyloseq: Update to 1.54.1. 
* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.54.1.

Change-Id: Iea5f1d1e11c729e3624d83be95650ab501a7bfed
 2026-03-07 11:57:38 +01:00
Ricardo Wurmus
55637c3886 gnu: r-gsva: Update to 2.4.6. 
* gnu/packages/bioconductor.scm (r-gsva): Update to 2.4.6.

Change-Id: I55231b2e2db06e3d1612dbcc7e23075ca92b91c3
 2026-03-07 11:57:37 +01:00
Laurent Gatto
39258e011e gnu: Add r-scpdata. 
* gnu/packages/bioconductor.scm (r-scpdata): New variable.

Change-Id: Ia1dbede5d8b29bc771b16e8efa08880d8a5c2ab6
 2026-03-07 11:57:36 +01:00
Laurent Gatto
b63a857c57 gnu: Add r-scp. 
* gnu/packages/bioconductor.scm (r-scp): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: Id0ae426756e3ad77a120069ce6ec6f1841437bcc
 2026-03-07 11:57:36 +01:00
Laurent Gatto
eaab307c5c gnu: Add r-msdatahub. 
* gnu/packages/bioconductor.scm (r-msdatahub): New variable.

Change-Id: I63977e3c950b122c014108683e84aefa51972064
 2026-03-07 11:57:36 +01:00
Ricardo Wurmus
0bd81e3871 gnu: r-scran: Update to 1.38.1. 
* gnu/packages/bioconductor.scm (r-scran): Update to 1.38.1.

Change-Id: If3516e5464c47a7402428f01b848ca290c4e9612
 2026-03-07 11:57:34 +01:00
Ricardo Wurmus
cb9cd82cda gnu: r-scdblfinder: Update to 1.24.10. 
* gnu/packages/bioconductor.scm (r-scdblfinder): Update to 1.24.10.

Change-Id: Id7d60f86558fb0998b866886759544928d268e35
 2026-03-07 11:57:34 +01:00
Ricardo Wurmus
2c1330d185 gnu: r-mutationalpatterns: Update to 3.20.1. 
* gnu/packages/bioconductor.scm (r-mutationalpatterns): Update to 3.20.1.

Change-Id: I7f6dc949b0961b5d07904e590d9729bca042a195
 2026-03-07 11:57:34 +01:00
Ricardo Wurmus
a4d999679d gnu: r-gsva: Update to 2.4.5. 
* gnu/packages/bioconductor.scm (r-gsva): Update to 2.4.5.

Change-Id: I34e86dc4ef74c977488209fa42afafb889ac43de
 2026-03-07 11:57:34 +01:00
Ricardo Wurmus
f68c9af97e gnu: r-systempiperdata: Update to 2.14.5. 
* gnu/packages/bioconductor.scm (r-systempiperdata): Update to 2.14.5.

Change-Id: I619ea050473642025b458d76b0e68e65e2b3ba08
 2026-03-07 11:57:34 +01:00
Ricardo Wurmus
2fcfbdf8fc gnu: r-illuminahumanmethylationepicv2manifest: Update to 1.0.1. 
* gnu/packages/bioconductor.scm (r-illuminahumanmethylationepicv2manifest): Update to 1.0.1.

Change-Id: I237bfef2be1f9be21fbc93de5418a6874f44b8e9
 2026-03-07 11:57:34 +01:00
Ricardo Wurmus
28c5a19bbf gnu: r-illuminahumanmethylationepicv2anno-20a1-hg38: Update to 1.0.1. 
* gnu/packages/bioconductor.scm (r-illuminahumanmethylationepicv2anno-20a1-hg38): Update to 1.0.1.

Change-Id: Icc6a9069665b60c5bc76ad47412d45d04e337b09
 2026-03-07 11:57:34 +01:00
Ricardo Wurmus
5022deef41 gnu: r-survcomp: Update to 1.60.1. 
* gnu/packages/bioconductor.scm (r-survcomp): Update to 1.60.1.
[native-inputs]: Add r-biobase, r-biocmanager, and r-xtable.

Change-Id: Ia31f7785ac5510f78b68ca080e144fbd4db7e727
 2026-03-07 11:57:34 +01:00
Ricardo Wurmus
c87d544fab gnu: r-biomart: Update to 2.66.1. 
* gnu/packages/bioconductor.scm (r-biomart): Update to 2.66.1.

