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Author SHA1 Message Date
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
Ricardo Wurmus
055b6f725d
gnu: r-chromunity: Add missing input. 
* gnu/packages/bioinformatics.scm (r-chromunity)[native-inputs]: Add
r-testthat.

Change-Id: I5d208a5ab0cb63567ab49783d0fbe0733b08161a
 2024-12-03 10:54:30 +01:00
Ricardo Wurmus
39cc1b0ac0
gnu: r-cytoml: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-cytoml)[native-inputs]: Add
r-devtools, r-flowclust, r-flowstats, and r-flowworkspacedata.
[properties]: Tell updater to keep extra inputs and ignore others.

Change-Id: I64cfc0b2b424f537b086a7f2f91e1ef15631c461
 2024-12-03 10:54:30 +01:00
Ricardo Wurmus
94c88620db
gnu: r-variantfiltering: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-variantfiltering)[native-inputs]: Add
r-biocstyle, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db, and
r-txdb-hsapiens-ucsc-hg19-knowngene.
[properties]: Tell updater to keep extra inputs.
[arguments]: Add phase 'delete-bad-tests; disable vignettes.

Change-Id: I23e78f1bd49b348719c6e03a116228b5657ae379
 2024-12-03 10:54:30 +01:00
Ricardo Wurmus
a221786237
gnu: Add r-sift-hsapiens-dbsnp137. 
* gnu/packages/bioconductor.scm (r-sift-hsapiens-dbsnp137): New variable.

Change-Id: Ib71a322d3ed0e563f01620e04aca844b290ecc3b
 2024-12-03 10:54:29 +01:00
Ricardo Wurmus
e2c6a92357
gnu: Add r-polyphen-hsapiens-dbsnp131. 
* gnu/packages/bioconductor.scm (r-polyphen-hsapiens-dbsnp131): New variable.

Change-Id: I65ca94c82b3c9c8d9f0faf6f31a04d52e935f127
 2024-12-03 10:54:29 +01:00
Ricardo Wurmus
813ef6d487
gnu: Add r-mafdb-1kgenomes-phase1-hs37d5. 
* gnu/packages/bioconductor.scm (r-mafdb-1kgenomes-phase1-hs37d5): New variable.

Change-Id: Id8827d4a5d788ef2bc4d258048572e697e61b4d2
 2024-12-03 10:54:29 +01:00
Ricardo Wurmus
5cdd9cb901
gnu: r-mmuphin: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-mmuphin)[native-inputs]: Add r-testthat.

Change-Id: I24c838fb0c474cda16a49b48c469d8dfd7194e10
 2024-12-03 10:54:29 +01:00
Ricardo Wurmus
459906a4f8
gnu: r-lefser: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-lefser)[native-inputs]: Add r-mia and
r-withr; remove r-testthat.
[properties]: Tell updater to keep r-mia.

Change-Id: I791e6626a3d000f12a149cdc87979389aee886f0
 2024-12-03 10:54:29 +01:00
Ricardo Wurmus
4e5674c0da
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 10:54:29 +01:00
Ricardo Wurmus
d0226e377b
gnu: r-liana: Add missing input. 
* gnu/packages/bioinformatics.scm (r-liana)[native-inputs]: Add r-testthat.

Change-Id: I04c9c5f60842e1ed0a0415e51c25b46b64a60104
 2024-12-03 10:54:29 +01:00
Ricardo Wurmus
e9a79e867f
gnu: r-abaenrichment: Add missing input. 
* gnu/packages/bioconductor.scm (r-abaenrichment)[native-inputs]: Add
r-testthat.

Change-Id: I3a5a43d3a1b9f7ff81c589efc0a0aade1e666553
 2024-12-03 10:54:29 +01:00
Ricardo Wurmus
b877e65a1d
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 10:54:29 +01:00
Ricardo Wurmus
34071e280e
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 10:54:29 +01:00
Ricardo Wurmus
696172d9d5
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 10:54:29 +01:00
Ricardo Wurmus
ff4b517d8d
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 10:54:29 +01:00
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