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* gnu: r-msnid: Disable vignettes.Ricardo Wurmus2024-12-031-2/+6
| | | | | | * gnu/packages/bioconductor.scm (r-msnid)[arguments]: Disable vignettes. Change-Id: I47dc4cf5b6d80699d4f22b2b92382ada7ca3322a
* gnu: r-pcaexplorer: Add missing inputs.Ricardo Wurmus2024-12-031-1/+1
| | | | | | | * gnu/packages/bioconductor.scm (r-pcaexplorer)[native-inputs]: Add r-airway and r-org-hs-eg-db. Change-Id: Id559bea8cd4308058a06158e74d3e13d7f645572
* gnu: Add r-airway.Ricardo Wurmus2024-12-031-0/+31
| | | | | | * gnu/packages/bioconductor.scm (r-airway): New variable. Change-Id: I521c1bf868566f80997c8ba80609fd5709a95694
* gnu: r-reportingtools: Add missing inputs.Ricardo Wurmus2024-12-031-2/+15
| | | | | | | | | * 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
* gnu: Add r-faahko.Ricardo Wurmus2024-12-031-0/+24
| | | | | | * gnu/packages/bioconductor.scm (r-faahko): New variable. Change-Id: I70cd662bdd202ac78f5f25235fb7b9b9e7d60b37
* gnu: r-xcms: Disable tests.Ricardo Wurmus2024-12-031-1/+7
| | | | | | | | * gnu/packages/bioconductor.scm (r-xcms)[arguments]: Disable tests. [properties]: Tell updater to ignore r-faahko. [native-inputs]: Add r-msdata. Change-Id: I2ee167828534a4046d15d740f6f25d8eff9d589f
* gnu: r-biodb: Disable tests.Ricardo Wurmus2024-12-031-0/+5
| | | | | | * gnu/packages/bioconductor.scm (r-biodb)[arguments]: Disable tests. Change-Id: I40746a3fbfad0801058b7f34182edc358a863fa2
* gnu: r-rcas: Add missing inputsRicardo Wurmus2024-12-031-1/+16
| | | | | | | * gnu/packages/bioconductor.scm (r-rcas)[native-inputs]: Add r-biocmanager. [arguments]: Add phases 'skip-bad-tests and 'set-HOME. Change-Id: I952ae31347776dc35cf012aaa8146f38b375957a
* gnu: r-affyplm: Add missing inputs and disable tests.Ricardo Wurmus2024-12-031-1/+6
| | | | | | | | | * 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
* gnu: Add r-hgu95av2cdf.Ricardo Wurmus2024-12-031-0/+21
| | | | | | * gnu/packages/bioconductor.scm (r-hgu95av2cdf): New variable. Change-Id: I12095d54198b563a81c0d3967699016fef0f2de0
* gnu: Remove r-bioconcotk.Ricardo Wurmus2024-12-031-46/+0
| | | | | | | | | 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
* gnu: r-bigmelon: Add missing inputs.Ricardo Wurmus2024-12-031-1/+1
| | | | | | | * gnu/packages/bioconductor.scm (r-bigmelon)[native-inputs]: Add r-biocstyle and r-knitr. Change-Id: Ie24831140e5b38d330435231d8ea976a060b4800
* gnu: r-chipexoqual: Add missing input.Ricardo Wurmus2024-12-031-1/+1
| | | | | | | * gnu/packages/bioconductor.scm (r-chipexoqual)[native-inputs]: Add r-chipexoqualexample. Change-Id: I68e5ac7ce3d0c00cfc1838ef7d6b4e2e5410bb50
* gnu: Add r-chipexoqualexample.Ricardo Wurmus2024-12-031-0/+22
| | | | | | * gnu/packages/bioconductor.scm (r-chipexoqualexample): New variable. Change-Id: I181bb085e441d056d886d4110a46668d92cd39f4
* gnu: r-genomicstate: Disable tests.Ricardo Wurmus2024-12-031-0/+2
| | | | | | * gnu/packages/bioconductor.scm (r-genomicstate)[arguments]: Disable tests. Change-Id: Ia2a43c0b20af344e74306f88c3306c6bd40267b0
* gnu: r-gqtlstats: Add missing input and disable tests.Ricardo Wurmus2024-12-031-1/+3
| | | | | | | * gnu/packages/bioconductor.scm (r-gqtlstats)[native-inputs]: Add r-runit. [arguments]: Disable tests. Change-Id: I1b11251e88826970d16f32a1304a92f9c4923bd5
* gnu: r-gostats: Add missing inputs.Ricardo Wurmus2024-12-031-1/+1
