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2024-12-03import: utils: Wrap function names in @code.Ricardo Wurmus
* guix/import/utils.scm (beautify-description): Adjust to include "()" in @code wrapper. * tests/import-utils.scm ("beautify-description: wrap function names in @code"): New test. Change-Id: I2b58728571a18ce8302c1b6f98b0c16dbe5931c3
2024-12-03gnu: r-msexperiment: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-msexperiment)[native-inputs]: Add r-msbackendsql, r-msdata, r-mzr, and r-rsqlite. [properties]: Tell updater to keep r-mzr. Change-Id: I7fda0e9fd6b369506686970926f0ab53364a6503
2024-12-03gnu: Add r-msbackendsql.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-msbackendsql): New variable. Change-Id: Ie7937f5bcbe26cd53035e9944fe5befbb35efe27
2024-12-03gnu: r-tradeseq: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tradeseq)[native-inputs]: Add r-delayedmatrixstats and r-dplyr. Change-Id: I049a5cc83128d065a5524e6e1d8b93fa9ab6c8a8
2024-12-03gnu: r-monocle: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-monocle)[arguments]: Disable tests and add phase 'patch-tests. Change-Id: I430617a0edf56b977f882e9bd2b79dcb4a34542d
2024-12-03gnu: r-doubletcollection: Add missing input and disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-doubletcollection)[native-inputs]: Add r-testthat. [arguments]: Disable tests. Change-Id: I8802f703ecfd8d69e6e457cffb28e34d3f4f2b06
2024-12-03gnu: r-gsva: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gsva)[native-inputs]: Add r-gsvadata. Change-Id: I81da88cbbef78885863fe199a5a4e51d67e0c0bf
2024-12-03gnu: Add r-gsvadata.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gsvadata): New variable. Change-Id: Ic3bbcf3cff9b0f98597f143041b1b79298215e56
2024-12-03gnu: Add r-hgu95a-db.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-hgu95a-db): New variable. Change-Id: I9eb2e8182689a2e1ba38c180d476dd60363f3c51
2024-12-03gnu: r-curatedtcgadata: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-curatedtcgadata)[native-inputs]: Add r-testthat. Change-Id: I9379295f854ab66a88321326c25f8d7a15fe2e26
2024-12-03gnu: r-pando: Add missing inputs and disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-pando)[native-inputs]: Add r-bsgenome-hsapiens-ucsc-hg38, r-devtools, r-doparallel, and r-ensdb-hsapiens-v86. [arguments]: Disable tests. Change-Id: Ic66679e2b8c4cdb9835ce08dc4dbb0a42e35e291
2024-12-03gnu: r-anpan: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-anpan)[native-inputs]: Add r-testthat. Change-Id: I69be3fa82db5f9c4e1302c9a3bd2d4f5253bde13
2024-12-03gnu: r-caretensemble: Add missing inputs.Ricardo Wurmus
* gnu/packages/cran.scm (r-caretensemble)[native-inputs]: Add r-catools, r-earth, r-glmnet, r-mlbench, and r-randomforest. Change-Id: I66037e22d86b1cadc5e57f84bfebb4e37396c705
2024-12-03gnu: r-parsnip: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-parsnip)[native-inputs]: Add r-earth. [arguments]: Remove phase 'delete-bad-tests. Change-Id: I64f4000afc59ab838476f6f08cc331f9121e802b
2024-12-03gnu: Add r-earth.Ricardo Wurmus
* gnu/packages/cran.scm (r-earth): New variable. Change-Id: If6ae39912cade13d0d81c1e5178eb20c5017ccb3
2024-12-03gnu: r-openmx: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-openmx)[native-inputs]: Add r-numderiv. Change-Id: I7ed2872021b5f164d256704180076bf4618f5e8f
2024-12-03gnu: Add r-plotmo.Ricardo Wurmus
