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Author SHA1 Message Date
Ricardo Wurmus
71f82174a5
import/cran: Enhance import pattern. 
* guix/import/cran.scm (import-pattern): Comment; capture direct namespace
imports as well as silent imports.

Change-Id: Ia54035d6f230d695aa950adb3e691cbce4f2d416
 2024-12-03 10:54:33 +01:00
Ricardo Wurmus
066d769293
import/cran: Also add set-HOME phase when R.cache exists. 
* guix/import/cran.scm (phases-for-inputs): Add "R.cache" to the list.

Change-Id: Ia65beb7cd535de10b024d108a97db0169045fe1f
 2024-12-03 10:54:33 +01:00
Ricardo Wurmus
2ec838c630
gnu: r-msnid: Disable vignettes. 
* gnu/packages/bioconductor.scm (r-msnid)[arguments]: Disable vignettes.

Change-Id: I47dc4cf5b6d80699d4f22b2b92382ada7ca3322a
 2024-12-03 10:54:33 +01:00
Ricardo Wurmus
7c37518d76
gnu: r-pcaexplorer: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-pcaexplorer)[native-inputs]: Add
r-airway and r-org-hs-eg-db.

Change-Id: Id559bea8cd4308058a06158e74d3e13d7f645572
 2024-12-03 10:54:33 +01:00
Ricardo Wurmus
c2511ab60f
gnu: Add r-airway. 
* gnu/packages/bioconductor.scm (r-airway): New variable.

Change-Id: I521c1bf868566f80997c8ba80609fd5709a95694
 2024-12-03 10:54:33 +01:00
Ricardo Wurmus
161518633d
gnu: r-reportingtools: Add missing inputs. 
* 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
 2024-12-03 10:54:33 +01:00
Ricardo Wurmus
7410d8fc1b
gnu: Add r-faahko. 
* gnu/packages/bioconductor.scm (r-faahko): New variable.

Change-Id: I70cd662bdd202ac78f5f25235fb7b9b9e7d60b37
 2024-12-03 10:54:33 +01:00
Ricardo Wurmus
6ea00f5ca2
gnu: r-xcms: Disable tests. 
* gnu/packages/bioconductor.scm (r-xcms)[arguments]: Disable tests.
[properties]: Tell updater to ignore r-faahko.
[native-inputs]: Add r-msdata.

Change-Id: I2ee167828534a4046d15d740f6f25d8eff9d589f
 2024-12-03 10:54:33 +01:00
Ricardo Wurmus
9ee9113651
gnu: r-httpgd: Disable tests. 
* gnu/packages/statistics.scm (r-httpgd)[arguments]: Disable tests.
[synopsis]: Use lower case and remove extraneous quotes.

Change-Id: I25e69987b6c647d14cc51ba01ba2fcfb1163c568
 2024-12-03 10:54:33 +01:00
Ricardo Wurmus
c9d6db397a
gnu: r-mcmc: Disable vignettes. 
* gnu/packages/cran.scm (r-mcmc)[arguments]: Disable vignettes.

Change-Id: I0453d3a812d8e5fea52ab38d16e82f9c5ea439ac
 2024-12-03 10:54:33 +01:00
Ricardo Wurmus
05398b8be6
gnu: r-biodb: Disable tests. 
* gnu/packages/bioconductor.scm (r-biodb)[arguments]: Disable tests.

Change-Id: I40746a3fbfad0801058b7f34182edc358a863fa2
 2024-12-03 10:54:33 +01:00
Ricardo Wurmus
db47c695d6
gnu: discrover: Add missing input. 
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add
texlive-etoolbox.

Change-Id: I42075c05a36a031c40c335a668a8b46a7603b4dd
 2024-12-03 10:54:33 +01:00
Ricardo Wurmus
26040524c6
gnu: r-rtk: Add missing input. 
* gnu/packages/cran.scm (r-rtk)[native-inputs]: Add r-testthat.

