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Author SHA1 Message Date
Ricardo Wurmus
e90cc282f1
gnu: r-sesamedata: Disable tests. 
* gnu/packages/bioconductor.scm (r-sesamedata)[arguments]: Disable tests.
[properties]: Tell updater to ignore r-sesame.

Change-Id: I42e3a2d83963e79a21db70f4c1f8ddf92107943f
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
64e941ef7a
gnu: r-liana: Add missing input. 
* gnu/packages/bioinformatics.scm (r-liana)[native-inputs]: Add r-testthat.

Change-Id: I04c9c5f60842e1ed0a0415e51c25b46b64a60104
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
d8ad680471
gnu: r-abaenrichment: Add missing input. 
* gnu/packages/bioconductor.scm (r-abaenrichment)[native-inputs]: Add
r-testthat.

Change-Id: I3a5a43d3a1b9f7ff81c589efc0a0aade1e666553
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
8dcf48ab94
gnu: r-mosdef: Add missing inputs. 
* 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
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
587ec117f4
gnu: r-diffbind: Add missing inputs and skip vignettes. 
* 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
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
3c2964c923
gnu: r-quasr: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-quasr)[native-inputs]: Add
r-genomicalignments and r-rhisat2.
[properties]: Tell updater to keep r-rhisat2.

Change-Id: I304824e27d39f76a1de2aeb1e77c32f5d6faf70e
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
8f9b6c3137
gnu: r-bgeecall: Add missing inputs and disable tests. 
* gnu/packages/bioconductor.scm (r-bgeecall)[native-inputs]: Add
r-annotationhub and r-httr.
[arguments]: Disable tests.

Change-Id: Ic2ea9e81075c70501d53df556ab9548d46ac24ae
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
17c1e8ef1b
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 16:59:57 +01:00
Ricardo Wurmus
84c3b169b9
gnu: r-conos: Add missing input. 
* gnu/packages/bioconductor.scm (r-conos)[native-inputs]: Add r-pagoda2.

Change-Id: I9b12a3c3ba727d7e6101fa2566c42c0a6858d601
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
3e72995a28
gnu: r-maaslin2: Add missing input. 
* gnu/packages/bioconductor.scm (r-maaslin2)[native-inputs]: Add r-testthat.

Change-Id: I044a9bf1f1e53f0988760f84b822beb6b6779291
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
324ea9c11d
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 16:59:56 +01:00
Ricardo Wurmus
f6b6eb26b9
gnu: r-circus: Add missing input. 
* gnu/packages/bioinformatics.scm (r-circus)[native-inputs]: Add r-testthat.

Change-Id: I7178baece0a8134923fd550e2f1cc303f32aaaea
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
23251014aa
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 16:59:56 +01:00
Ricardo Wurmus
ddb2a9572e
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 16:59:56 +01:00
Ricardo Wurmus
f0a93b18b4
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 16:59:56 +01:00
Ricardo Wurmus
8c6114b920
gnu: r-xbseq: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-xbseq)[native-inputs]: Add r-testthat.

Change-Id: I7b8eb1c7a7ffcac81b9ead33969b1e57d99a68f3
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
8762488487
gnu: r-numbat: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-numbat)[native-inputs]: Add r-testthat.

Change-Id: I3a3db09ba1c69c27a9bc6a67be9346098710fde3
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
e3bbf678e3
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 16:59:56 +01:00
Ricardo Wurmus
dff6f58688
gnu: r-spectre: Disable tests. 
* gnu/packages/bioinformatics.scm (r-spectre)[arguments]: Disable tests.

Change-Id: I7978b05d0c1c2de3ada6b1b490ae36b28171f17c
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
e2561d2ec8
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 16:59:56 +01:00
Ricardo Wurmus
d2d2b4d4cb
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 16:59:56 +01:00
Ricardo Wurmus
f0480849b8
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 16:59:56 +01:00
Ricardo Wurmus
b935741c09
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 16:59:56 +01:00
Ricardo Wurmus
d19945f198
gnu: Add r-flowworkspacedata. 
* gnu/packages/bioconductor.scm (r-flowworkspacedata): New variable.

Change-Id: Ie2add925d3fcd3540bc3885427982fb0cee5a146
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
0eec5846bb
gnu: r-bodymaprat: Disable tests. 
* gnu/packages/bioconductor.scm (r-bodymaprat)[arguments]: Disable tests.

Change-Id: Icaa4428e4890a898c35444ae1bedd4258527ee37
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
cd9f1389d3
gnu: Add r-methylaiddata. 
* gnu/packages/bioconductor.scm (r-methylaiddata): New variable.

Change-Id: I7711a18b6a5d8e7a431d6a3c713bb3fa26a12e96
 2024-12-03 16:59:55 +01:00
Ricardo Wurmus
3dcb5dcfb7
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 16:59:55 +01:00
Ricardo Wurmus
f9e84b561a
gnu: Add r-minfidataepic. 
* gnu/packages/bioconductor.scm (r-minfidataepic): New variable.