* gnu/packages/cran.scm (r-plotmo): New variable. Change-Id: Id0803e02acc72f1f98429f023b1d673453fde302
2024-12-03gnu: r-kmer: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-kmer)[native-inputs]: Add r-knitr. Change-Id: Ia28f582637d27c87413af1169ae816ee05377652
2024-12-03gnu: r-devtools: Add missing input.Ricardo Wurmus
* gnu/packages/statistics.scm (r-devtools)[native-inputs]: Add r-mockery. Change-Id: I2d67a549e9eaee339b5362dac54d417deec850b9
2024-12-03gnu: r-hdwgcna: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdwgcna)[native-inputs]: Add r-devtools and r-testthat. Change-Id: I553d4fc2f1a682e5d552862c5e50a31140528073
2024-12-03gnu: r-rcmdcheck: Add missing inputs.Ricardo Wurmus
* gnu/packages/cran.scm (r-rcmdcheck)[native-inputs]: Add r-mockery and r-webfakes. Change-Id: Id4389d7c6d1c8bce5af67bcbf6d3e04956f58c9b
2024-12-03gnu: r-haplo-stats: Fix vignettes.Ricardo Wurmus
* gnu/packages/cran.scm (r-haplo-stats)[arguments]: Add phase 'set-HOME. Change-Id: Ia1f5e5c33753b2261c7b4dc2ffa40322e9c840a9
2024-12-03gnu: r-celldex: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-celldex)[arguments]: Disable tests. Change-Id: I1881b1793f2fe8bc870697976a5c3434147760ca
2024-12-03gnu: r-ihw: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ihw)[native-inputs]: Add r-ggplot2 and r-scales. Change-Id: Ib52a30442b00ae4303d307a816578012563aa612
2024-12-03gnu: r-ewastools: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ewastools)[native-inputs]: Add r-enmix, r-illuminahumanmethylationepicanno-ilm10b4-hg19, r-minfi, r-stringi, and r-testthat. Change-Id: I8ba2b1c46a4898b27874a7dc8648bb142f4b5a70
2024-12-03gnu: r-enmix: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-enmix)[native-inputs]: Add r-minfidata. Change-Id: I0afa8a677c1b91ffec7463b2ed11aadd01a16797
2024-12-03gnu: r-untb: Add missing inputs and disable vignettes.Ricardo Wurmus
* gnu/packages/cran.scm (r-untb)[arguments]: Skip building vignettes. [native-inputs]: Add r-vdiffr. Change-Id: I0e3a8a075fd34f28cee1a76a443c215f500e5012
2024-12-03gnu: r-dalex: Add test inputs.Ricardo Wurmus
* gnu/packages/cran.scm (r-dalex)[native-inputs]: Add r-gower and r-ranger. Change-Id: I2a2de0275dff4a664fbfb660f7cbf065928dddc0
2024-12-03gnu: r-minfi: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-minfi)[arguments]: Disable tests. Change-Id: I6fdb8d78c176c2ebbfbd9289a00833b79448c7a2
2024-12-03gnu: r-bamutils: Add test inputs and disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bamutils)[arguments]: Disable tests. [native-inputs]: Add r-testthat and samtools. Change-Id: I781c38fb59355a51f2cd27a833d7ed5dbe5277ab
2024-12-03gnu: r-bamutils: Update to 0.0.0.9000-2.0a7d2d9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bamutils): Update to 0.0.0.9000-2.0a7d2d9. Change-Id: I04e86c2ff1059f23a34615ac6067926cdd9cb355
2024-12-03gnu: r-rbamtools: Disable tests.Ricardo Wurmus
* gnu/packages/cran.scm (r-rbamtools)[arguments]: Disable tests. Change-Id: I6a16095454d3d58de23786bec21b54245dc5a462
2024-12-03gnu: r-chippeakanno: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chippeakanno)[native-inputs]: Add r-biomart, r-bsgenome-celegans-ucsc-ce10, r-bsgenome-drerio-ucsc-danrer7, r-bsgenome-hsapiens-ucsc-hg19, r-ensdb-hsapiens-v79, r-org-ce-eg-db, r-org-hs-eg-db, r-reactome-db, and r-txdb-hsapiens-ucsc-hg38-knowngene. Change-Id: Ifd3e71dcca3297c03c9cc93da6c677a274c58b2c
