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2024-12-03gnu: r-xbseq: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-xbseq)[native-inputs]: Add r-testthat. Change-Id: I7b8eb1c7a7ffcac81b9ead33969b1e57d99a68f3
2024-12-03gnu: r-numbat: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-numbat)[native-inputs]: Add r-testthat. Change-Id: I3a3db09ba1c69c27a9bc6a67be9346098710fde3
2024-12-03gnu: Remove r-numbat.Ricardo Wurmus
This is a duplicate of a package in (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-numbat): Delete variable. Change-Id: Ic1f5d9779a594432a0dd8bd0be9059423a2f5b34
2024-12-03gnu: r-spectre: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-spectre)[arguments]: Disable tests. Change-Id: I7978b05d0c1c2de3ada6b1b490ae36b28171f17c
2024-12-03gnu: r-gchain: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gchain)[native-inputs]: Add r-pwalign and r-testthat. [arguments]: Add phase 'skip-bad-tests. Change-Id: Ia11c6e50e0d2886762ec551df3e5d73ef98547f8
2024-12-03gnu: r-flowstats: Add missing inputs.Ricardo Wurmus
* 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
2024-12-03gnu: r-ggcyto: Add missing inputs.Ricardo Wurmus
* 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
2024-12-03gnu: r-opencyto: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-opencyto)[native-inputs]: Add r-flowworkspacedata. [properties]: Tell updater to add r-flowworkspacedata. Change-Id: Ife446af466fb4be221f9fdaba53c84bbe80dec86
2024-12-03gnu: Add r-flowworkspacedata.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-flowworkspacedata): New variable. Change-Id: Ie2add925d3fcd3540bc3885427982fb0cee5a146
2024-12-03gnu: r-bodymaprat: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bodymaprat)[arguments]: Disable tests. Change-Id: Icaa4428e4890a898c35444ae1bedd4258527ee37
2024-12-03gnu: Add r-methylaiddata.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-methylaiddata): New variable. Change-Id: I7711a18b6a5d8e7a431d6a3c713bb3fa26a12e96
2024-12-03gnu: r-methylaid: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-methylaid)[native-inputs]: Add r-geoquery, r-minfidata, and r-minfidataepic. [properties]: Tell updater to ignore r-methylaiddata. Change-Id: I11b0e7e76e5ccf4768165634aae86b45606abe40
2024-12-03gnu: Add r-minfidataepic.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-minfidataepic): New variable. Change-Id: Icce76beb123c0ad45bac09ec88a259b1b271141f
2024-12-03gnu: Add r-illuminahumanmethylationepicanno-ilm10b2-hg19.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-illuminahumanmethylationepicanno-ilm10b2-hg19): New variable. Change-Id: I110d1b71fa45bc1c5e81399de0a89aab99d45031
2024-12-03gnu: r-escape: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-escape)[native-inputs]: Add r-seurat. [arguments]: Add phase 'delete-bad-tests. Change-Id: Ie86501a4d283e3dab863bcda5e6cc63cd98d847c
2024-12-03gnu: r-pathview: Disable vignettes.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-pathview)[arguments]: Skip vignettes. Change-Id: I8ab4558fba53a44db4d6e1dceee560ce6b3e67dd
2024-12-03gnu: r-brms: Fix vignettes.Ricardo Wurmus
* gnu/packages/cran.scm (r-brms)[arguments]: Add phase 'set-HOME. Change-Id: Ife0fcc2352b8bf47356c1684687fdf26b0281f6f
2024-12-03gnu: r-cycombine: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-cycombine)[native-inputs]: Add r-testthat. Change-Id: I101d0109153f04dbf3b9a3d96c2b1c9a9f676f63
2024-12-03gnu: r-catalyst: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-catalyst)[native-inputs]: Add r-diffcyt. Change-Id: Ifa4bf1c432bb23e2b3570595c6bbe0b4279e27e9
