mirror/guix
1
0
Fork 0
mirror of https://git.savannah.gnu.org/git/guix.git synced 2025-01-19 14:07:01 +01:00
Code Issues Projects Releases Packages Wiki Activity Actions
148241 commits 90 branches 36 tags 694 MiB
Commit graph

148241 commits

This branch
This branch
All branches
Author SHA1 Message Date
Ricardo Wurmus
baef0f8bb3
gnu: Add r-cytoexplorerdata. 
* gnu/packages/bioinformatics.scm (r-cytoexplorerdata): New variable.

Change-Id: I5565dff552f033c951bee5bac474cb05c7034066
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
ed7d8f576a
gnu: r-vsn: Add missing input. 
* gnu/packages/bioconductor.scm (r-vsn)[native-inputs]: Add r-biocstyle.

Change-Id: I12b619b0ae134132a4536b0e54e1182a55ea816c
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
61c16f3e55
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 16:59:58 +01:00
Ricardo Wurmus
e335531bbd
gnu: r-cicero-monocle3: Disable failing test. 
* gnu/packages/bioconductor.scm (r-cicero-monocle3)[arguments]: Disable
failing test.

Change-Id: I92d3878ee189403478309837214e09fe66874b69
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
1e335d0c52
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 16:59:58 +01:00
Ricardo Wurmus
bd109162b3
gnu: r-scseqcomm: Remove commented inputs. 
* gnu/packages/bioinformatics.scm (r-scseqcomm): Remove comments.

Change-Id: I537f6377da44637674a0413a30ddd6b70a620ad3
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
0b3aa43797
gnu: r-chromunity: Add missing input. 
* gnu/packages/bioinformatics.scm (r-chromunity)[native-inputs]: Add
r-testthat.

Change-Id: I5d208a5ab0cb63567ab49783d0fbe0733b08161a
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
cec92c060e
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 16:59:58 +01:00
Ricardo Wurmus
18c5a3b324
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 16:59:57 +01:00
Ricardo Wurmus
8dd751f114
gnu: Add r-sift-hsapiens-dbsnp137. 
* gnu/packages/bioconductor.scm (r-sift-hsapiens-dbsnp137): New variable.

Change-Id: Ib71a322d3ed0e563f01620e04aca844b290ecc3b
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
a9dc352e79
gnu: Add r-polyphen-hsapiens-dbsnp131. 
* gnu/packages/bioconductor.scm (r-polyphen-hsapiens-dbsnp131): New variable.

Change-Id: I65ca94c82b3c9c8d9f0faf6f31a04d52e935f127
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
8417b0f27a
gnu: Add r-mafdb-1kgenomes-phase1-hs37d5. 
* gnu/packages/bioconductor.scm (r-mafdb-1kgenomes-phase1-hs37d5): New variable.

Change-Id: Id8827d4a5d788ef2bc4d258048572e697e61b4d2
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
f1d03188a6
gnu: r-mmuphin: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-mmuphin)[native-inputs]: Add r-testthat.

Change-Id: I24c838fb0c474cda16a49b48c469d8dfd7194e10
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
12968c7675
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 16:59:57 +01:00
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