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8773 Commits

Author SHA1 Message Date
Ricardo Wurmus
55e96e1eac gnu: r-sparsearray: Update to 1.10.10. 
* gnu/packages/bioconductor.scm (r-sparsearray): Update to 1.10.10.

Change-Id: I2264aeaf24c41263c7f89b8e78f78746d2c3e1dd
 2026-04-02 07:37:27 +02:00
Ricardo Wurmus
ab9cf79f94 gnu: r-multiassayexperiment: Update to 1.36.2. 
* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.36.2.

Change-Id: I9141df279c08861fa1a0169155af36b86e6b7f4b
 2026-04-02 07:37:27 +02:00
Ricardo Wurmus
accbae6d83 gnu: r-animalcules: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-animalcules)[arguments]: Remove phase
'skip-bad-tests; specify #:skipped-tests instead.

Change-Id: Ie5f3befab21d5dae3e006aa06116f0d6039d4d9b
 2026-04-02 07:37:26 +02:00
Ricardo Wurmus
240cf8850a gnu: r-annotationhubdata: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-annotationhubdata)[arguments]: Remove phase
'disable-bad-tests; specify #:skipped-tests instead.

Change-Id: I9e2dda16fcf59db72d41048ad5ca9471e3652994
 2026-04-02 07:37:26 +02:00
Ricardo Wurmus
17526fa4ed gnu: r-biocmake: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-biocmake)[arguments]: Remove phase
'disable-bad-tests; specify #:skipped-tests instead.

Change-Id: I53f6872b261fa004967b0a332a8c3c461d010a39
 2026-04-02 07:37:26 +02:00
Ricardo Wurmus
17864135c3 gnu: r-coregx: Enable all tests. 
* gnu/packages/bioconductor.scm (r-coregx)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: I84c99eb508a02bc86b23c9567ffc4af375987c44
 2026-04-02 07:37:26 +02:00
Ricardo Wurmus
31f5309cad gnu: r-metabocoreutils: Remove obsolete build phase. 
* gnu/packages/bioconductor.scm (r-metabocoreutils)[arguments]: Remove phase
'testthat-compatibility.

Change-Id: Id36f100ae3ed9ccd7c5841f61e11b165164f6d51
 2026-04-02 07:37:26 +02:00
Ricardo Wurmus
873620fbbd gnu: r-phyloseq: Remove obsolete build phase. 
* gnu/packages/bioconductor.scm (r-phyloseq)[arguments]: Remove phase
'testthat-compatibility.

Change-Id: I1fad7dbde4c97113553e613a0aa794c249a428a6
 2026-04-02 07:37:25 +02:00
Ricardo Wurmus
ed4dba483a gnu: r-ballgown: Remove obsolete build phase. 
* gnu/packages/bioconductor.scm (r-ballgown)[arguments]: Remove phase
'testthat-compatibility.

Change-Id: I8e07774d6e3580356fab6d690935d22f1fa6b761
 2026-04-02 07:37:25 +02:00
Ricardo Wurmus
7969f5281f gnu: r-isva: Update to 1.10. 
* gnu/packages/bioconductor.scm (r-isva): Update to 1.10.

Change-Id: I40aee88fee31b47d18526f5ce68fee0b76ab22c7
 2026-04-02 07:37:21 +02:00
Ricardo Wurmus
02e7f5bd3c gnu: r-gwascat: Update to 2.42.1. 
* gnu/packages/bioconductor.scm (r-gwascat): Update to 2.42.1.
[propagated-inputs]: Remove r-snpstats.

Change-Id: I169b53b7320b89bfd24e19f745752d003e7eba38
 2026-04-02 07:37:20 +02:00
Ricardo Wurmus
7ff3cecc72 gnu: r-scater: Update to 1.38.1. 
* gnu/packages/bioconductor.scm (r-scater): Update to 1.38.1.

Change-Id: I7ccc3a0c9b5377b4196e7806cba863c691895fa0
 2026-04-02 07:37:20 +02:00
Ricardo Wurmus
cadd11f0cd gnu: r-beadarray: Update to 2.60.1. 
* gnu/packages/bioconductor.scm (r-beadarray): Update to 2.60.1.

Change-Id: Ie6b49f29346bc7de56484fcf273ff089868d8736
 2026-04-02 07:37:20 +02:00
Ricardo Wurmus
e128f915f2 gnu: r-biocviews: Update to 1.78.1. 
* gnu/packages/bioconductor.scm (r-biocviews): Update to 1.78.1.