Change-Id: I7b44de4ba1bb980ca4c6de8b774f8652bbc3df17
 2026-03-07 11:57:24 +01:00
Ricardo Wurmus
0a9c3f1338 gnu: r-animalcules: Update to 1.26.1. 
* gnu/packages/bioconductor.scm (r-animalcules): Update to 1.26.1.

Change-Id: I57738b1fec6dc5b393a6f26fc87cf9e0ea1f6f76
 2026-03-07 11:57:24 +01:00
Ricardo Wurmus
34df487128 gnu: r-cytoml: Update list of ignored native inputs. 
* gnu/packages/bioconductor.scm (r-cytoml)[properties]: Update
updater-extra-native-inputs.

Change-Id: Iac49c82eb7321c1488ed4737794fa3dee1197215
 2026-03-07 11:57:24 +01:00
Ricardo Wurmus
eabee0d297 gnu: r-msnid: Update to 1.44.2. 
* gnu/packages/bioconductor.scm (r-msnid): Update to 1.44.2.

Change-Id: I72fb5b0040742d30980f507d3fbe69a5f82c0459
 2026-03-07 11:57:18 +01:00
Ricardo Wurmus
8ee03aaf64 gnu: r-nebulosa: Update to 1.20.1. 
* gnu/packages/bioconductor.scm (r-nebulosa): Update to 1.20.1.

Change-Id: I2f37d3e2396ab5dd0d3ff8e6ff8f62d94cafa489
 2026-03-07 11:57:18 +01:00
Ricardo Wurmus
174b346917 gnu: r-ggpicrust2: Update to 2.5.10. 
* gnu/packages/bioconductor.scm (r-ggpicrust2): Update to 2.5.10.
[properties]: Record updater-extra-native-inputs.
[native-inputs]: Remove r-devtools, r-ggvenndiagram, r-mockery, and r-upsetr;
add r-aldex2, r-ggally, r-knitr, and r-limma.

Change-Id: I8c674943eba6559c0b4a2364445fc63e2b7d6828
 2026-03-07 11:57:15 +01:00
Ricardo Wurmus
e817a66e7b gnu: r-anndatar: Update to 1.0.1. 
anndataR is now on Bioconductor.

* gnu/packages/bioinformatics.scm (r-anndatar): Move from here...
* gnu/packages/bioconductor.scm (r-anndatar): ...to here; update to 1.0.1.
[properties]: Remove updater-extra-native-inputs.
[inputs]: Add python-wrapper and python-anndata.
[native-inputs]: Add r-processx, r-s4vectors, r-seurat, r-spelling, and
r-withr; remove r-vctrs.
[propagated-inputs]: Add r-cli, r-lifecycle, r-purrr, r-reticulate, and
r-rlang.

Change-Id: I2410f00b33451c60d8b1657ac30a6c1b014e260d
 2026-02-20 14:15:00 +01:00
Ricardo Wurmus
0f6d6c36d3 gnu: r-biobroom: Replace call of deprecated procedure. 
* gnu/packages/bioconductor.scm (r-biobroom)[arguments]: Add phase
'dplyr-compatibility.
[propagated-inputs]: Add r-tibble.

Change-Id: I6cfb08e430c55b7ae910d87b54c38b6c9192b848
 2026-02-14 12:28:11 +01:00
Ricardo Wurmus
c8dc645fbd gnu: r-tximeta: Update to 1.28.3. 
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.28.3.

Change-Id: Idfae2347d58ba6c8b58c8d9a6b84bd36e768cf53
 2026-02-14 10:18:25 +01:00
Ricardo Wurmus
458277137b gnu: r-rgreat: Update to 2.12.2. 
* gnu/packages/bioconductor.scm (r-rgreat): Update to 2.12.2.

Change-Id: Id2b7fe1fbe014eb7374ca2655d9a29b7f82966e6
 2026-02-14 10:18:25 +01:00
Ricardo Wurmus
94b82f7c44 gnu: r-pcatools: Update to 2.22.4. 
* gnu/packages/bioconductor.scm (r-pcatools): Update to 2.22.4.
[propagated-inputs]: Add r-assorthead.

