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Author SHA1 Message Date
Ricardo Wurmus
1afde387f5
gnu: r-pathview: Disable vignettes. 
* gnu/packages/bioconductor.scm (r-pathview)[arguments]: Skip vignettes.

Change-Id: I8ab4558fba53a44db4d6e1dceee560ce6b3e67dd
 2024-12-03 10:54:27 +01:00
Ricardo Wurmus
50d88e2b55
gnu: r-brms: Fix vignettes. 
* gnu/packages/cran.scm (r-brms)[arguments]: Add phase 'set-HOME.

Change-Id: Ife0fcc2352b8bf47356c1684687fdf26b0281f6f
 2024-12-03 10:54:27 +01:00
Ricardo Wurmus
988da04606
gnu: r-cycombine: Add missing input. 
* gnu/packages/bioconductor.scm (r-cycombine)[native-inputs]: Add r-testthat.

Change-Id: I101d0109153f04dbf3b9a3d96c2b1c9a9f676f63
 2024-12-03 10:54:27 +01:00
Ricardo Wurmus
1315e2c9b8
gnu: r-catalyst: Add missing input. 
* gnu/packages/bioconductor.scm (r-catalyst)[native-inputs]: Add r-diffcyt.

Change-Id: Ifa4bf1c432bb23e2b3570595c6bbe0b4279e27e9
 2024-12-03 10:54:27 +01:00
Ricardo Wurmus
e611a4cb97
gnu: r-adductomicsr: Disable tests. 
* gnu/packages/bioconductor.scm (r-adductomicsr)[arguments]: Disable tests.

Change-Id: Ibcacce27e8a62038bb5d24864125986889733e8c
 2024-12-03 10:54:27 +01:00
Ricardo Wurmus
3fdaf73f4f
gnu: r-seraster: Add missing input. 
* gnu/packages/bioinformatics.scm (r-seraster)[native-inputs]: Add r-testthat.

Change-Id: I88fb4a51831aff1b08437ef08adb62e344185a07
 2024-12-03 10:54:27 +01:00
Ricardo Wurmus
610f7ad281
gnu: r-httpgd: Add missing input. 
* gnu/packages/statistics.scm (r-httpgd)[native-inputs]: Add r-testthat.

Change-Id: Iefadbf9fd0bba743210d3c55b8355b793fcb2b25
 2024-12-03 10:54:26 +01:00
Ricardo Wurmus
d6e9f37b8e
gnu: r-flowviz: Disable tests. 
* gnu/packages/bioconductor.scm (r-flowviz)[arguments]: Disable tests.
[properties]: Tell updater to ignore r-flowstats.
[native-inputs]: Add r-ncdfflow.

Change-Id: Ic6123c745dbfc25c026646e92a230a62db483306
 2024-12-03 10:54:26 +01:00
Ricardo Wurmus
b7f66aca6e
gnu: r-derfinder: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-derfinder)[native-inputs]: Add
r-derfinderdata and r-txdb-hsapiens-ucsc-hg19-knowngene.
[arguments]: Add phase 'delete-bad-tests.

Change-Id: I2c0e5b6ea514c6b0024022e8e663d171dd8868da
 2024-12-03 10:54:26 +01:00
Ricardo Wurmus
37c346a229
gnu: Add r-derfinderdata. 
* gnu/packages/bioconductor.scm (r-derfinderdata): New variable.

Change-Id: I735030fad98b4eb20e0898d7f4779cd4c06ec82c
 2024-12-03 10:54:26 +01:00
Ricardo Wurmus
6e9bc2465e
gnu: r-psmatch: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-psmatch)[native-inputs]: Add r-msdata,
r-mzid, r-mzr, and r-spectra.

Change-Id: Idda7d88adf8ce6bdd9ec29033b80b029f22b9c84
 2024-12-03 10:54:26 +01:00
Ricardo Wurmus
a29c7cf8b4
gnu: r-riboprofiling: Add missing input. 
* gnu/packages/bioconductor.scm (r-riboprofiling)[native-inputs]: Add
r-txdb-hsapiens-ucsc-hg19-knowngene

Change-Id: I448e1535c3ec6513ba6590e932c1e20ff1c34bb4
 2024-12-03 10:54:26 +01:00
Ricardo Wurmus
d7ccc1dfe3
gnu: r-flowclust: Add missing input. 
* gnu/packages/bioconductor.scm (r-flowclust)[native-inputs]: Add
r-flowworkspace.
[properties]: Tell updater not to add r-opencyto.
[arguments]: Add phases 'delete-bad-tests.

