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2024-12-03gnu: Add r-chipexoqualexample.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chipexoqualexample): New variable. Change-Id: I181bb085e441d056d886d4110a46668d92cd39f4
2024-12-03gnu: r-chk: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-chk)[native-inputs]: Add tzdata-for-tests. [properties]: Tell updater to keep it. Change-Id: I86058064135869dadb79d490f16a8b7ea5fd4661
2024-12-03gnu: r-btools: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-btools)[arguments]: Disable tests. Change-Id: I0fc83672a3c09908296551b649244ae1993ac01d
2024-12-03gnu: r-genomicstate: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomicstate)[arguments]: Disable tests. Change-Id: Ia2a43c0b20af344e74306f88c3306c6bd40267b0
2024-12-03gnu: r-googlesheets: Add missing inputs.Ricardo Wurmus
* gnu/packages/statistics.scm (r-googlesheets)[native-inputs]: Add r-knitr and r-testthat. Change-Id: I8ac8ec40c9bbcdb01509dc199b4937e95563aad6
2024-12-03gnu: r-gqtlstats: Add missing input and disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gqtlstats)[native-inputs]: Add r-runit. [arguments]: Disable tests. Change-Id: I1b11251e88826970d16f32a1304a92f9c4923bd5
2024-12-03gnu: r-gostats: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gostats)[native-inputs]: Add r-biocgenerics and r-hgu95av2-db. Change-Id: I4e5ee933154dc102efe4c034f993c959b2924671
2024-12-03gnu: r-mumin: Add missing inputs.Ricardo Wurmus
* gnu/packages/statistics.scm (r-mumin)[native-inputs]: Add r-mgcv and r-survival. Change-Id: Id5b1a558af6020018d1fbdc88179682681bd625c
2024-12-03gnu: r-nabor: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-nabor)[native-inputs]: Add r-rann. Change-Id: Ie177502c2f902a6d4e76a94a2d2d30537c747df6
2024-12-03gnu: r-msnbase: Add missing inputs.Ricardo Wurmus
* 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
2024-12-03gnu: Add r-prolocdata.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-prolocdata): New variable. Change-Id: Iac4da738f793e2a746d1ef8a17251a3b27c2e599
2024-12-03gnu: Add r-rpx.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rpx): New variable. Change-Id: Id8b70a61d2657dfe5588f1cb67074d6fe5f1988c
2024-12-03gnu: r-cytoexplorer: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-cytoexplorer)[native-inputs]: Drop labels; add r-cytoexplorerdata, r-mockery, and r-testthat. [arguments]: Add phase 'skip-bad-tests. Change-Id: I5060b1ae4ad42ae122a46db018f10910340985d6
2024-12-03gnu: r-rnbeads: Add missing inputs.Ricardo Wurmus
* 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
2024-12-03gnu: Add r-rnbeads-hg19.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rnbeads-hg19): New variable. Change-Id: I48ad7e0e3831edc280b8241b3d525fb73f95805f
2024-12-03gnu: r-protviz: Add missing inputs.Ricardo Wurmus
* gnu/packages/cran.scm (r-protviz)[native-inputs]: Add r-lattice and r-xtable. Change-Id: Ibc1f437c3abeef8fbf063864256fc526cdeb0441
2024-12-03gnu: Add r-cytoexplorerdata.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-cytoexplorerdata): New variable. Change-Id: I5565dff552f033c951bee5bac474cb05c7034066
2024-12-03gnu: r-vsn: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-vsn)[native-inputs]: Add r-biocstyle. Change-Id: I12b619b0ae134132a4536b0e54e1182a55ea816c
2024-12-03gnu: r-skitools: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-skitools)[native-inputs]: Add r-bsgenome-hsapiens-ucsc-hg19. Change-Id: I8331e0df21bda001d6e3ec944f02791c0a9301b6
2024-12-03gnu: r-cicero-monocle3: Disable failing test.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-cicero-monocle3)[arguments]: Disable failing test. Change-Id: I92d3878ee189403478309837214e09fe66874b69
2024-12-03gnu: r-cicero-monocle3: Update to 1.3.9-1.495ef0d.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-cicero-monocle3): Update to 1.3.9-1.495ef0d. Change-Id: Ic3939f8374818cfaaf6a77dee42710d998968021
2024-12-03gnu: r-scseqcomm: Remove commented inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scseqcomm): Remove comments. Change-Id: I537f6377da44637674a0413a30ddd6b70a620ad3
2024-12-03gnu: r-chromunity: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-chromunity)[native-inputs]: Add r-testthat. Change-Id: I5d208a5ab0cb63567ab49783d0fbe0733b08161a
2024-12-03gnu: r-cytoml: Add missing inputs.Ricardo Wurmus
* 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
2024-12-03gnu: r-variantfiltering: Add missing inputs.Ricardo Wurmus
* 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
2024-12-03gnu: Add r-sift-hsapiens-dbsnp137.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-sift-hsapiens-dbsnp137): New variable. Change-Id: Ib71a322d3ed0e563f01620e04aca844b290ecc3b
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
2024-12-03import/cran: Recurse for all R packages.Ricardo Wurmus
* guix/import/cran.scm (description->package): Return all R packages, not just all propagated inputs. Change-Id: Id1c6ded681e25e29dcef8f8aed1a6be47b36c4a0
2024-12-03import/cran: Restore memoization for download procedure.Ricardo Wurmus
Fixes <https://issues.guix.gnu.org/44256>. * guix/import/cran.scm (cran-package-inputs): Avoid passing "#:method #f", so that there is only one memoization key in the default case. (fetch-description): Use the full list returned by BIOCONDUCTOR-URI. Change-Id: I532812b14f4e4d9542bfb9248555be1b09f7d92f
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
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