Change-Id: I40426c8a05626d73e7e0bbe05cf66c949e464d6a
 2026-02-14 10:18:25 +01:00
Ricardo Wurmus
c4b88e5e25 gnu: r-biocpkgtools: Update to 1.28.3. 
* gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.28.3.

Change-Id: Ic2481c53616d8700ad96ae9e2d37bcf717051e65
 2026-02-14 10:18:25 +01:00
Ricardo Wurmus
2b62bf4f2e gnu: r-gtrellis: Update to 1.42.1. 
* gnu/packages/bioconductor.scm (r-gtrellis): Update to 1.42.1.

Change-Id: I261281d68121866b814e54cb18b0dc7f19c5d7f6
 2026-02-14 10:18:24 +01:00
Ricardo Wurmus
1852f5e39d gnu: r-enrichedheatmap: Update to 1.40.1. 
* gnu/packages/bioconductor.scm (r-enrichedheatmap): Update to 1.40.1.

Change-Id: I981995b30c57168e999079d22154be3720181dc6
 2026-02-14 10:18:24 +01:00
Ricardo Wurmus
f1a3a0999a gnu: r-ggtreeextra: Update to 1.20.1. 
* gnu/packages/bioconductor.scm (r-ggtreeextra): Update to 1.20.1.
[propagated-inputs]: Add r-yulab-utils.

Change-Id: I527b401b1acec94ecedf40e28c6c24df25c6be76
 2026-02-14 10:18:24 +01:00
Ricardo Wurmus
69ad88eb91 gnu: r-vsn: Update to 3.78.1. 
* gnu/packages/bioconductor.scm (r-vsn): Update to 3.78.1.

Change-Id: I452833ad630d094227e342f38dece2aeb70bca37
 2026-02-14 10:18:24 +01:00
Ricardo Wurmus
9fc268a8ea gnu: r-scds: Update to 1.26.1. 
* gnu/packages/bioconductor.scm (r-scds): Update to 1.26.1.

Change-Id: Iab8249219e3819b1450ee1cc5c325d935fd36f9a
 2026-02-14 10:18:24 +01:00
Ricardo Wurmus
5200b1bed5 gnu: r-simplifyenrichment: Update to 2.4.1. 
* gnu/packages/bioconductor.scm (r-simplifyenrichment): Update to 2.4.1.

Change-Id: Ic3c156ab1e6384e5a18ca5dce957b73098cb7345
 2026-02-14 10:18:24 +01:00
Ricardo Wurmus
5782124bb4 gnu: r-simona: Update to 1.8.1. 
* gnu/packages/bioconductor.scm (r-simona): Update to 1.8.1.

Change-Id: I0160004aadf58174b0f9ec023648164cc532f231
 2026-02-14 10:18:24 +01:00
Ricardo Wurmus
8c886b250a gnu: r-seqarray: Update to 1.50.1. 
* gnu/packages/bioconductor.scm (r-seqarray): Update to 1.50.1.

Change-Id: I36d5c3947cdbb531e46d0a1211ce34bdb5bd4a4b
 2026-02-14 10:18:24 +01:00
Ricardo Wurmus
f24609ef4c gnu: r-scannotatr: Update to 1.16.1. 
* gnu/packages/bioconductor.scm (r-scannotatr): Update to 1.16.1.

Change-Id: I644db2d421bff2d8c734eb6029572e9875126fc2
 2026-02-14 10:18:24 +01:00
Ricardo Wurmus
5ecec28dd7 gnu: r-msnid: Update to 1.44.1. 
* gnu/packages/bioconductor.scm (r-msnid): Update to 1.44.1.

Change-Id: I5c4c3b49b7f54f42307354a72decaf3ccc5522f8
 2026-02-14 10:18:24 +01:00
Ricardo Wurmus
a5b56cd6e4 gnu: r-enmix: Update to 1.46.1. 
* gnu/packages/bioconductor.scm (r-enmix): Update to 1.46.1.

Change-Id: Ifbb853fc68b3c1b887c8f8a9d3d9b7932968b7c2
 2026-02-14 10:18:24 +01:00
Ricardo Wurmus
972a988cb5 gnu: r-complexheatmap: Update to 2.26.1. 
* gnu/packages/bioconductor.scm (r-complexheatmap): Update to 2.26.1.

