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2024-12-03gnu: Add r-polyphen-hsapiens-dbsnp131.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-polyphen-hsapiens-dbsnp131): New variable. Change-Id: I65ca94c82b3c9c8d9f0faf6f31a04d52e935f127
2024-12-03gnu: Add r-mafdb-1kgenomes-phase1-hs37d5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mafdb-1kgenomes-phase1-hs37d5): New variable. Change-Id: Id8827d4a5d788ef2bc4d258048572e697e61b4d2
2024-12-03gnu: r-mmuphin: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mmuphin)[native-inputs]: Add r-testthat. Change-Id: I24c838fb0c474cda16a49b48c469d8dfd7194e10
2024-12-03gnu: r-lefser: Add missing inputs.Ricardo Wurmus
* 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
2024-12-03gnu: r-sesamedata: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-sesamedata)[arguments]: Disable tests. [properties]: Tell updater to ignore r-sesame. Change-Id: I42e3a2d83963e79a21db70f4c1f8ddf92107943f
2024-12-03gnu: r-liana: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-liana)[native-inputs]: Add r-testthat. Change-Id: I04c9c5f60842e1ed0a0415e51c25b46b64a60104
2024-12-03gnu: r-abaenrichment: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-abaenrichment)[native-inputs]: Add r-testthat. Change-Id: I3a5a43d3a1b9f7ff81c589efc0a0aade1e666553
2024-12-03gnu: r-mosdef: Add missing inputs.Ricardo Wurmus
* 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
2024-12-03gnu: r-diffbind: Add missing inputs and skip vignettes.Ricardo Wurmus
* 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
2024-12-03gnu: r-quasr: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-quasr)[native-inputs]: Add r-genomicalignments and r-rhisat2. [properties]: Tell updater to keep r-rhisat2. Change-Id: I304824e27d39f76a1de2aeb1e77c32f5d6faf70e
2024-12-03gnu: r-bgeecall: Add missing inputs and disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bgeecall)[native-inputs]: Add r-annotationhub and r-httr. [arguments]: Disable tests. Change-Id: Ic2ea9e81075c70501d53df556ab9548d46ac24ae
2024-12-03gnu: r-milor: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-milor)[native-inputs]: Add r-mass, r-mvtnorm, r-scater, and r-scran. Change-Id: Icdfa0e9a89a21ace0d994800a00b968a803d41ea
2024-12-03gnu: r-conos: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-conos)[native-inputs]: Add r-pagoda2. Change-Id: I9b12a3c3ba727d7e6101fa2566c42c0a6858d601
2024-12-03gnu: r-maaslin2: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-maaslin2)[native-inputs]: Add r-testthat. Change-Id: I044a9bf1f1e53f0988760f84b822beb6b6779291
2024-12-03gnu: r-simona: Add missing input.Ricardo Wurmus
* 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
2024-12-03gnu: r-circus: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-circus)[native-inputs]: Add r-testthat. Change-Id: I7178baece0a8134923fd550e2f1cc303f32aaaea
2024-12-03gnu: r-gviz: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gviz)[native-inputs]: Add r-bsgenome-hsapiens-ucsc-hg19. Change-Id: I2be88201e9219cc55be39217592483f1324e456f
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
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