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2024-12-04gnu: packages/python-science: Update copyright header.Sharlatan Hellseher
* gnu/packages/python-science.scm: Update copyright header for Antero Mejr <antero@mailbox.org> . Change-Id: I4153d51d74f7de1629d5a7851346021b77e7352d
2024-12-04gnu: Add python-scikit-surprise.Antero Mejr
* gnu/packages/python-science.scm (python-scikit-surprise): New variable. Change-Id: I9b5e13f0c985f34bb0bd759e76ebd27221a340a4 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-12-04gnu: ikiwiki: Fix build by disabling a test.Janneke Nieuwenhuizen
* gnu/packages/web.scm (ikiwiki)[arguments]: In stage "pre-check", disable failing "t/t.po" test. Change-Id: I4fc1240512b4d3df3ece837521116aee5746e181
2024-12-03gnu: r-rcdt: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-rcdt)[native-inputs]: Add r-testthat. Change-Id: Ic5358aee6d5174052266dc01b81f618edf931cd2
2024-12-03gnu: r-msnid: Disable vignettes.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-msnid)[arguments]: Disable vignettes. Change-Id: I47dc4cf5b6d80699d4f22b2b92382ada7ca3322a
2024-12-03gnu: r-pcaexplorer: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-pcaexplorer)[native-inputs]: Add r-airway and r-org-hs-eg-db. Change-Id: Id559bea8cd4308058a06158e74d3e13d7f645572
2024-12-03gnu: Add r-airway.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-airway): New variable. Change-Id: I521c1bf868566f80997c8ba80609fd5709a95694
2024-12-03gnu: r-reportingtools: Add missing inputs.Ricardo Wurmus
* 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
2024-12-03gnu: Add r-faahko.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-faahko): New variable. Change-Id: I70cd662bdd202ac78f5f25235fb7b9b9e7d60b37
2024-12-03gnu: r-xcms: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-xcms)[arguments]: Disable tests. [properties]: Tell updater to ignore r-faahko. [native-inputs]: Add r-msdata. Change-Id: I2ee167828534a4046d15d740f6f25d8eff9d589f
2024-12-03gnu: r-httpgd: Disable tests.Ricardo Wurmus
* gnu/packages/statistics.scm (r-httpgd)[arguments]: Disable tests. [synopsis]: Use lower case and remove extraneous quotes. Change-Id: I25e69987b6c647d14cc51ba01ba2fcfb1163c568
2024-12-03gnu: r-mcmc: Disable vignettes.Ricardo Wurmus
* gnu/packages/cran.scm (r-mcmc)[arguments]: Disable vignettes. Change-Id: I0453d3a812d8e5fea52ab38d16e82f9c5ea439ac
2024-12-03gnu: r-biodb: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biodb)[arguments]: Disable tests. Change-Id: I40746a3fbfad0801058b7f34182edc358a863fa2
2024-12-03gnu: discrover: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add texlive-etoolbox. Change-Id: I42075c05a36a031c40c335a668a8b46a7603b4dd
2024-12-03gnu: r-rtk: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-rtk)[native-inputs]: Add r-testthat. Change-Id: I22bd9756036270cf9e60fcdf1b09f8be8aace74d
2024-12-03gnu: r-assertive: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-assertive)[native-inputs]: Add r-testthat. Change-Id: I0119786699e4353b9254f4a4858a2b0820a85e31
2024-12-03gnu: r-assertive-data: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-assertive-data)[native-inputs]: Add r-testthat. Change-Id: Ie47c9aaa6dc8f9bf3f627555bde01eff38b58b7f
2024-12-03gnu: r-assertive-data-uk: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-assertive-data-uk)[native-inputs]: Add r-testthat. Change-Id: I9a388538bc3a7b8192132da7139eb6d37ba785c6
2024-12-03gnu: r-assertive-data-us: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-assertive-data-us)[native-inputs]: Add r-testthat. Change-Id: Ib2e5540aa6fb409cf807b51871eb80f87d221c5b
2024-12-03gnu: r-assertive-datetimes: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-assertive-datetimes)[native-inputs]: Add r-testthat. Change-Id: I41cf25fde0519a2552e2bfabf88325c9790b9598
2024-12-03gnu: r-assertive-code: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-assertive-code)[native-inputs]: Add r-testthat. Change-Id: Iab971756002abbe84f7472092db82f62eb9acc55
2024-12-03gnu: r-assertive-strings: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-assertive-strings)[native-inputs]: Add r-testthat. Change-Id: Ib4f6eb638105f7d1aaa54972176b8d66704ed2a4
2024-12-03gnu: r-rcas: Add missing inputsRicardo Wurmus
* gnu/packages/bioconductor.scm (r-rcas)[native-inputs]: Add r-biocmanager. [arguments]: Add phases 'skip-bad-tests and 'set-HOME. Change-Id: I952ae31347776dc35cf012aaa8146f38b375957a
2024-12-03gnu: r-affyplm: Add missing inputs and disable tests.Ricardo Wurmus
* 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
2024-12-03gnu: Add r-hgu95av2cdf.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-hgu95av2cdf): New variable. Change-Id: I12095d54198b563a81c0d3967699016fef0f2de0
2024-12-03gnu: r-assertive-files: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-assertive-files)[native-inputs]: Add r-testthat. [arguments]: Add phases 'set-HOME. Change-Id: Icd6d2dc145b31b25fcad1c0482ba87928165c7f7
2024-12-03gnu: r-assertive-types: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-assertive-types)[native-inputs]: Add r-testthat. Change-Id: I58ef096504602989de101b744362b115fcb67f27
2024-12-03gnu: Remove r-bioconcotk.Ricardo Wurmus
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
2024-12-03gnu: r-bigmelon: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bigmelon)[native-inputs]: Add r-biocstyle and r-knitr. Change-Id: Ie24831140e5b38d330435231d8ea976a060b4800
2024-12-03gnu: r-chipexoqual: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chipexoqual)[native-inputs]: Add r-chipexoqualexample. Change-Id: I68e5ac7ce3d0c00cfc1838ef7d6b4e2e5410bb50
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
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