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Author SHA1 Message Date
Ricardo Wurmus
da259387c3
gnu: r-trackviewer: Fix reference. 
* gnu/packages/bioconductor.scm (r-trackviewer)[arguments]: Use correct label
for reference to origin.

Change-Id: I6c66ab468e19025ee9e912a531c8e6ca458e750b
 2025-01-20 21:38:03 +01:00
Ricardo Wurmus
332a7bb631
gnu: r-motifstack: Fix reference. 
* gnu/packages/bioconductor.scm (r-motifstack)[arguments]: Use correct label
for reference to origin.

Change-Id: Ia9b3222f15c9630bd703713111e79937126e20fd
 2025-01-20 21:38:03 +01:00
Ricardo Wurmus
105f58850b
gnu: r-reportingtools: Fix reference. 
* gnu/packages/bioconductor.scm (r-reportingtools)[arguments]: Use correct
label for reference to origin.

Change-Id: Id3b509c369bd35e12fff2fb2f4822bef4152aff1
 2025-01-20 21:38:03 +01:00
Ricardo Wurmus
46badc09bd
gnu: r-msnid: Disable vignettes. 
* gnu/packages/bioconductor.scm (r-msnid)[arguments]: Disable vignettes.

Change-Id: I47dc4cf5b6d80699d4f22b2b92382ada7ca3322a
 2024-12-03 17:00:01 +01:00
Ricardo Wurmus
2f4814e95c
gnu: r-pcaexplorer: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-pcaexplorer)[native-inputs]: Add
r-airway and r-org-hs-eg-db.

Change-Id: Id559bea8cd4308058a06158e74d3e13d7f645572
 2024-12-03 17:00:01 +01:00
Ricardo Wurmus
0b64bb6ee5
gnu: Add r-airway. 
* gnu/packages/bioconductor.scm (r-airway): New variable.

Change-Id: I521c1bf868566f80997c8ba80609fd5709a95694
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
dedc157d71
gnu: r-reportingtools: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-reportingtools)[native-inputs]: Add
r-all, r-genefilter, r-hgu95av2-db, r-org-hs-eg-db, r-org-mm-eg-db,
r-org-sc-sgd-db, r-pasilla, and r-shiny.
[properties]: Tell updater to ignore r-gsealm.

Change-Id: I9512bbc7a96c328ee05e15bc898969494dca4be0
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
f8bbfe1ea9
gnu: Add r-faahko. 
* gnu/packages/bioconductor.scm (r-faahko): New variable.

Change-Id: I70cd662bdd202ac78f5f25235fb7b9b9e7d60b37
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
9e72ac0e0c
gnu: r-xcms: Disable tests. 
* gnu/packages/bioconductor.scm (r-xcms)[arguments]: Disable tests.
[properties]: Tell updater to ignore r-faahko.
[native-inputs]: Add r-msdata.

Change-Id: I2ee167828534a4046d15d740f6f25d8eff9d589f
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
014b08cbc8
gnu: r-biodb: Disable tests. 
* gnu/packages/bioconductor.scm (r-biodb)[arguments]: Disable tests.

Change-Id: I40746a3fbfad0801058b7f34182edc358a863fa2
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
8f7196cbae
gnu: r-rcas: Add missing inputs 
* gnu/packages/bioconductor.scm (r-rcas)[native-inputs]: Add r-biocmanager.
[arguments]: Add phases 'skip-bad-tests and 'set-HOME.

Change-Id: I952ae31347776dc35cf012aaa8146f38b375957a
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
eb04b8ca59
gnu: r-affyplm: Add missing inputs and disable tests. 
* gnu/packages/bioconductor.scm (r-affyplm)[native-inputs]: Add r-affydata and
r-hgu95av2cdf.
[arguments]: Disable tests.
[properties]: Tell updater to keep extra input.

Change-Id: I05778ba527078d46e955a752a2b1af075508fdf0
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
0e1b5c7d44
gnu: Add r-hgu95av2cdf. 
* gnu/packages/bioconductor.scm (r-hgu95av2cdf): New variable.

Change-Id: I12095d54198b563a81c0d3967699016fef0f2de0
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
ee88301053
gnu: Remove r-bioconcotk. 
This package has been removed from Bioconductor and tests depend on a package
that has also been removed.

* gnu/packages/bioconductor.scm (r-bioconcotk): Remove variable.

Change-Id: If444fb7a10aea71a5339b4a488683148c84bb236
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
4b0c460719
gnu: r-bigmelon: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-bigmelon)[native-inputs]: Add
r-biocstyle and r-knitr.

Change-Id: Ie24831140e5b38d330435231d8ea976a060b4800
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
436869bdf9
gnu: r-chipexoqual: Add missing input. 
* gnu/packages/bioconductor.scm (r-chipexoqual)[native-inputs]: Add
r-chipexoqualexample.

Change-Id: I68e5ac7ce3d0c00cfc1838ef7d6b4e2e5410bb50
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
5f8f7435a2
gnu: Add r-chipexoqualexample. 
* gnu/packages/bioconductor.scm (r-chipexoqualexample): New variable.