| | | | | | | * gnu/packages/bioconductor.scm (r-gostats)[native-inputs]: Add r-biocgenerics and r-hgu95av2-db. Change-Id: I4e5ee933154dc102efe4c034f993c959b2924671
* gnu: r-msnbase: Add missing inputs.Ricardo Wurmus2024-12-031-2/+38
| | | | | | | | | * 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
* gnu: Add r-prolocdata.Ricardo Wurmus2024-12-031-0/+23
| | | | | | * gnu/packages/bioconductor.scm (r-prolocdata): New variable. Change-Id: Iac4da738f793e2a746d1ef8a17251a3b27c2e599
* gnu: Add r-rpx.Ricardo Wurmus2024-12-031-0/+23
| | | | | | * gnu/packages/bioconductor.scm (r-rpx): New variable. Change-Id: Id8b70a61d2657dfe5588f1cb67074d6fe5f1988c
* gnu: r-rnbeads: Add missing inputs.Ricardo Wurmus2024-12-031-5/+37
| | | | | | | | | | | | | * 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
* gnu: Add r-rnbeads-hg19.Ricardo Wurmus2024-12-031-0/+21
| | | | | | * gnu/packages/bioconductor.scm (r-rnbeads-hg19): New variable. Change-Id: I48ad7e0e3831edc280b8241b3d525fb73f95805f
* gnu: r-vsn: Add missing input.Ricardo Wurmus2024-12-031-1/+1
| | | | | | * gnu/packages/bioconductor.scm (r-vsn)[native-inputs]: Add r-biocstyle. Change-Id: I12b619b0ae134132a4536b0e54e1182a55ea816c
* gnu: r-cicero-monocle3: Disable failing test.Ricardo Wurmus2024-12-031-0/+10
| | | | | | | * gnu/packages/bioconductor.scm (r-cicero-monocle3)[arguments]: Disable failing test. Change-Id: I92d3878ee189403478309837214e09fe66874b69
* gnu: r-cicero-monocle3: Update to 1.3.9-1.495ef0d.Ricardo Wurmus2024-12-031-3/+3
| | | | | | | * gnu/packages/bioconductor.scm (r-cicero-monocle3): Update to 1.3.9-1.495ef0d. Change-Id: Ic3939f8374818cfaaf6a77dee42710d998968021
* gnu: r-cytoml: Add missing inputs.Ricardo Wurmus2024-12-031-2/+10
| | | | | | | | * 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
* gnu: r-variantfiltering: Add missing inputs.Ricardo Wurmus2024-12-031-2/+24
| | | | | | | | | | * 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
* gnu: Add r-sift-hsapiens-dbsnp137.Ricardo Wurmus2024-12-031-0/+21
| | | | | | * gnu/packages/bioconductor.scm (r-sift-hsapiens-dbsnp137): New variable. Change-Id: Ib71a322d3ed0e563f01620e04aca844b290ecc3b
* gnu: Add r-polyphen-hsapiens-dbsnp131.Ricardo Wurmus2024-12-031-0/+21
| | | | | | * gnu/packages/bioconductor.scm (r-polyphen-hsapiens-dbsnp131): New variable. Change-Id: I65ca94c82b3c9c8d9f0faf6f31a04d52e935f127
* gnu: Add r-mafdb-1kgenomes-phase1-hs37d5.Ricardo Wurmus2024-12-031-0/+28
| | | | | | * gnu/packages/bioconductor.scm (r-mafdb-1kgenomes-phase1-hs37d5): New variable. Change-Id: Id8827d4a5d788ef2bc4d258048572e697e61b4d2
* gnu: r-mmuphin: Add missing inputs.Ricardo Wurmus2024-12-031-1/+1
| | | | | | * gnu/packages/bioconductor.scm (r-mmuphin)[native-inputs]: Add r-testthat. Change-Id: I24c838fb0c474cda16a49b48c469d8dfd7194e10
* gnu: r-lefser: Add missing inputs.Ricardo Wurmus2024-12-031-2/+4
| | | | | | | | * 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
* gnu: r-sesamedata: Disable tests.Ricardo Wurmus2024-12-031-1/+6
| | | | | | | * gnu/packages/bioconductor.scm (r-sesamedata)[arguments]: Disable tests. [properties]: Tell updater to ignore r-sesame. Change-Id: I42e3a2d83963e79a21db70f4c1f8ddf92107943f
* gnu: r-abaenrichment: Add missing input.Ricardo Wurmus2024-12-031-1/+1
| | | | | | | * gnu/packages/bioconductor.scm (r-abaenrichment)[native-inputs]: Add r-testthat. Change-Id: I3a5a43d3a1b9f7ff81c589efc0a0aade1e666553