2024-12-03gnu: r-adductomicsr: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-adductomicsr)[arguments]: Disable tests. Change-Id: Ibcacce27e8a62038bb5d24864125986889733e8c
2024-12-03gnu: r-seraster: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seraster)[native-inputs]: Add r-testthat. Change-Id: I88fb4a51831aff1b08437ef08adb62e344185a07
2024-12-03gnu: r-httpgd: Add missing input.Ricardo Wurmus
* gnu/packages/statistics.scm (r-httpgd)[native-inputs]: Add r-testthat. Change-Id: Iefadbf9fd0bba743210d3c55b8355b793fcb2b25
2024-12-03gnu: r-flowviz: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-flowviz)[arguments]: Disable tests. [properties]: Tell updater to ignore r-flowstats. [native-inputs]: Add r-ncdfflow. Change-Id: Ic6123c745dbfc25c026646e92a230a62db483306
2024-12-03gnu: r-derfinder: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-derfinder)[native-inputs]: Add r-derfinderdata and r-txdb-hsapiens-ucsc-hg19-knowngene. [arguments]: Add phase 'delete-bad-tests. Change-Id: I2c0e5b6ea514c6b0024022e8e663d171dd8868da
2024-12-03gnu: Add r-derfinderdata.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-derfinderdata): New variable. Change-Id: I735030fad98b4eb20e0898d7f4779cd4c06ec82c
2024-12-03gnu: r-psmatch: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-psmatch)[native-inputs]: Add r-msdata, r-mzid, r-mzr, and r-spectra. Change-Id: Idda7d88adf8ce6bdd9ec29033b80b029f22b9c84
2024-12-03gnu: r-riboprofiling: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-riboprofiling)[native-inputs]: Add r-txdb-hsapiens-ucsc-hg19-knowngene Change-Id: I448e1535c3ec6513ba6590e932c1e20ff1c34bb4
2024-12-03gnu: r-flowclust: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-flowclust)[native-inputs]: Add r-flowworkspace. [properties]: Tell updater not to add r-opencyto. [arguments]: Add phases 'delete-bad-tests. Change-Id: Ie82854c0ff52c290e7482f67771aa9ef82a83343
2024-12-03gnu: r-flowworkspace: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-flowworkspace)[arguments]: Disable tests. Change-Id: Idb8abe5b056c3f67c44377782869b35620370aa9
2024-12-03gnu: r-ncdfflow: Delete bad tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ncdfflow)[arguments]: Add phase 'delete-bad-tests. [properties]: Tell updater not to add r-flowstats. Change-Id: I3ba5519d907890d606ea1160d4b715ce82392e36
2024-12-03gnu: r-gqtlbase: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gqtlbase)[arguments]: Disable tests; remove trailing #T from 'fix-imports phase. [native-inputs]: Add r-runit. Change-Id: Ic05a67edccfb5eebe312811d461d65bc49929ec9
2024-12-03gnu: r-monocle3: Update to 1.3.7.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-monocle3): Update to 1.3.7. [propagated-inputs]: Remove r-htmlwidgets, r-matrix-utils, r-pryr, r-rcppparallel, and r-reticulate; add r-biocparallel, r-delayedarray, r-digest, r-future, r-ggrastr, r-hdf5array, r-lme4, r-openssl, r-plyr, r-rcolorbrewer, r-rcppannoy, r-rcpphnsw, r-s4vectors, r-sf, and r-summarizedexperiment. [native-inputs]: Add r-testthat. [description]: Expand. [arguments]: Disable tests. Change-Id: I0331c5148dce5b282d25edf93e0ccc80397f78ec
2024-12-03gnu: r-chromstar: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chromstar)[native-inputs]: Add r-testthat. Change-Id: I29897bb94f587adf210395dd28b6e3dc480ac74c
2024-12-03gnu: r-gtrack: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gtrack)[native-inputs]: Add r-testthat. Change-Id: I7b0cad1b8fd27d88ff766c5a46bd01dae2933422
