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Author SHA1 Message Date
Ricardo Wurmus
ae3947de67
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 16:59:54 +01:00
Ricardo Wurmus
9fda4a5ac6
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 16:59:54 +01:00
Ricardo Wurmus
ecc52f514d
gnu: r-annotationhubdata: Delete bad tests. 
* gnu/packages/bioconductor.scm (r-annotationhubdata)[arguments]: Add phase
'delete-bad-tests.

Change-Id: Id14228ace239fca4524d92bd09a9298c556b9399
 2024-12-03 16:59:54 +01:00
Ricardo Wurmus
eac2074a6d
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 16:59:54 +01:00
Ricardo Wurmus
4a06a1aca3
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 16:59:54 +01:00
Ricardo Wurmus
8bee3a5910
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 16:59:54 +01:00
Ricardo Wurmus
c851b73e79
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 16:59:54 +01:00
Ricardo Wurmus
716f8a779b
gnu: Add r-msbackendsql. 
* gnu/packages/bioconductor.scm (r-msbackendsql): New variable.

Change-Id: Ie7937f5bcbe26cd53035e9944fe5befbb35efe27
 2024-12-03 16:59:54 +01:00
Ricardo Wurmus
cb19766706
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 16:59:54 +01:00
Ricardo Wurmus
c4d7e1cd4f
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 16:59:53 +01:00
Ricardo Wurmus
10296b8cae
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 16:59:53 +01:00
Ricardo Wurmus
7e64097a9d
gnu: r-gsva: Add missing input. 
* gnu/packages/bioconductor.scm (r-gsva)[native-inputs]: Add r-gsvadata.

Change-Id: I81da88cbbef78885863fe199a5a4e51d67e0c0bf
 2024-12-03 16:59:53 +01:00
Ricardo Wurmus
1065128341
gnu: Add r-gsvadata. 
* gnu/packages/bioconductor.scm (r-gsvadata): New variable.

Change-Id: Ic3bbcf3cff9b0f98597f143041b1b79298215e56
 2024-12-03 16:59:53 +01:00
Ricardo Wurmus
d509499eff
gnu: Add r-hgu95a-db. 
* gnu/packages/bioconductor.scm (r-hgu95a-db): New variable.

Change-Id: I9eb2e8182689a2e1ba38c180d476dd60363f3c51
 2024-12-03 16:59:53 +01:00
Ricardo Wurmus
78db646a99
gnu: r-curatedtcgadata: Add missing input. 
* gnu/packages/bioconductor.scm (r-curatedtcgadata)[native-inputs]: Add
r-testthat.

Change-Id: I9379295f854ab66a88321326c25f8d7a15fe2e26
 2024-12-03 16:59:53 +01:00
Ricardo Wurmus
bb939442b0
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 16:59:53 +01:00
Ricardo Wurmus
066b53965c
gnu: r-anpan: Add missing input. 
* gnu/packages/bioinformatics.scm (r-anpan)[native-inputs]: Add r-testthat.

Change-Id: I69be3fa82db5f9c4e1302c9a3bd2d4f5253bde13
 2024-12-03 16:59:53 +01:00
Ricardo Wurmus
72895370c8
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 16:59:53 +01:00
Ricardo Wurmus
494fcdd782
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 16:59:53 +01:00
Ricardo Wurmus
faec0f7595
gnu: Add r-earth. 
* gnu/packages/cran.scm (r-earth): New variable.

Change-Id: If6ae39912cade13d0d81c1e5178eb20c5017ccb3
 2024-12-03 16:59:53 +01:00
Ricardo Wurmus
eeacb3d98a
gnu: r-openmx: Add missing input. 
* gnu/packages/cran.scm (r-openmx)[native-inputs]: Add r-numderiv.

Change-Id: I7ed2872021b5f164d256704180076bf4618f5e8f
 2024-12-03 16:59:53 +01:00
Ricardo Wurmus
efed932ad9
gnu: Add r-plotmo. 
* gnu/packages/cran.scm (r-plotmo): New variable.

Change-Id: Id0803e02acc72f1f98429f023b1d673453fde302
 2024-12-03 16:59:53 +01:00
Ricardo Wurmus
b0e687ae7d
gnu: r-kmer: Add missing input. 
* gnu/packages/cran.scm (r-kmer)[native-inputs]: Add r-knitr.