Change-Id: I660d44487d25d7c19ad6cff239024bc5e829599c
 2026-04-02 07:37:20 +02:00
Ricardo Wurmus
8b4eaa339a gnu: r-variancepartition: Update to 1.40.2. 
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.40.2.

Change-Id: Iea9427a9df269d1260b8fdf17a25518865fcb2da
 2026-04-02 07:37:20 +02:00
Ricardo Wurmus
69a93344fa gnu: r-cicero: Update to 1.28.3. 
* gnu/packages/bioconductor.scm (r-cicero): Update to 1.28.3.

Change-Id: Ia93dd658d5dc9d3ef82702adcfb873b79a9151f0
 2026-04-02 07:37:20 +02:00
Ricardo Wurmus
83651e17f9 gnu: r-ggtree: Update to 4.0.5. 
* gnu/packages/bioconductor.scm (r-ggtree): Update to 4.0.5.

Change-Id: Id4ae9e94369b63c8e48c760d2c44a101ef413441
 2026-04-02 07:37:20 +02:00
Ricardo Wurmus
dc668775f9 gnu: r-tcgautils: Update to 1.30.3. 
* gnu/packages/bioconductor.scm (r-tcgautils): Update to 1.30.3.

Change-Id: I755d9857120c38f153696f55368d893cac47baa8
 2026-04-02 07:37:20 +02:00
Ricardo Wurmus
057667a9f9 gnu: r-mmuphin: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-mmuphin): Update to 1.24.0.

Change-Id: I6b966eb1c8637e31beffe6af6e44cbff2882ca96
 2026-04-02 07:37:19 +02:00
Ricardo Wurmus
e46379066d gnu: r-maaslin2: Update to 1.24.1. 
* gnu/packages/bioconductor.scm (r-maaslin2): Update to 1.24.1.

Change-Id: I28de568df289efcadf6afe01badfd0c09f89cb37
 2026-04-02 07:37:19 +02:00
Ricardo Wurmus
f5483a2145 gnu: r-gsva: Update to 2.4.8. 
* gnu/packages/bioconductor.scm (r-gsva): Update to 2.4.8.

Change-Id: Id9f7f1bb7599d9350e42c2e511e447fad1193501
 2026-04-02 07:37:19 +02:00
Ricardo Wurmus
040e86256b gnu: r-arrayqualitymetrics: Update to 3.66.0. 
* gnu/packages/bioconductor.scm (r-arrayqualitymetrics): Update to 3.66.0.
[native-inputs]: Add r-biocstyle.

Change-Id: Ia1f0ac427117dbc01ce182190ff749dc578a54ea
 2026-04-02 07:37:19 +02:00
Ricardo Wurmus
86ea888ceb gnu: r-biomformat: Update to 1.38.3. 
* gnu/packages/bioconductor.scm (r-biomformat): Update to 1.38.3.
[arguments]: Remove phase 'testthat-compatibility.
[propagated-inputs]: Remove r-plyr.

Change-Id: I67e973b606f8135b0c4ef0dbf2d29229d87522a4
 2026-04-02 07:37:19 +02:00
Ricardo Wurmus
c0ca73afdd gnu: r-biomart: Update to 2.66.2. 
* gnu/packages/bioconductor.scm (r-biomart): Update to 2.66.2.

Change-Id: I42fcda6dd4d5d59d65c8c111f7dbd7878e2bcadb
 2026-04-02 07:37:13 +02:00
Ricardo Wurmus
ebbd626dd2 gnu: r-activedriverwgs: Update to 1.2.1. 
* gnu/packages/bioconductor.scm (r-activedriverwgs): Update to 1.2.1.
[propagated-inputs]: Remove r-bsgenome-hsapiens-ucsc-hg19, r-bsgenome-hsapiens-ucsc-hg38,
r-bsgenome-mmusculus-ucsc-mm9, and r-bsgenome-mmusculus-ucsc-mm10.
[native-inputs]: Add r-bsgenome-hsapiens-ucsc-hg19.

Change-Id: I95a0dca9fca9c818d1c100cd1d6279338e28bc71
 2026-04-02 07:37:11 +02:00
Ricardo Wurmus
1bac2be5e3 gnu: r-systempiperdata: Update to 2.14.6. 
* gnu/packages/bioconductor.scm (r-systempiperdata): Update to 2.14.6.