2024-12-03gnu: r-biocpkgtools: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocpkgtools)[arguments]: Disable tests. Change-Id: Id96ca07103e762fa267c83a178c4367855cdc5c8
2024-12-03gnu: r-damefinder: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-damefinder)[native-inputs]: Add r-bsgenome-hsapiens-ucsc-hg19. Change-Id: I9f3eeeb597d8c9672f201ab89f4e57118b8e6e72
2024-12-03gnu: r-stringdb: Add missing input and disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-stringdb)[arguments]: Disable tests. [native-inputs]: Add r-biocgenerics. Change-Id: I534f7102e4397111bba7c58353ba5fc74c8bd2cf
2024-12-03gnu: r-category: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-category)[arguments]: Add phase 'delete-bad-tests; skip building vignettes. [native-inputs]: Add r-all, r-geneplotter, r-hgu95av2-db, r-karyoploter, r-keggrest, r-lattice, r-limma, r-org-sc-sgd-db, and r-rcolorbrewer. [properties]: Tell updater to ignore r-gostats. Change-Id: I186b7a92437a20f85960bd605ae25ed5c29bf5b2
2024-12-03gnu: r-annotationhubdata: Delete bad tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotationhubdata)[arguments]: Add phase 'delete-bad-tests. Change-Id: Id14228ace239fca4524d92bd09a9298c556b9399
2024-12-03gnu: r-msexperiment: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-msexperiment)[native-inputs]: Add r-msbackendsql, r-msdata, r-mzr, and r-rsqlite. [properties]: Tell updater to keep r-mzr. Change-Id: I7fda0e9fd6b369506686970926f0ab53364a6503
2024-12-03gnu: Add r-msbackendsql.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-msbackendsql): New variable. Change-Id: Ie7937f5bcbe26cd53035e9944fe5befbb35efe27
2024-12-03gnu: r-tradeseq: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tradeseq)[native-inputs]: Add r-delayedmatrixstats and r-dplyr. Change-Id: I049a5cc83128d065a5524e6e1d8b93fa9ab6c8a8
2024-12-03gnu: r-monocle: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-monocle)[arguments]: Disable tests and add phase 'patch-tests. Change-Id: I430617a0edf56b977f882e9bd2b79dcb4a34542d
2024-12-03gnu: r-doubletcollection: Add missing input and disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-doubletcollection)[native-inputs]: Add r-testthat. [arguments]: Disable tests. Change-Id: I8802f703ecfd8d69e6e457cffb28e34d3f4f2b06
2024-12-03gnu: r-gsva: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gsva)[native-inputs]: Add r-gsvadata. Change-Id: I81da88cbbef78885863fe199a5a4e51d67e0c0bf
2024-12-03gnu: Add r-gsvadata.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gsvadata): New variable. Change-Id: Ic3bbcf3cff9b0f98597f143041b1b79298215e56
2024-12-03gnu: Add r-hgu95a-db.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-hgu95a-db): New variable. Change-Id: I9eb2e8182689a2e1ba38c180d476dd60363f3c51
2024-12-03gnu: r-curatedtcgadata: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-curatedtcgadata)[native-inputs]: Add r-testthat. Change-Id: I9379295f854ab66a88321326c25f8d7a15fe2e26
2024-12-03gnu: r-pando: Add missing inputs and disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-pando)[native-inputs]: Add r-bsgenome-hsapiens-ucsc-hg38, r-devtools, r-doparallel, and r-ensdb-hsapiens-v86. [arguments]: Disable tests. Change-Id: Ic66679e2b8c4cdb9835ce08dc4dbb0a42e35e291
2024-12-03gnu: r-anpan: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-anpan)[native-inputs]: Add r-testthat. Change-Id: I69be3fa82db5f9c4e1302c9a3bd2d4f5253bde13
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