Change-Id: Icce76beb123c0ad45bac09ec88a259b1b271141f
 2024-12-03 16:59:55 +01:00
Ricardo Wurmus
81d799711c
gnu: Add r-illuminahumanmethylationepicanno-ilm10b2-hg19. 
* gnu/packages/bioconductor.scm
(r-illuminahumanmethylationepicanno-ilm10b2-hg19): New variable.

Change-Id: I110d1b71fa45bc1c5e81399de0a89aab99d45031
 2024-12-03 16:59:55 +01:00
Ricardo Wurmus
aae349d50f
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 16:59:55 +01:00
Ricardo Wurmus
3e956d6adf
gnu: r-pathview: Disable vignettes. 
* gnu/packages/bioconductor.scm (r-pathview)[arguments]: Skip vignettes.

Change-Id: I8ab4558fba53a44db4d6e1dceee560ce6b3e67dd
 2024-12-03 16:59:55 +01:00
Ricardo Wurmus
5f6d02dbe7
gnu: r-brms: Fix vignettes. 
* gnu/packages/cran.scm (r-brms)[arguments]: Add phase 'set-HOME.

Change-Id: Ife0fcc2352b8bf47356c1684687fdf26b0281f6f
 2024-12-03 16:59:55 +01:00
Ricardo Wurmus
694d3a4e8a
gnu: r-cycombine: Add missing input. 
* gnu/packages/bioconductor.scm (r-cycombine)[native-inputs]: Add r-testthat.

Change-Id: I101d0109153f04dbf3b9a3d96c2b1c9a9f676f63
 2024-12-03 16:59:55 +01:00
Ricardo Wurmus
32b097e015
gnu: r-catalyst: Add missing input. 
* gnu/packages/bioconductor.scm (r-catalyst)[native-inputs]: Add r-diffcyt.

Change-Id: Ifa4bf1c432bb23e2b3570595c6bbe0b4279e27e9
 2024-12-03 16:59:55 +01:00
Ricardo Wurmus
07d3a6f19a
gnu: r-adductomicsr: Disable tests. 
* gnu/packages/bioconductor.scm (r-adductomicsr)[arguments]: Disable tests.

Change-Id: Ibcacce27e8a62038bb5d24864125986889733e8c
 2024-12-03 16:59:55 +01:00
Ricardo Wurmus
5d6561a87d
gnu: r-seraster: Add missing input. 
* gnu/packages/bioinformatics.scm (r-seraster)[native-inputs]: Add r-testthat.

Change-Id: I88fb4a51831aff1b08437ef08adb62e344185a07
 2024-12-03 16:59:55 +01:00
Ricardo Wurmus
cc5c5ad67e
gnu: r-httpgd: Add missing input. 
* gnu/packages/statistics.scm (r-httpgd)[native-inputs]: Add r-testthat.

Change-Id: Iefadbf9fd0bba743210d3c55b8355b793fcb2b25
 2024-12-03 16:59:55 +01:00
Ricardo Wurmus
f577adac87
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 16:59:55 +01:00
Ricardo Wurmus
951bdcc925
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 16:59:55 +01:00
Ricardo Wurmus
041a02c2ad
gnu: Add r-derfinderdata. 
* gnu/packages/bioconductor.scm (r-derfinderdata): New variable.

Change-Id: I735030fad98b4eb20e0898d7f4779cd4c06ec82c
 2024-12-03 16:59:55 +01:00
Ricardo Wurmus
6a03ed4b28
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 16:59:54 +01:00
Ricardo Wurmus
571dcd7e3b
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 16:59:54 +01:00
Ricardo Wurmus
8971ac5f4f
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 16:59:54 +01:00
Ricardo Wurmus
a71eb95c0f
gnu: r-flowworkspace: Disable tests. 
* gnu/packages/bioconductor.scm (r-flowworkspace)[arguments]: Disable tests.

Change-Id: Idb8abe5b056c3f67c44377782869b35620370aa9
 2024-12-03 16:59:54 +01:00
Ricardo Wurmus
62c0eda7f4
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 16:59:54 +01:00
Ricardo Wurmus
1bdde11073
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 16:59:54 +01:00
Ricardo Wurmus
a4a110c6c6
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 16:59:54 +01:00
Ricardo Wurmus
014ee99b5f
gnu: r-chromstar: Add missing input. 
* gnu/packages/bioconductor.scm (r-chromstar)[native-inputs]: Add r-testthat.

Change-Id: I29897bb94f587adf210395dd28b6e3dc480ac74c
 2024-12-03 16:59:54 +01:00
Ricardo Wurmus
88ce625adb
gnu: r-gtrack: Add missing input. 
* gnu/packages/bioinformatics.scm (r-gtrack)[native-inputs]: Add r-testthat.

Change-Id: I7b0cad1b8fd27d88ff766c5a46bd01dae2933422
 2024-12-03 16:59:54 +01:00
Ricardo Wurmus
47d6e1bab7
gnu: r-biocpkgtools: Disable tests. 
* gnu/packages/bioconductor.scm (r-biocpkgtools)[arguments]: Disable tests.

Change-Id: Id96ca07103e762fa267c83a178c4367855cdc5c8
 2024-12-03 16:59:54 +01:00