Change-Id: I22bd9756036270cf9e60fcdf1b09f8be8aace74d
 2024-12-03 10:54:33 +01:00
Ricardo Wurmus
7c3e664e0c
gnu: r-assertive: Add missing input. 
* gnu/packages/cran.scm (r-assertive)[native-inputs]: Add r-testthat.

Change-Id: I0119786699e4353b9254f4a4858a2b0820a85e31
 2024-12-03 10:54:32 +01:00
Ricardo Wurmus
16528c9709
gnu: r-assertive-data: Add missing input. 
* gnu/packages/cran.scm (r-assertive-data)[native-inputs]: Add r-testthat.

Change-Id: Ie47c9aaa6dc8f9bf3f627555bde01eff38b58b7f
 2024-12-03 10:54:32 +01:00
Ricardo Wurmus
4e339d7403
gnu: r-assertive-data-uk: Add missing input. 
* gnu/packages/cran.scm (r-assertive-data-uk)[native-inputs]: Add r-testthat.

Change-Id: I9a388538bc3a7b8192132da7139eb6d37ba785c6
 2024-12-03 10:54:32 +01:00
Ricardo Wurmus
93f9e60a9d
gnu: r-assertive-data-us: Add missing input. 
* gnu/packages/cran.scm (r-assertive-data-us)[native-inputs]: Add r-testthat.

Change-Id: Ib2e5540aa6fb409cf807b51871eb80f87d221c5b
 2024-12-03 10:54:32 +01:00
Ricardo Wurmus
f9af512739
gnu: r-assertive-datetimes: Add missing input. 
* gnu/packages/cran.scm (r-assertive-datetimes)[native-inputs]: Add
r-testthat.

Change-Id: I41cf25fde0519a2552e2bfabf88325c9790b9598
 2024-12-03 10:54:32 +01:00
Ricardo Wurmus
f491970085
gnu: r-assertive-code: Add missing input. 
* gnu/packages/cran.scm (r-assertive-code)[native-inputs]: Add r-testthat.

Change-Id: Iab971756002abbe84f7472092db82f62eb9acc55
 2024-12-03 10:54:32 +01:00
Ricardo Wurmus
f8bc1e5a63
gnu: r-assertive-strings: Add missing input. 
* gnu/packages/cran.scm (r-assertive-strings)[native-inputs]: Add r-testthat.

Change-Id: Ib4f6eb638105f7d1aaa54972176b8d66704ed2a4
 2024-12-03 10:54:32 +01:00
Ricardo Wurmus
45fb3f85f4
gnu: r-rcas: Add missing inputs 
* gnu/packages/bioconductor.scm (r-rcas)[native-inputs]: Add r-biocmanager.
[arguments]: Add phases 'skip-bad-tests and 'set-HOME.

Change-Id: I952ae31347776dc35cf012aaa8146f38b375957a
 2024-12-03 10:54:32 +01:00
Ricardo Wurmus
7af4765204
gnu: r-affyplm: Add missing inputs and disable tests. 
* 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
 2024-12-03 10:54:32 +01:00
Ricardo Wurmus
5a8accfaaf
gnu: Add r-hgu95av2cdf. 
* gnu/packages/bioconductor.scm (r-hgu95av2cdf): New variable.

Change-Id: I12095d54198b563a81c0d3967699016fef0f2de0
 2024-12-03 10:54:32 +01:00
Ricardo Wurmus
8020893722
gnu: r-assertive-files: Add missing input. 
* gnu/packages/cran.scm (r-assertive-files)[native-inputs]: Add r-testthat.
[arguments]: Add phases 'set-HOME.

Change-Id: Icd6d2dc145b31b25fcad1c0482ba87928165c7f7
 2024-12-03 10:54:32 +01:00
Ricardo Wurmus
4db537df94
gnu: r-assertive-types: Add missing input. 
* gnu/packages/cran.scm (r-assertive-types)[native-inputs]: Add r-testthat.