Change-Id: Ie82854c0ff52c290e7482f67771aa9ef82a83343
 2024-12-03 10:54:26 +01:00
Ricardo Wurmus
54b89fb948
gnu: r-flowworkspace: Disable tests. 
* gnu/packages/bioconductor.scm (r-flowworkspace)[arguments]: Disable tests.

Change-Id: Idb8abe5b056c3f67c44377782869b35620370aa9
 2024-12-03 10:54:26 +01:00
Ricardo Wurmus
b5b768a3d0
gnu: r-ncdfflow: Delete bad tests. 
* gnu/packages/bioconductor.scm (r-ncdfflow)[arguments]: Add phase
'delete-bad-tests.
[properties]: Tell updater not to add r-flowstats.

Change-Id: I3ba5519d907890d606ea1160d4b715ce82392e36
 2024-12-03 10:54:26 +01:00
Ricardo Wurmus
0bfb0dde32
gnu: r-gqtlbase: Disable tests. 
* gnu/packages/bioconductor.scm (r-gqtlbase)[arguments]: Disable tests; remove
trailing #T from 'fix-imports phase.
[native-inputs]: Add r-runit.

Change-Id: Ic05a67edccfb5eebe312811d461d65bc49929ec9
 2024-12-03 10:54:26 +01:00
Ricardo Wurmus
8ba2261df5
gnu: r-monocle3: Update to 1.3.7. 
* gnu/packages/bioconductor.scm (r-monocle3): Update to 1.3.7.
[propagated-inputs]: Remove r-htmlwidgets, r-matrix-utils, r-pryr,
r-rcppparallel, and r-reticulate; add r-biocparallel, r-delayedarray,
r-digest, r-future, r-ggrastr, r-hdf5array, r-lme4, r-openssl, r-plyr,
r-rcolorbrewer, r-rcppannoy, r-rcpphnsw, r-s4vectors, r-sf, and
r-summarizedexperiment.
[native-inputs]: Add r-testthat.
[description]: Expand.
[arguments]: Disable tests.

Change-Id: I0331c5148dce5b282d25edf93e0ccc80397f78ec
 2024-12-03 10:54:26 +01:00
Ricardo Wurmus
1ac18c2c7f
gnu: r-chromstar: Add missing input. 
* gnu/packages/bioconductor.scm (r-chromstar)[native-inputs]: Add r-testthat.

Change-Id: I29897bb94f587adf210395dd28b6e3dc480ac74c
 2024-12-03 10:54:26 +01:00
Ricardo Wurmus
37161d1289
gnu: r-gtrack: Add missing input. 
* gnu/packages/bioinformatics.scm (r-gtrack)[native-inputs]: Add r-testthat.

Change-Id: I7b0cad1b8fd27d88ff766c5a46bd01dae2933422
 2024-12-03 10:54:26 +01:00
Ricardo Wurmus
60ebe23d09
gnu: r-biocpkgtools: Disable tests. 
* gnu/packages/bioconductor.scm (r-biocpkgtools)[arguments]: Disable tests.

Change-Id: Id96ca07103e762fa267c83a178c4367855cdc5c8
 2024-12-03 10:54:26 +01:00
Ricardo Wurmus
a06f572036
gnu: r-damefinder: Add missing input. 
* gnu/packages/bioconductor.scm (r-damefinder)[native-inputs]: Add
r-bsgenome-hsapiens-ucsc-hg19.

Change-Id: I9f3eeeb597d8c9672f201ab89f4e57118b8e6e72
 2024-12-03 10:54:25 +01:00
Ricardo Wurmus
b3d65982ca
gnu: r-stringdb: Add missing input and disable tests. 
* gnu/packages/bioconductor.scm (r-stringdb)[arguments]: Disable tests.
[native-inputs]: Add r-biocgenerics.

Change-Id: I534f7102e4397111bba7c58353ba5fc74c8bd2cf
 2024-12-03 10:54:25 +01:00
Ricardo Wurmus
494a413178
gnu: r-category: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-category)[arguments]: Add phase
'delete-bad-tests; skip building vignettes.
[native-inputs]: Add r-all, r-geneplotter, r-hgu95av2-db, r-karyoploter,
r-keggrest, r-lattice, r-limma, r-org-sc-sgd-db, and r-rcolorbrewer.
[properties]: Tell updater to ignore r-gostats.

