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2024-12-03gnu: r-spectra: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-spectra)[arguments]: Disable tests. [native-inputs]: Add missing inputs r-mzr and r-patrick. Change-Id: I7d9dca3c1f17c0a57d7b6cc7479e08ea5bb11843
2024-12-03gnu: Add r-betareg.Ricardo Wurmus
* gnu/packages/cran.scm (r-betareg): New variable. Change-Id: I67839c22e6374dcd9e9f0c12d08770d8103ead6d
2024-12-03gnu: r-powertcr: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-powertcr)[native-inputs]: Add r-biocgenerics. Change-Id: Ieb0f7f2bd4362a9f1d6c4a0b9b937e8be81b7323
2024-12-03gnu: r-freetypeharfbuzz: Disable tests.Ricardo Wurmus
* gnu/packages/cran.scm (r-freetypeharfbuzz)[arguments]: Disable tests. [native-inputs]: Add r-testthat. Change-Id: Ibd82aacff87c79b2c3f061035b14bb750fcee239
2024-12-03gnu: r-mzr: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mzr)[native-inputs]: Add r-codetools, r-msdata, r-mzid, and r-xml. Change-Id: Iaeb8286a19ddb1bc750710a0e5d5a5cee59b3901
2024-12-03gnu: r-depmixs4: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-depmixs4)[native-inputs]: Add r-gamlss. Change-Id: Ib7f2ab4f656bda824f2375d0d3ea59908ad1aa5c
2024-12-03gnu: r-sanssouci: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-sanssouci)[native-inputs]: Add r-ggplot2 and r-testthat. [arguments]: Add phase 'delete-bad-tests. Change-Id: I902b4e4a2163f5ed9cf07d186dfe80068a8ef4a5
2024-12-03gnu: r-unigd: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-unigd)[native-inputs]: Add r-xml2. Change-Id: Ice50673f8092cf37b2e26bc47bd2b1040e5e652a
2024-12-03gnu: r-birewire: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-birewire)[native-inputs]: Add r-biocgenerics. Change-Id: I3d07db1bd5cafd88f05afe67fc7bf43e07946365
2024-12-03gnu: r-seurat5: Deprecate.Ricardo Wurmus
* gnu/packages/cran.scm (r-seurat5): Deprecate in favor of r-seurat. Change-Id: I906ec3bf0d82f93db108ac5f58394bae40347f81
2024-12-03gnu: r-seurat5object: Deprecate.Ricardo Wurmus
* gnu/packages/cran.scm (r-seurat5object): Deprecate in favor of r-seuratobject. Change-Id: I44865a9a28b337071ff59462226cf77ad60e4f0f
2024-12-03gnu: r-downloader: Disable tests.Ricardo Wurmus
* gnu/packages/cran.scm (r-downloader)[arguments]: Disable tests. Change-Id: I69834c27c64153a046aa1022b32826bf0c383b5c
2024-12-03gnu: r-scico: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-scico)[native-inputs]: Add r-dplyr and r-ggplot2. Change-Id: Ia5a81c607bf9417413dbfcb396cc3b63191e4d15
2024-12-03gnu: r-tm: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-tm)[native-inputs]: Add r-snowballc. Change-Id: I55b18e9c64965746e7563519a483ea688830f6fc
2024-12-03gnu: r-stm: Disable vignettes, add test inputs.Ricardo Wurmus
* gnu/packages/cran.scm (r-stm)[arguments]: Disable vignettes. [native-inputs]: Add r-tm. Change-Id: Ib880a15c940b70054018fb03750e60537561f19b
2024-12-03gnu: r-bridgesampling: Fix vignettes.Ricardo Wurmus
* gnu/packages/cran.scm (r-bridgesampling)[arguments]: Add phase 'set-HOME. Change-Id: Ibde578ee3530fc56b2ee61dc28450260295d283b
2024-12-03gnu: r-readbitmap: Add missing inputs.Ricardo Wurmus
* gnu/packages/cran.scm (r-readbitmap)[native-inputs]: Add r-pixmap. Change-Id: I3f8132db83651c091fd8eef3445874f2eb3d98d8