2024-12-03gnu: r-arrow: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-arrow)[native-inputs]: Add glibc-utf8-locales, r-dplyr, r-hms, r-lubridate, r-stringr, r-tibble, and tzdata-for-tests. [arguments]: Add phases 'delete-bad-tests, 'set-test-locale, and 'set-timezone. Change-Id: Iece4e463ebe73d41a42594eff7850f2efa96b26f
2024-12-03gnu: r-annotatr: Disable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotatr)[arguments]: Disable tests. Change-Id: I819fe4bc651c39315ba6d42e34d36b505979003d
2024-12-03gnu: r-lpsymphony: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-lpsymphony)[native-inputs]: Add gfortran. Change-Id: Id5bcbdb1bf19364fc8cbee905efb18698893f771
2024-12-03gnu: r-multiassayexperiment: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-multiassayexperiment)[native-inputs]: Add r-hdf5array, r-raggedexperiment, and r-reshape2. [arguments]: Add phase 'set-HOME. Change-Id: Ifafc630ebd32cc255a4d7fd1c190a885e2f7020f
2024-12-03gnu: r-phylogram: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-phylogram)[native-inputs]: Add r-knitr. Change-Id: Ib2e4816c516cc5af9f9495c925e9e244453d30c9
2024-12-03gnu: r-dicekriging: Add missing inputs.Ricardo Wurmus
* gnu/packages/cran.scm (r-dicekriging)[native-inputs]: Add r-numderiv. Change-Id: Ie5ac8b8e7d9c809ee06d26988c582d91d78fdfe6
2024-12-03gnu: r-mvnfast: Disable tests.Ricardo Wurmus
* gnu/packages/cran.scm (r-mvnfast)[arguments]: Disable tests. Change-Id: I2c4ad28984200081faa328fbd606aff22c2bd0cb
2024-12-03gnu: r-janitor: Fix tests.Ricardo Wurmus
* gnu/packages/cran.scm (r-janitor)[native-inputs]: Add tzdata-for-tests. [arguments]: Add phases 'set-timezone and 'delete-bad-tests. Change-Id: Ibbea9ef585d6697e93c31d46b1ff7cc4e23e0e17
2024-12-03gnu: r-trajectoryutils: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-trajectoryutils)[native-inputs]: Add r-biocneighbors and r-delayedmatrixstats. Change-Id: Id49b6e481ebae657f40aba4692dda4de4e2d5bd1
2024-12-03gnu: r-reinforcelearn: Add missing inputs.Ricardo Wurmus
* gnu/packages/cran.scm (r-reinforcelearn)[native-inputs]: Add r-knitr and r-testthat. Change-Id: I71965722253610030cce43e34d299891760cdc9f
2024-12-03gnu: r-bigmemoryextras: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bigmemoryextras)[native-inputs]: Add r-testthat. Change-Id: Iafc29855c30e74c055f157303e3c2f351f0e7aeb
2024-12-03gnu: r-leidenbase: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-leidenbase)[native-inputs]: Add r-knitr and r-testthat. Change-Id: I35e5aebbe6a5e44dea1743f011e4a3a362f6efb1
2024-12-03gnu: r-spacyr: Fix tests.Ricardo Wurmus
* gnu/packages/cran.scm (r-spacyr)[argumenst]: Add phase 'set-HOME. Change-Id: I990c80dd94388da09aa1592e3cc0dd8d14a65d94
2024-12-03gnu: r-quantmod: Disable tests.Ricardo Wurmus
* gnu/packages/cran.scm (r-quantmod)[arguments]: Disable tests. Change-Id: If5ef32ec14ef1bfaca5f5ef983ad0b0e8971837b
2024-12-03gnu: r-partitions: Skip vignettes.Ricardo Wurmus
* gnu/packages/cran.scm (r-partitions)[arguments]: Skip building vignettes. Change-Id: I66d86a439d4ce0922dc74a86c3e4c53a0c632e07
2024-12-03gnu: r-nnlm: Add missing input.Ricardo Wurmus
* gnu/packages/statistics.scm (r-nnlm)[native-inputs]: Add r-testthat. Change-Id: Id0acc0730f43e87d764b2938a299e3a0734358d5
2024-12-03gnu: r-arsenal: Add missing input.Ricardo Wurmus
* gnu/packages/cran.scm (r-arsenal)[native-inputs]: Add r-broom. Change-Id: I442b99b481b73d401e178a69d593fa7a4566fe6a
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