Change-Id: Ia3f002b8ab76bd4a49790396ef7825db48c2acc6
 2026-02-14 10:18:24 +01:00
Ricardo Wurmus
a6d16216e2 gnu: r-bambu: Update to 3.12.1. 
* gnu/packages/bioconductor.scm (r-bambu): Update to 3.12.1.

Change-Id: I04b82f0693afe8805dda6b039150c2ab0c6d9be3
 2026-02-14 10:18:24 +01:00
Ricardo Wurmus
ed5af8efe4 gnu: r-anvil: Update to 1.22.5. 
* gnu/packages/bioconductor.scm (r-anvil): Update to 1.22.5.

Change-Id: I26c35de22804a20ca4155777305004f3b06120c2
 2026-02-14 10:18:23 +01:00
Ricardo Wurmus
446a5a0bc5 gnu: r-systempiperdata: Update to 2.14.4. 
* gnu/packages/bioconductor.scm (r-systempiperdata): Update to 2.14.4.

Change-Id: Id543f3da8de708bbb29dd035ce5e19e38fc52634
 2026-02-14 10:18:23 +01:00
Ricardo Wurmus
adee6ce457 gnu: r-wgcna: Update to 1.74. 
* gnu/packages/bioconductor.scm (r-wgcna): Update to 1.74.
[propagated-inputs]: Remove r-annotationdbi and r-go-db.

Change-Id: I886508cc01aabff7a107b7f6e606e4984a5135e6
 2026-02-14 10:18:17 +01:00
Ricardo Wurmus
d5cae29268 gnu: r-scistreer: Update to 1.2.1. 
* gnu/packages/bioconductor.scm (r-scistreer): Update to 1.2.1.

Change-Id: I6a00643cdc0a8bedae568de38ec3d34c1ec770e1
 2026-02-14 10:18:17 +01:00
Ricardo Wurmus
6dd51a46bf gnu: r-numbat: Update to 1.5.2. 
* gnu/packages/bioconductor.scm (r-numbat): Update to 1.5.2.
[propagated-inputs]: Remove r-pryr.

Change-Id: I72614a7dc7033174a6cdae8c84265544dd265d28
 2026-02-14 10:18:17 +01:00
Ricardo Wurmus
1508dd68d1 gnu: r-pcatools: Update to 2.22.1. 
* gnu/packages/bioconductor.scm (r-pcatools): Update to 2.22.1.

Change-Id: Id61b5bd7a63d18652d62235d830723e8654b8488
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
 2026-01-25 21:30:23 +01:00
Ricardo Wurmus
e90b7a88b0 gnu: r-flames: Update to 2.4.2. 
* gnu/packages/bioconductor.scm (r-flames): Update to 2.4.2.

Change-Id: Id6bb3f280dcf8fdd595b2d8e9e6b1b21ebe13df7
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
 2026-01-25 21:30:22 +01:00
Ricardo Wurmus
ed1ea054c5 gnu: r-netgsa: Update to 4.0.7. 
* gnu/packages/bioconductor.scm (r-netgsa): Update to 4.0.7.
[propagated-inputs]: Remove r-org-hs-eg-db.

Change-Id: I3e40676dc5e4fdecf988c003d2dd2f338526e317
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
 2026-01-25 21:29:37 +01:00
Ricardo Wurmus
d7d5770b54 gnu: Add r-rarr. 
* gnu/packages/bioconductor.scm (r-rarr): New variable.

Change-Id: Ia302b53f601295663246e66b9587c427a6ffd926
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
 2026-01-25 21:29:27 +01:00
Ricardo Wurmus
4847b6e749 gnu: r-msnid: Disable one test. 
* gnu/packages/bioconductor.scm (r-msnid)[arguments]: Add phase
'disable-bad-tests.

Change-Id: I188a069530c1aa7da663b438a079b736866e8bb5
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
 2026-01-25 21:29:25 +01:00
Ricardo Wurmus
723d092168 gnu: r-tximeta: Update to 1.28.1. 
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.28.1.

Change-Id: Id10c5bdd793e8efcb051bce989fb06519bf0e739
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
 2026-01-25 21:29:25 +01:00