Change-Id: I181bb085e441d056d886d4110a46668d92cd39f4
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
dcd3f1660d
gnu: r-genomicstate: Disable tests. 
* gnu/packages/bioconductor.scm (r-genomicstate)[arguments]: Disable tests.

Change-Id: Ia2a43c0b20af344e74306f88c3306c6bd40267b0
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
38e85d78ad
gnu: r-gqtlstats: Add missing input and disable tests. 
* gnu/packages/bioconductor.scm (r-gqtlstats)[native-inputs]: Add r-runit.
[arguments]: Disable tests.

Change-Id: I1b11251e88826970d16f32a1304a92f9c4923bd5
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
91b5e69b29
gnu: r-gostats: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-gostats)[native-inputs]: Add r-biocgenerics
and r-hgu95av2-db.

Change-Id: I4e5ee933154dc102efe4c034f993c959b2924671
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
169c4e612b
gnu: r-msnbase: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-msnbase)[native-inputs]: Add r-msdata,
r-rpx, r-summarizedexperiment, and r-xml.
[arguments]: Add phases 'set-HOME and 'delete-bad-tests.
[properties]: Tell updater to avoid a dependency cycle.

Change-Id: I49f6ec0c516f610785c3e79e0d4a4ad74a9ac38c
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
594d64569d
gnu: Add r-prolocdata. 
* gnu/packages/bioconductor.scm (r-prolocdata): New variable.

Change-Id: Iac4da738f793e2a746d1ef8a17251a3b27c2e599
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
6a216a8317
gnu: Add r-rpx. 
* gnu/packages/bioconductor.scm (r-rpx): New variable.

Change-Id: Id8b70a61d2657dfe5588f1cb67074d6fe5f1988c
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
1c559a129c
gnu: r-rnbeads: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-rnbeads)[native-inputs]: Add ghostscript,
r-doparallel, r-impute, r-missmethyl, r-qvalue, r-rnbeads-hg19, and
r-rtracklayer.
[inputs]: Add kentutils.
[source]: Add snippet to delete bundled binaries.
[arguments]: Add phase 'link-to-executables; disable vignettes.
[properties]: Tell updater what inputs to ignore and what to keep.
[description]: Reflow paragraph.

Change-Id: Ied81eeee2210fac43c3868d268aa20c1d0a0fb50
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
d09ff90cb6
gnu: Add r-rnbeads-hg19. 
* gnu/packages/bioconductor.scm (r-rnbeads-hg19): New variable.

Change-Id: I48ad7e0e3831edc280b8241b3d525fb73f95805f
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
ed7d8f576a
gnu: r-vsn: Add missing input. 
* gnu/packages/bioconductor.scm (r-vsn)[native-inputs]: Add r-biocstyle.

Change-Id: I12b619b0ae134132a4536b0e54e1182a55ea816c
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
e335531bbd
gnu: r-cicero-monocle3: Disable failing test. 
* gnu/packages/bioconductor.scm (r-cicero-monocle3)[arguments]: Disable
failing test.

Change-Id: I92d3878ee189403478309837214e09fe66874b69
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
1e335d0c52
gnu: r-cicero-monocle3: Update to 1.3.9-1.495ef0d. 
* gnu/packages/bioconductor.scm (r-cicero-monocle3): Update to
1.3.9-1.495ef0d.

Change-Id: Ic3939f8374818cfaaf6a77dee42710d998968021
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
cec92c060e
gnu: r-cytoml: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-cytoml)[native-inputs]: Add
r-devtools, r-flowclust, r-flowstats, and r-flowworkspacedata.
[properties]: Tell updater to keep extra inputs and ignore others.

Change-Id: I64cfc0b2b424f537b086a7f2f91e1ef15631c461
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
18c5a3b324
gnu: r-variantfiltering: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-variantfiltering)[native-inputs]: Add
r-biocstyle, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db, and
r-txdb-hsapiens-ucsc-hg19-knowngene.
[properties]: Tell updater to keep extra inputs.
[arguments]: Add phase 'delete-bad-tests; disable vignettes.

Change-Id: I23e78f1bd49b348719c6e03a116228b5657ae379
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
8dd751f114
gnu: Add r-sift-hsapiens-dbsnp137. 
* gnu/packages/bioconductor.scm (r-sift-hsapiens-dbsnp137): New variable.

Change-Id: Ib71a322d3ed0e563f01620e04aca844b290ecc3b
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
a9dc352e79
gnu: Add r-polyphen-hsapiens-dbsnp131. 
* gnu/packages/bioconductor.scm (r-polyphen-hsapiens-dbsnp131): New variable.

Change-Id: I65ca94c82b3c9c8d9f0faf6f31a04d52e935f127
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
8417b0f27a
gnu: Add r-mafdb-1kgenomes-phase1-hs37d5. 
* gnu/packages/bioconductor.scm (r-mafdb-1kgenomes-phase1-hs37d5): New variable.