2024-12-03gnu: r-dyngen: Fix tests.Ricardo Wurmus
* gnu/packages/cran.scm (r-dyngen)[arguments]: Add phase 'set-HOME. Change-Id: If47090b0f9f1d4a0a794ca00ef2ed90226148ab3
2024-12-03gnu: r-variancepartition: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-variancepartition)[native-inputs]: Add r-edger and r-rfast. Change-Id: I5b9bd4e378d0e7dbd5bc3efc67b96bd1beb563b1
2024-12-03gnu: r-annotationhub: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotationhub)[arguments]: Disable tests. Change-Id: I00a9778eb5d8cd031b956c583f12f42921fec4e2
2024-12-03gnu: r-treeio: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-treeio)[native-inputs]: Add r-igraph and r-xml2. [arguments]: Add phase 'delete-bad-tests. Change-Id: I0c5e8ef566acbc8593c6c27a6cc7776778937876
2024-12-03gnu: r-gofuncr: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gofuncr)[native-inputs]: Add r-homo-sapiens. Change-Id: I66d6e9985fc420c93eaf77afa348b7bbd29381c7
2024-12-03gnu: r-organismdbi: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-organismdbi)[arguments]: Disable tests. Change-Id: I1a669db2ffc8f9e5bf00666bdfbc53a060508dc6
2024-12-03gnu: r-txdbmaker: Add test inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-txdbmaker)[native-inputs]: Add r-rmariadb. [arguments]: Add phase 'delete-bad-tests. Change-Id: I22fe422410a41998e4fa3552cfaa1dba3e245c10
2024-12-03gnu: Add r-rmariadb.Ricardo Wurmus
* gnu/packages/cran.scm (r-rmariadb): New variable. Change-Id: I12ec88bb93170b4d59f62e3d89bf3d0e110b0eae
2024-12-03gnu: r-biomart: Add test inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biomart)[native-inputs]: Add r-httptest2 and r-mockery. [arguments]: Add phase 'delete-bad-tests. Change-Id: I07aacb1f73a8afd49a1645da8c1bf2d22dde7873
2024-12-03gnu: Add r-httptest2.Ricardo Wurmus
* gnu/packages/cran.scm (r-httptest2): New variable. Change-Id: Iaaf40d07c1bea2213359857eeae86eeead90fbc4
2024-12-03gnu: Add r-webfakes.Ricardo Wurmus
* gnu/packages/cran.scm (r-webfakes): New variable. Change-Id: Ia7bcf571bfbefe046b6fbd129a969fd118cf0760
2024-12-03gnu: r-metagenomeseq: Add test inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-metagenomeseq)[native-inputs]: Add r-testthat. [arguments]: Add phase 'delete-bad-tests. Change-Id: I702d02695fe0b078bd2b97b958a0bbde73d0c2d5
2024-12-03gnu: r-ioniser: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ioniser)[native-inputs]: Add r-minionsummarydata. Change-Id: Ie478db21c33c6d279937678b8103cca5df228a09
2024-12-03gnu: Add r-minionsummarydata.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-minionsummarydata): New variable. Change-Id: I61318a1338bbff117e38d3ce5963dd061e5175a9
2024-12-03gnu: r-rnacrosslinkoo: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rnacrosslinkoo)[native-inputs]: Add r-testthat. Change-Id: Iedd2dee7a32dcd19a99d25d92b6f453dd197f5b4
2024-12-03gnu: r-glimma: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-glimma)[native-inputs]: Add r-pryr. Change-Id: I9109cc636e758df436aaae38c3b2bd735b1e4cc0
2024-12-03gnu: r-systempiper: Add missing inputs and disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-systempiper)[native-inputs]: Add r-systempiperdata. [arguments]: Disable tests. Change-Id: Ic071bbcb53ef9fb96385fbbdb5725ed2a4490db7