Change-Id: I186b7a92437a20f85960bd605ae25ed5c29bf5b2
 2024-12-03 10:54:25 +01:00
Ricardo Wurmus
312b5e5880
gnu: r-annotationhubdata: Delete bad tests. 
* gnu/packages/bioconductor.scm (r-annotationhubdata)[arguments]: Add phase
'delete-bad-tests.

Change-Id: Id14228ace239fca4524d92bd09a9298c556b9399
 2024-12-03 10:54:25 +01:00
Ricardo Wurmus
db1597f6ea
import/cran: Detect test and vignette inputs. 
* guix/import/cran.scm (import-pattern): New variable.
(needed-test-inputs-in-directory, needed-vignettes-inputs-in-directory): New
procedures.
(source-dir->dependencies): Add native inputs from result of
NEEDED-TEST-INPUTS-IN-DIRECTORY and NEEDED-VIGNETTES-INPUTS-IN-DIRECTORY.
(cran-package-inputs): Clean up and delete duplicates from source-derived
inputs.

Change-Id: Id139c144fc6e866e4aaf8f05201b0d2687744fb6
 2024-12-03 10:54:25 +01:00
Ricardo Wurmus
cb172bf9fb
import/cran: Set HOME when R.rsp is among inputs. 
* guix/import/cran.scm (phases-for-inputs): Also add 'set-HOME phase when
R.rsp is among the inputs.

Change-Id: Ib00d981cc623da8ec487086913570f937a76aeb5
 2024-12-03 10:54:25 +01:00
Ricardo Wurmus
808b5a619f
import: utils: Wrap function names in @code. 
* 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
 2024-12-03 10:54:25 +01:00
Ricardo Wurmus
ab111d373f
gnu: r-msexperiment: Add missing inputs. 
* 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
 2024-12-03 10:54:25 +01:00
Ricardo Wurmus
2128090200
gnu: Add r-msbackendsql. 
* gnu/packages/bioconductor.scm (r-msbackendsql): New variable.

Change-Id: Ie7937f5bcbe26cd53035e9944fe5befbb35efe27
 2024-12-03 10:54:25 +01:00
Ricardo Wurmus
471e9aa1be
gnu: r-tradeseq: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-tradeseq)[native-inputs]: Add
r-delayedmatrixstats and r-dplyr.

Change-Id: I049a5cc83128d065a5524e6e1d8b93fa9ab6c8a8
 2024-12-03 10:54:25 +01:00
Ricardo Wurmus
eb7250bda1
gnu: r-monocle: Disable tests. 
* gnu/packages/bioconductor.scm (r-monocle)[arguments]: Disable tests and add
phase 'patch-tests.

Change-Id: I430617a0edf56b977f882e9bd2b79dcb4a34542d
 2024-12-03 10:54:25 +01:00
Ricardo Wurmus
98c1c91c06
gnu: r-doubletcollection: Add missing input and disable tests. 
* gnu/packages/bioinformatics.scm (r-doubletcollection)[native-inputs]: Add
r-testthat.
[arguments]: Disable tests.

Change-Id: I8802f703ecfd8d69e6e457cffb28e34d3f4f2b06
 2024-12-03 10:54:25 +01:00
Ricardo Wurmus
dcf6eb9fb4
gnu: r-gsva: Add missing input. 
* gnu/packages/bioconductor.scm (r-gsva)[native-inputs]: Add r-gsvadata.

Change-Id: I81da88cbbef78885863fe199a5a4e51d67e0c0bf
 2024-12-03 10:54:25 +01:00
Ricardo Wurmus
710a2915b4
gnu: Add r-gsvadata. 
* gnu/packages/bioconductor.scm (r-gsvadata): New variable.

Change-Id: Ic3bbcf3cff9b0f98597f143041b1b79298215e56
 2024-12-03 10:54:25 +01:00
Ricardo Wurmus
2e915f8611
gnu: Add r-hgu95a-db. 
* gnu/packages/bioconductor.scm (r-hgu95a-db): New variable.

Change-Id: I9eb2e8182689a2e1ba38c180d476dd60363f3c51
 2024-12-03 10:54:24 +01:00
Ricardo Wurmus
9a51c0bb0a
gnu: r-curatedtcgadata: Add missing input. 
* gnu/packages/bioconductor.scm (r-curatedtcgadata)[native-inputs]: Add
r-testthat.