* gnu: r-mosdef: Add missing inputs.Ricardo Wurmus2024-12-031-2/+5
| | | | | | | | * 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
* gnu: r-diffbind: Add missing inputs and skip vignettes.Ricardo Wurmus2024-12-031-2/+6
| | | | | | | | | * 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
* gnu: r-quasr: Add missing inputs.Ricardo Wurmus2024-12-031-2/+4
| | | | | | | | * gnu/packages/bioconductor.scm (r-quasr)[native-inputs]: Add r-genomicalignments and r-rhisat2. [properties]: Tell updater to keep r-rhisat2. Change-Id: I304824e27d39f76a1de2aeb1e77c32f5d6faf70e
* gnu: r-bgeecall: Add missing inputs and disable tests.Ricardo Wurmus2024-12-031-1/+3
| | | | | | | | * gnu/packages/bioconductor.scm (r-bgeecall)[native-inputs]: Add r-annotationhub and r-httr. [arguments]: Disable tests. Change-Id: Ic2ea9e81075c70501d53df556ab9548d46ac24ae
* gnu: r-milor: Add missing inputs.Ricardo Wurmus2024-12-031-1/+6
| | | | | | | * gnu/packages/bioconductor.scm (r-milor)[native-inputs]: Add r-mass, r-mvtnorm, r-scater, and r-scran. Change-Id: Icdfa0e9a89a21ace0d994800a00b968a803d41ea
* gnu: r-conos: Add missing input.Ricardo Wurmus2024-12-031-1/+1
| | | | | | * gnu/packages/bioconductor.scm (r-conos)[native-inputs]: Add r-pagoda2. Change-Id: I9b12a3c3ba727d7e6101fa2566c42c0a6858d601
* gnu: r-maaslin2: Add missing input.Ricardo Wurmus2024-12-031-1/+1
| | | | | | * gnu/packages/bioconductor.scm (r-maaslin2)[native-inputs]: Add r-testthat. Change-Id: I044a9bf1f1e53f0988760f84b822beb6b6779291
* gnu: r-simona: Add missing input.Ricardo Wurmus2024-12-031-2/+5
| | | | | | | | * 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
* gnu: r-gviz: Add missing input.Ricardo Wurmus2024-12-031-1/+1
| | | | | | | * gnu/packages/bioconductor.scm (r-gviz)[native-inputs]: Add r-bsgenome-hsapiens-ucsc-hg19. Change-Id: I2be88201e9219cc55be39217592483f1324e456f
* gnu: r-xbseq: Add missing inputs.Ricardo Wurmus2024-12-031-1/+1
| | | | | | * gnu/packages/bioconductor.scm (r-xbseq)[native-inputs]: Add r-testthat. Change-Id: I7b8eb1c7a7ffcac81b9ead33969b1e57d99a68f3
* gnu: r-numbat: Add missing inputs.Ricardo Wurmus2024-12-031-0/+1
| | | | | | * gnu/packages/bioconductor.scm (r-numbat)[native-inputs]: Add r-testthat. Change-Id: I3a3db09ba1c69c27a9bc6a67be9346098710fde3
* gnu: r-flowstats: Add missing inputs.Ricardo Wurmus2024-12-031-1/+8
| | | | | | | | * 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
* gnu: r-ggcyto: Add missing inputs.Ricardo Wurmus2024-12-031-2/+6
| | | | | | | | * 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
* gnu: r-opencyto: Add missing inputs.Ricardo Wurmus2024-12-031-2/+4
| | | | | | | | * gnu/packages/bioconductor.scm (r-opencyto)[native-inputs]: Add r-flowworkspacedata. [properties]: Tell updater to add r-flowworkspacedata. Change-Id: Ife446af466fb4be221f9fdaba53c84bbe80dec86
* gnu: Add r-flowworkspacedata.Ricardo Wurmus2024-12-031-0/+23
| | | | | | * gnu/packages/bioconductor.scm (r-flowworkspacedata): New variable. Change-Id: Ie2add925d3fcd3540bc3885427982fb0cee5a146
* gnu: r-bodymaprat: Disable tests.Ricardo Wurmus2024-12-031-0/+2
| | | | | | * gnu/packages/bioconductor.scm (r-bodymaprat)[arguments]: Disable tests. Change-Id: Icaa4428e4890a898c35444ae1bedd4258527ee37
generated by cgit v1.2.3 (git 2.47.1) at 2025-01-22 00:33:04 +0000