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Author SHA1 Message Date
Ricardo Wurmus
a3b9248e0e
gnu: r-milor: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-milor)[native-inputs]: Add r-mass,
r-mvtnorm, r-scater, and r-scran.

Change-Id: Icdfa0e9a89a21ace0d994800a00b968a803d41ea
 2024-12-03 10:54:29 +01:00
Ricardo Wurmus
70623fbc5c
gnu: r-conos: Add missing input. 
* gnu/packages/bioconductor.scm (r-conos)[native-inputs]: Add r-pagoda2.

Change-Id: I9b12a3c3ba727d7e6101fa2566c42c0a6858d601
 2024-12-03 10:54:29 +01:00
Ricardo Wurmus
103d2f9803
gnu: r-maaslin2: Add missing input. 
* gnu/packages/bioconductor.scm (r-maaslin2)[native-inputs]: Add r-testthat.

Change-Id: I044a9bf1f1e53f0988760f84b822beb6b6779291
 2024-12-03 10:54:28 +01:00
Ricardo Wurmus
ce41b48b23
gnu: r-simona: Add missing input. 
* 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
 2024-12-03 10:54:28 +01:00
Ricardo Wurmus
9cdeb21219
gnu: r-circus: Add missing input. 
* gnu/packages/bioinformatics.scm (r-circus)[native-inputs]: Add r-testthat.

Change-Id: I7178baece0a8134923fd550e2f1cc303f32aaaea
 2024-12-03 10:54:28 +01:00
Ricardo Wurmus
4f2c3aa4c7
gnu: r-gviz: Add missing input. 
* gnu/packages/bioconductor.scm (r-gviz)[native-inputs]: Add
r-bsgenome-hsapiens-ucsc-hg19.

Change-Id: I2be88201e9219cc55be39217592483f1324e456f
 2024-12-03 10:54:28 +01:00
Ricardo Wurmus
75b91fb8bc
import/cran: Recurse for all R packages. 
* guix/import/cran.scm (description->package): Return all R packages, not just
all propagated inputs.

Change-Id: Id1c6ded681e25e29dcef8f8aed1a6be47b36c4a0
 2024-12-03 10:54:28 +01:00
Ricardo Wurmus
6aefd74304
import/cran: Restore memoization for download procedure. 
Fixes <https://issues.guix.gnu.org/44256>.

* guix/import/cran.scm (cran-package-inputs): Avoid passing "#:method #f", so
that there is only one memoization key in the default case.
(fetch-description): Use the full list returned by BIOCONDUCTOR-URI.

Change-Id: I532812b14f4e4d9542bfb9248555be1b09f7d92f
 2024-12-03 10:54:28 +01:00
Ricardo Wurmus
64de165862
gnu: r-xbseq: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-xbseq)[native-inputs]: Add r-testthat.

Change-Id: I7b8eb1c7a7ffcac81b9ead33969b1e57d99a68f3
 2024-12-03 10:54:28 +01:00
Ricardo Wurmus
d4683ff6f6
gnu: r-numbat: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-numbat)[native-inputs]: Add r-testthat.

Change-Id: I3a3db09ba1c69c27a9bc6a67be9346098710fde3
 2024-12-03 10:54:28 +01:00
Ricardo Wurmus
e9e10d311a
gnu: Remove r-numbat. 
This is a duplicate of a package in (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-numbat): Delete variable.

Change-Id: Ic1f5d9779a594432a0dd8bd0be9059423a2f5b34
 2024-12-03 10:54:28 +01:00
Ricardo Wurmus
7ed6c6de0b
gnu: r-spectre: Disable tests. 
* gnu/packages/bioinformatics.scm (r-spectre)[arguments]: Disable tests.

Change-Id: I7978b05d0c1c2de3ada6b1b490ae36b28171f17c
 2024-12-03 10:54:28 +01:00
Ricardo Wurmus
4bb5fa3824
gnu: r-gchain: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-gchain)[native-inputs]: Add
r-pwalign and r-testthat.
[arguments]: Add phase 'skip-bad-tests.

Change-Id: Ia11c6e50e0d2886762ec551df3e5d73ef98547f8
 2024-12-03 10:54:28 +01:00
Ricardo Wurmus
6319836971
gnu: r-flowstats: Add missing inputs. 
* 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
 2024-12-03 10:54:28 +01:00
Ricardo Wurmus
76068dcaae
gnu: r-ggcyto: Add missing inputs. 
* 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
 2024-12-03 10:54:28 +01:00
Ricardo Wurmus
9ba2ddfe40
gnu: r-opencyto: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-opencyto)[native-inputs]: Add
r-flowworkspacedata.
[properties]: Tell updater to add r-flowworkspacedata.

Change-Id: Ife446af466fb4be221f9fdaba53c84bbe80dec86
 2024-12-03 10:54:28 +01:00
Ricardo Wurmus
4e3069a271
gnu: Add r-flowworkspacedata. 
* gnu/packages/bioconductor.scm (r-flowworkspacedata): New variable.

Change-Id: Ie2add925d3fcd3540bc3885427982fb0cee5a146
 2024-12-03 10:54:27 +01:00
Ricardo Wurmus
c132195c1e
gnu: r-bodymaprat: Disable tests. 
* gnu/packages/bioconductor.scm (r-bodymaprat)[arguments]: Disable tests.

Change-Id: Icaa4428e4890a898c35444ae1bedd4258527ee37
 2024-12-03 10:54:27 +01:00
Ricardo Wurmus
ee9754f526
gnu: Add r-methylaiddata. 
* gnu/packages/bioconductor.scm (r-methylaiddata): New variable.

Change-Id: I7711a18b6a5d8e7a431d6a3c713bb3fa26a12e96
 2024-12-03 10:54:27 +01:00
Ricardo Wurmus
96e2c094cb
gnu: r-methylaid: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-methylaid)[native-inputs]: Add r-geoquery,
r-minfidata, and r-minfidataepic.
[properties]: Tell updater to ignore r-methylaiddata.

Change-Id: I11b0e7e76e5ccf4768165634aae86b45606abe40
 2024-12-03 10:54:27 +01:00
Ricardo Wurmus
1fbe57aafa
gnu: Add r-minfidataepic. 
* gnu/packages/bioconductor.scm (r-minfidataepic): New variable.

Change-Id: Icce76beb123c0ad45bac09ec88a259b1b271141f
 2024-12-03 10:54:27 +01:00
Ricardo Wurmus
b3ce31d35f
gnu: Add r-illuminahumanmethylationepicanno-ilm10b2-hg19. 
* gnu/packages/bioconductor.scm
(r-illuminahumanmethylationepicanno-ilm10b2-hg19): New variable.

Change-Id: I110d1b71fa45bc1c5e81399de0a89aab99d45031
 2024-12-03 10:54:27 +01:00
Ricardo Wurmus
d7530d8008
gnu: r-escape: Add missing input. 
* gnu/packages/bioconductor.scm (r-escape)[native-inputs]: Add r-seurat.
[arguments]: Add phase 'delete-bad-tests.

Change-Id: Ie86501a4d283e3dab863bcda5e6cc63cd98d847c
 2024-12-03 10:54:27 +01:00
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