Change-Id: I9379295f854ab66a88321326c25f8d7a15fe2e26
 2024-12-03 10:54:24 +01:00
Ricardo Wurmus
5f91ef23b8
gnu: r-pando: Add missing inputs and disable tests. 
* 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
 2024-12-03 10:54:24 +01:00
Ricardo Wurmus
8bc8f6f8d7
gnu: r-anpan: Add missing input. 
* gnu/packages/bioinformatics.scm (r-anpan)[native-inputs]: Add r-testthat.

Change-Id: I69be3fa82db5f9c4e1302c9a3bd2d4f5253bde13
 2024-12-03 10:54:24 +01:00
Ricardo Wurmus
d62869da55
gnu: r-caretensemble: Add missing inputs. 
* gnu/packages/cran.scm (r-caretensemble)[native-inputs]: Add r-catools,
r-earth, r-glmnet, r-mlbench, and r-randomforest.

Change-Id: I66037e22d86b1cadc5e57f84bfebb4e37396c705
 2024-12-03 10:54:24 +01:00
Ricardo Wurmus
a872aa23e6
gnu: r-parsnip: Add missing input. 
* gnu/packages/cran.scm (r-parsnip)[native-inputs]: Add r-earth.
[arguments]: Remove phase 'delete-bad-tests.

Change-Id: I64f4000afc59ab838476f6f08cc331f9121e802b
 2024-12-03 10:54:24 +01:00
Ricardo Wurmus
b1406d22e5
gnu: Add r-earth. 
* gnu/packages/cran.scm (r-earth): New variable.

Change-Id: If6ae39912cade13d0d81c1e5178eb20c5017ccb3
 2024-12-03 10:54:24 +01:00
Ricardo Wurmus
affd500ba2
gnu: r-openmx: Add missing input. 
* gnu/packages/cran.scm (r-openmx)[native-inputs]: Add r-numderiv.

Change-Id: I7ed2872021b5f164d256704180076bf4618f5e8f
 2024-12-03 10:54:24 +01:00
Ricardo Wurmus
0bc427e19f
gnu: Add r-plotmo. 
* gnu/packages/cran.scm (r-plotmo): New variable.

Change-Id: Id0803e02acc72f1f98429f023b1d673453fde302
 2024-12-03 10:54:24 +01:00
Ricardo Wurmus
d252496834
gnu: r-kmer: Add missing input. 
* gnu/packages/cran.scm (r-kmer)[native-inputs]: Add r-knitr.

Change-Id: Ia28f582637d27c87413af1169ae816ee05377652
 2024-12-03 10:54:24 +01:00
Ricardo Wurmus
feeef70afe
gnu: r-devtools: Add missing input. 
* gnu/packages/statistics.scm (r-devtools)[native-inputs]: Add r-mockery.

Change-Id: I2d67a549e9eaee339b5362dac54d417deec850b9
 2024-12-03 10:54:24 +01:00
Ricardo Wurmus
0587d6280d
gnu: r-hdwgcna: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-hdwgcna)[native-inputs]: Add r-devtools
and r-testthat.

Change-Id: I553d4fc2f1a682e5d552862c5e50a31140528073
 2024-12-03 10:54:24 +01:00
Ricardo Wurmus
ede924f945
gnu: r-rcmdcheck: Add missing inputs. 
* gnu/packages/cran.scm (r-rcmdcheck)[native-inputs]: Add r-mockery and
r-webfakes.

Change-Id: Id4389d7c6d1c8bce5af67bcbf6d3e04956f58c9b
 2024-12-03 10:54:24 +01:00
Ricardo Wurmus
feea9b4577
gnu: r-haplo-stats: Fix vignettes. 
* gnu/packages/cran.scm (r-haplo-stats)[arguments]: Add phase 'set-HOME.

Change-Id: Ia1f5e5c33753b2261c7b4dc2ffa40322e9c840a9
 2024-12-03 10:54:23 +01:00
Ricardo Wurmus
80b206c4b1
gnu: r-celldex: Disable tests. 
* gnu/packages/bioconductor.scm (r-celldex)[arguments]: Disable tests.

Change-Id: I1881b1793f2fe8bc870697976a5c3434147760ca
 2024-12-03 10:54:23 +01:00
Ricardo Wurmus
b715e861bc
gnu: r-ihw: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-ihw)[native-inputs]: Add r-ggplot2 and
r-scales.

Change-Id: Ib52a30442b00ae4303d307a816578012563aa612
 2024-12-03 10:54:23 +01:00