Change-Id: I8fae8955722d4691477042489c051f4c607ffee4
 2026-04-02 07:37:10 +02:00
Ricardo Wurmus
d563d8c242 gnu: r-rliger: Update to 2.2.1. 
* gnu/packages/cran.scm (r-rliger, r-liger): Move variable definitions from here...
* gnu/packages/bioconductor.scm (r-rliger, r-liger): ...to here; update to 2.2.1.
[source]: Update source URL; remove obsolete snippet.
[arguments]: Remove phases 'strip-jar-timestamps and 'build-java-part.
[native-inputs]: Remove icedtea, optimizer-src, unzip, and zip; add
r-circlize, r-complexheatmap, r-testthat, and r-viridis.
[propagated-inputs]: Remove r-cowplot, r-dosnow, r-fnn, r-foreach, r-ggrepel,
r-hmisc, r-ica, r-irlba, r-mclust, r-plyr, r-rann-l1, r-riverplot, and
r-rtsne; add r-cli, r-delayedarray, r-hdf5array, r-hdf5r, r-leidenalg, r-lifecycle,
r-magrittr, r-rann, r-rcppplanc, r-rcppprogress, r-rlang, r-s4vectors,
r-scales, and r-uwot.

Change-Id: I35bcdd94954f6fdf5aa641f9756c65a0efe1008e
 2026-04-02 07:37:08 +02:00
Ricardo Wurmus
9aee49d65d gnu: r-phyloseq: Update to 1.54.2. 
* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.54.2.

Change-Id: Ide709c5d2e6186c9d816c65acbe3786917b549b4
 2026-04-02 07:37:04 +02:00
Ricardo Wurmus
e360849ac5 gnu: r-sparsearray: Update to 1.10.9. 
* gnu/packages/bioconductor.scm (r-sparsearray): Update to 1.10.9.

Change-Id: I9ca97aae122e788997d3f74872c1df1229be4bca
 2026-04-02 07:37:04 +02:00
Ricardo Wurmus
2184edcc66 gnu: r-enrichplot: Update to 1.30.5. 
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.30.5.

Change-Id: I5e3ee050327a5ea536e46a8136f2349e4440aefe
 2026-04-02 07:37:04 +02:00
Ricardo Wurmus
f767cfc824 gnu: r-systempiper: Update to 2.16.4. 
* gnu/packages/bioconductor.scm (r-systempiper): Update to 2.16.4.

Change-Id: Iac7cf251a58614b71e3d2c82e52a7180f44a55a8
 2026-04-02 07:37:04 +02:00
Ricardo Wurmus
1c564df9fe gnu: r-gsva: Update to 2.4.7. 
* gnu/packages/bioconductor.scm (r-gsva): Update to 2.4.7.

Change-Id: I0b8d1dbf0d5563463b7af9ecf3ac5617a19c679e
 2026-04-02 07:37:03 +02:00
Ricardo Wurmus
17b3d6f8b5 gnu: r-anndatar: Update to 1.0.2. 
* gnu/packages/bioconductor.scm (r-anndatar): Update to 1.0.2.

Change-Id: Ib9e3b5a62fad67efa950b8ab50ac7ee5645f5f85
 2026-04-02 07:37:03 +02:00
Ricardo Wurmus
e36dc2ae2a gnu: r-microbiomestat: Update to 1.4. 
* gnu/packages/bioconductor.scm (r-microbiomestat): Update to 1.4.
[propagated-inputs]: Remove r-bbmisc, r-lhs, r-mlr, r-mlrmbo, r-paramhelpers, and
r-smoof; add r-bbotk, r-mlr3, r-mlr3mbo, and r-paradox.

Change-Id: Idc8342d33e47af8a4f9b0d104bce410dfca9417d
 2026-04-02 07:37:00 +02:00
Ricardo Wurmus
de1af38bce gnu: r-codedepends: Update to 0.6.7. 
* gnu/packages/bioconductor.scm (r-codedepends): Update to 0.6.7.

Change-Id: I9d35a67f25515137d58bc45f7dc8468f99f56395
 2026-04-02 07:37:00 +02:00
Ricardo Wurmus
f41346ad63 gnu: r-xllim: Update to 2.3.1. 
* gnu/packages/bioconductor.scm (r-xllim): Update to 2.3.1.

Change-Id: I0881a5df658b4ea7c6e76c5f17ca6f0c98da1753
 2026-04-02 07:36:59 +02:00
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