Change-Id: Id8827d4a5d788ef2bc4d258048572e697e61b4d2
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
f1d03188a6
gnu: r-mmuphin: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-mmuphin)[native-inputs]: Add r-testthat.

Change-Id: I24c838fb0c474cda16a49b48c469d8dfd7194e10
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
12968c7675
gnu: r-lefser: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-lefser)[native-inputs]: Add r-mia and
r-withr; remove r-testthat.
[properties]: Tell updater to keep r-mia.

Change-Id: I791e6626a3d000f12a149cdc87979389aee886f0
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
e90cc282f1
gnu: r-sesamedata: Disable tests. 
* gnu/packages/bioconductor.scm (r-sesamedata)[arguments]: Disable tests.
[properties]: Tell updater to ignore r-sesame.

Change-Id: I42e3a2d83963e79a21db70f4c1f8ddf92107943f
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
d8ad680471
gnu: r-abaenrichment: Add missing input. 
* gnu/packages/bioconductor.scm (r-abaenrichment)[native-inputs]: Add
r-testthat.

Change-Id: I3a5a43d3a1b9f7ff81c589efc0a0aade1e666553
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
8dcf48ab94
gnu: r-mosdef: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-mosdef)[native-inputs]: Add r-macrophage
and r-org-hs-eg-db.
[properties]: Tell updater to ignore r-pcaexplorer.

Change-Id: I27258d7119cbe5de244c2db6d91ec8c5b0bd0975
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
587ec117f4
gnu: r-diffbind: Add missing inputs and skip vignettes. 
* gnu/packages/bioconductor.scm (r-diffbind)[native-inputs]: Add
r-biocstyle and r-xtable.
[properties]: Tell updater to keep r-biocstyle.
[arguments]: Skip building vignettes.

Change-Id: I0a8515301c949c99d890816f37b7da82181b094c
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
3c2964c923
gnu: r-quasr: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-quasr)[native-inputs]: Add
r-genomicalignments and r-rhisat2.
[properties]: Tell updater to keep r-rhisat2.

Change-Id: I304824e27d39f76a1de2aeb1e77c32f5d6faf70e
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
8f9b6c3137
gnu: r-bgeecall: Add missing inputs and disable tests. 
* gnu/packages/bioconductor.scm (r-bgeecall)[native-inputs]: Add
r-annotationhub and r-httr.
[arguments]: Disable tests.

Change-Id: Ic2ea9e81075c70501d53df556ab9548d46ac24ae
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
17c1e8ef1b
gnu: r-milor: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-milor)[native-inputs]: Add r-mass,
r-mvtnorm, r-scater, and r-scran.

Change-Id: Icdfa0e9a89a21ace0d994800a00b968a803d41ea
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
84c3b169b9
gnu: r-conos: Add missing input. 
* gnu/packages/bioconductor.scm (r-conos)[native-inputs]: Add r-pagoda2.

Change-Id: I9b12a3c3ba727d7e6101fa2566c42c0a6858d601
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
3e72995a28
gnu: r-maaslin2: Add missing input. 
* gnu/packages/bioconductor.scm (r-maaslin2)[native-inputs]: Add r-testthat.

Change-Id: I044a9bf1f1e53f0988760f84b822beb6b6779291
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
324ea9c11d
gnu: r-simona: Add missing input. 
* gnu/packages/bioconductor.scm (r-simona)[native-inputs]: Add r-go-db,
r-org-hs-eg-db, and r-proxyc.
[properties]: Tell the updater to keep these inputs.

Change-Id: I253374be87eda5c844cda1937895024b8c609d1b
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
23251014aa
gnu: r-gviz: Add missing input. 
* gnu/packages/bioconductor.scm (r-gviz)[native-inputs]: Add
r-bsgenome-hsapiens-ucsc-hg19.

Change-Id: I2be88201e9219cc55be39217592483f1324e456f
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
8c6114b920
gnu: r-xbseq: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-xbseq)[native-inputs]: Add r-testthat.

Change-Id: I7b8eb1c7a7ffcac81b9ead33969b1e57d99a68f3
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
8762488487
gnu: r-numbat: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-numbat)[native-inputs]: Add r-testthat.

Change-Id: I3a3db09ba1c69c27a9bc6a67be9346098710fde3
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
d2d2b4d4cb
gnu: r-flowstats: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-flowstats)[native-inputs]: Add
r-devtools, r-ggcyto, r-ggridges, r-gridextra, r-opencyto, r-scales, and
r-xtable.

Change-Id: I5f2621939b33ece9339f0bbfcbeba2850acf3376
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
f0480849b8
gnu: r-ggcyto: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-ggcyto)[native-inputs]: Add
r-flowworkspacedata, r-opencyto, and r-vdiffr.
[properties]: Tell updater to add r-flowworkspacedata and ignore r-flowstats.

Change-Id: If281e4b930f99e18ccbd07fed7028ba932496c3c
 2024-12-03 16:59:56 +01:00