2024-12-03gnu: r-roar: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-roar)[native-inputs]: Add r-rnaseqdata-hnrnpc-bam-chr14. Change-Id: Ic5fa181d52e87ba7039e0000f5610eb46150bbfc
2024-12-03gnu: Add r-systempiperdata.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-systempiperdata): New variable. Change-Id: I125e8003073ffc5fa7f20d3efa0f3ead71eaafe3
2024-12-03gnu: r-sgseq: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-sgseq)[native-inputs]: Add r-bsgenome-hsapiens-ucsc-hg19. [arguments]: Add phase 'delete-bad-tests. Change-Id: I5ff9e2af754700e5ba70ad7bdd1be5ec952946a3
2024-12-03gnu: Add r-rnaseqdata-hnrnpc-bam-chr14.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rnaseqdata-hnrnpc-bam-chr14): New variable. Change-Id: If2f9bf10e3e1396cfd31e3278020d623ce2253e0
2024-12-03gnu: r-bedtorch: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bedtorch)[arguments]: Disable tests. [native-inputs]: Add r-testthat. Change-Id: Ia06aca330528eb2b9eea569d5d12db0f12d6511e
2024-12-03gnu: r-bioqc: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bioqc)[native-inputs]: Add r-ineq. Change-Id: I090a0d25f87d23119e66a69ca37c16d7b384a01a
2024-12-03gnu: r-organism-dplyr: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-organism-dplyr)[native-inputs]: Add r-txdb-hsapiens-ucsc-hg38-knowngene and r-txdb-mmusculus-ucsc-mm10-ensgene. Change-Id: I1dbf8d71f9a29d1a95e70a4b44042155af4a1222
2024-12-03gnu: r-genomicdatacommons: Delete bad tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomicdatacommons)[arguments]: Add phase 'delete-bad-tests. Change-Id: I9e09a99cc3e07d4d3a568d1058c717a74de925bc
2024-12-03gnu: Add r-txdb-mmusculus-ucsc-mm10-ensgene.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm10-ensgene): New variable. Change-Id: I5caa7d292ea0f81df5acf3f522fd3cf1ca9acb13
2024-12-03gnu: r-ctrdata: Fix vignettes.Ricardo Wurmus
* gnu/packages/cran.scm (r-ctrdata)[arguments]: Add phase 'set-HOME. Change-Id: I0191e69b9970fd0fe2c85dffa19839b94760befd
2024-12-03gnu: r-megadepth: Add missing inputs and disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-megadepth)[propagated-inputs]: Add megadepth. [arguments]: Disable tests. [inputs]: Remove empty field. [properties]: Tell updater to keep megadepth as a propagated input. Change-Id: Idbbc371c2d66aa7c0d7e2add13fa35a5b4f9cd77
2024-12-03gnu: r-alpine: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-alpine)[native-inputs]: Add r-testthat. Change-Id: I0dece0c9def13b5aed392b0a8404ee96e3d57ab5
2024-12-03gnu: r-tgutil: Add missing inputs.Ricardo Wurmus
* gnu/packages/statistics.scm (r-tgutil)[native-inputs]: Add r-testthat. Change-Id: Idb64f13cfcd01db56362fb77c4aca41095e4cf0a
2024-12-03gnu: r-biocdockermanager: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocdockermanager)[native-inputs]: Add r-testthat. Change-Id: I22918f6024bcd2e31f7707ee2dcd2a98061a6136
2024-12-03gnu: r-motifdb: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-motifdb)[native-inputs]: Add r-seqlogo. Change-Id: I4a2316e35ba4b2c79f01edb1d887702102b1106c
2024-12-03gnu: r-dittoseq: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dittoseq)[native-inputs]: Add r-complexheatmap, r-deseq2, r-edger r-ggplot-multistats, r-ggrastr, and r-plotly.
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