Change-Id: I58ef096504602989de101b744362b115fcb67f27
 2024-12-03 10:54:32 +01:00
Ricardo Wurmus
f880a4f96b
gnu: Remove r-bioconcotk. 
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
 2024-12-03 10:54:32 +01:00
Ricardo Wurmus
0dec8b3869
gnu: r-bigmelon: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-bigmelon)[native-inputs]: Add
r-biocstyle and r-knitr.

Change-Id: Ie24831140e5b38d330435231d8ea976a060b4800
 2024-12-03 10:54:31 +01:00
Ricardo Wurmus
b4d80e93d7
gnu: r-chipexoqual: Add missing input. 
* gnu/packages/bioconductor.scm (r-chipexoqual)[native-inputs]: Add
r-chipexoqualexample.

Change-Id: I68e5ac7ce3d0c00cfc1838ef7d6b4e2e5410bb50
 2024-12-03 10:54:31 +01:00
Ricardo Wurmus
eaa6bb26d9
gnu: Add r-chipexoqualexample. 
* gnu/packages/bioconductor.scm (r-chipexoqualexample): New variable.

Change-Id: I181bb085e441d056d886d4110a46668d92cd39f4
 2024-12-03 10:54:31 +01:00
Ricardo Wurmus
e02d5cb646
gnu: r-chk: Add missing input. 
* gnu/packages/cran.scm (r-chk)[native-inputs]: Add tzdata-for-tests.
[properties]: Tell updater to keep it.

Change-Id: I86058064135869dadb79d490f16a8b7ea5fd4661
 2024-12-03 10:54:31 +01:00
Ricardo Wurmus
a0032ff706
gnu: r-btools: Disable tests. 
* gnu/packages/bioinformatics.scm (r-btools)[arguments]: Disable tests.

Change-Id: I0fc83672a3c09908296551b649244ae1993ac01d
 2024-12-03 10:54:31 +01:00
Ricardo Wurmus
c25eb6304e
gnu: r-genomicstate: Disable tests. 
* gnu/packages/bioconductor.scm (r-genomicstate)[arguments]: Disable tests.

Change-Id: Ia2a43c0b20af344e74306f88c3306c6bd40267b0
 2024-12-03 10:54:31 +01:00
Ricardo Wurmus
6943f15a4e
gnu: r-googlesheets: Add missing inputs. 
* gnu/packages/statistics.scm (r-googlesheets)[native-inputs]: Add r-knitr and
r-testthat.

Change-Id: I8ac8ec40c9bbcdb01509dc199b4937e95563aad6
 2024-12-03 10:54:31 +01:00
Ricardo Wurmus
c2ebc147df
gnu: r-gqtlstats: Add missing input and disable tests. 
* gnu/packages/bioconductor.scm (r-gqtlstats)[native-inputs]: Add r-runit.
[arguments]: Disable tests.

Change-Id: I1b11251e88826970d16f32a1304a92f9c4923bd5
 2024-12-03 10:54:31 +01:00
Ricardo Wurmus
0950710e87
gnu: r-gostats: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-gostats)[native-inputs]: Add r-biocgenerics
and r-hgu95av2-db.

Change-Id: I4e5ee933154dc102efe4c034f993c959b2924671
 2024-12-03 10:54:31 +01:00
Ricardo Wurmus
78a2b77270
gnu: r-mumin: Add missing inputs. 
* gnu/packages/statistics.scm (r-mumin)[native-inputs]: Add r-mgcv and
r-survival.

Change-Id: Id5b1a558af6020018d1fbdc88179682681bd625c
 2024-12-03 10:54:31 +01:00
Ricardo Wurmus
349ee49226
gnu: r-nabor: Add missing input. 
* gnu/packages/cran.scm (r-nabor)[native-inputs]: Add r-rann.

Change-Id: Ie177502c2f902a6d4e76a94a2d2d30537c747df6
 2024-12-03 10:54:31 +01:00
Ricardo Wurmus
11debd4833
gnu: r-msnbase: Add missing inputs. 
* 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
 2024-12-03 10:54:31 +01:00
Ricardo Wurmus
3535a30b5d
gnu: Add r-prolocdata. 
* gnu/packages/bioconductor.scm (r-prolocdata): New variable.

Change-Id: Iac4da738f793e2a746d1ef8a17251a3b27c2e599
 2024-12-03 10:54:31 +01:00
Ricardo Wurmus
94a0d33650
gnu: Add r-rpx. 
* gnu/packages/bioconductor.scm (r-rpx): New variable.

Change-Id: Id8b70a61d2657dfe5588f1cb67074d6fe5f1988c
 2024-12-03 10:54:31 +01:00
Ricardo Wurmus
af5bf52c3a
gnu: r-cytoexplorer: Add missing inputs. 
* 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
 2024-12-03 10:54:30 +01:00
Ricardo Wurmus
25980b8f8e
gnu: r-rnbeads: Add missing inputs. 
* 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
 2024-12-03 10:54:30 +01:00
Ricardo Wurmus
399342bf6c
gnu: Add r-rnbeads-hg19. 
* gnu/packages/bioconductor.scm (r-rnbeads-hg19): New variable.

Change-Id: I48ad7e0e3831edc280b8241b3d525fb73f95805f
 2024-12-03 10:54:30 +01:00
Ricardo Wurmus
2caea483c4
gnu: r-protviz: Add missing inputs. 
* gnu/packages/cran.scm (r-protviz)[native-inputs]: Add r-lattice and
r-xtable.

Change-Id: Ibc1f437c3abeef8fbf063864256fc526cdeb0441
 2024-12-03 10:54:30 +01:00
Ricardo Wurmus
c20a815552
gnu: Add r-cytoexplorerdata. 
* gnu/packages/bioinformatics.scm (r-cytoexplorerdata): New variable.

Change-Id: I5565dff552f033c951bee5bac474cb05c7034066
 2024-12-03 10:54:30 +01:00
Ricardo Wurmus
8232deb3dc
gnu: r-vsn: Add missing input. 
* gnu/packages/bioconductor.scm (r-vsn)[native-inputs]: Add r-biocstyle.

Change-Id: I12b619b0ae134132a4536b0e54e1182a55ea816c
 2024-12-03 10:54:30 +01:00
Ricardo Wurmus
d9209e6326
gnu: r-skitools: Add missing input. 
* gnu/packages/bioinformatics.scm (r-skitools)[native-inputs]: Add
r-bsgenome-hsapiens-ucsc-hg19.

Change-Id: I8331e0df21bda001d6e3ec944f02791c0a9301b6
 2024-12-03 10:54:30 +01:00
Ricardo Wurmus
f4d0eb8ee4
gnu: r-cicero-monocle3: Disable failing test. 
* gnu/packages/bioconductor.scm (r-cicero-monocle3)[arguments]: Disable
failing test.

Change-Id: I92d3878ee189403478309837214e09fe66874b69
 2024-12-03 10:54:30 +01:00
Ricardo Wurmus
e2d5d339ab
gnu: r-cicero-monocle3: Update to 1.3.9-1.495ef0d. 
* gnu/packages/bioconductor.scm (r-cicero-monocle3): Update to
1.3.9-1.495ef0d.

Change-Id: Ic3939f8374818cfaaf6a77dee42710d998968021
 2024-12-03 10:54:30 +01:00
Ricardo Wurmus
3daa84e5d2
gnu: r-scseqcomm: Remove commented inputs. 
* gnu/packages/bioinformatics.scm (r-scseqcomm): Remove comments.

Change-Id: I537f6377da44637674a0413a30ddd6b70a620ad3
 2024-12-03 10:54:30 +01:00