Change-Id: Ia28f582637d27c87413af1169ae816ee05377652
 2024-12-03 16:59:53 +01:00
Ricardo Wurmus
b49b7e07ee
gnu: r-devtools: Add missing input. 
* gnu/packages/statistics.scm (r-devtools)[native-inputs]: Add r-mockery.

Change-Id: I2d67a549e9eaee339b5362dac54d417deec850b9
 2024-12-03 16:59:53 +01:00
Ricardo Wurmus
5a2ba07676
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 16:59:52 +01:00
Ricardo Wurmus
5ae3a6d466
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 16:59:52 +01:00
Ricardo Wurmus
0f2aef7905
gnu: r-haplo-stats: Fix vignettes. 
* gnu/packages/cran.scm (r-haplo-stats)[arguments]: Add phase 'set-HOME.

Change-Id: Ia1f5e5c33753b2261c7b4dc2ffa40322e9c840a9
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
1b3cc3e173
gnu: r-celldex: Disable tests. 
* gnu/packages/bioconductor.scm (r-celldex)[arguments]: Disable tests.

Change-Id: I1881b1793f2fe8bc870697976a5c3434147760ca
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
4bd824791d
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 16:59:52 +01:00
Ricardo Wurmus
4b78a0dde4
gnu: r-ewastools: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-ewastools)[native-inputs]: Add r-enmix,
r-illuminahumanmethylationepicanno-ilm10b4-hg19, r-minfi, r-stringi, and
r-testthat.

Change-Id: I8ba2b1c46a4898b27874a7dc8648bb142f4b5a70
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
1117a49258
gnu: r-enmix: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-enmix)[native-inputs]: Add r-minfidata.

Change-Id: I0afa8a677c1b91ffec7463b2ed11aadd01a16797
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
e40daf6a10
gnu: r-untb: Add missing inputs and disable vignettes. 
* gnu/packages/cran.scm (r-untb)[arguments]: Skip building vignettes.
[native-inputs]: Add r-vdiffr.

Change-Id: I0e3a8a075fd34f28cee1a76a443c215f500e5012
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
095516d897
gnu: r-dalex: Add test inputs. 
* gnu/packages/cran.scm (r-dalex)[native-inputs]: Add r-gower and r-ranger.

Change-Id: I2a2de0275dff4a664fbfb660f7cbf065928dddc0
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
142a2953a3
gnu: r-minfi: Disable tests. 
* gnu/packages/bioconductor.scm (r-minfi)[arguments]: Disable tests.

Change-Id: I6fdb8d78c176c2ebbfbd9289a00833b79448c7a2
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
387ca84d52
gnu: r-bamutils: Add test inputs and disable tests. 
* gnu/packages/bioinformatics.scm (r-bamutils)[arguments]: Disable tests.
[native-inputs]: Add r-testthat and samtools.

Change-Id: I781c38fb59355a51f2cd27a833d7ed5dbe5277ab
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
bf20a8fb15
gnu: r-bamutils: Update to 0.0.0.9000-2.0a7d2d9. 
* gnu/packages/bioinformatics.scm (r-bamutils): Update to
0.0.0.9000-2.0a7d2d9.

Change-Id: I04e86c2ff1059f23a34615ac6067926cdd9cb355
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
c39817a194
gnu: r-rbamtools: Disable tests. 
* gnu/packages/cran.scm (r-rbamtools)[arguments]: Disable tests.

Change-Id: I6a16095454d3d58de23786bec21b54245dc5a462
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
ec88f1db4e
gnu: r-chippeakanno: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-chippeakanno)[native-inputs]: Add
r-biomart, r-bsgenome-celegans-ucsc-ce10, r-bsgenome-drerio-ucsc-danrer7,
r-bsgenome-hsapiens-ucsc-hg19, r-ensdb-hsapiens-v79, r-org-ce-eg-db,
r-org-hs-eg-db, r-reactome-db, and r-txdb-hsapiens-ucsc-hg38-knowngene.

Change-Id: Ifd3e71dcca3297c03c9cc93da6c677a274c58b2c
 2024-12-03 16:59:51 +01:00
Ricardo Wurmus
0af4107d9f
gnu: r-arrow: Add missing input. 
* gnu/packages/cran.scm (r-arrow)[native-inputs]: Add glibc-utf8-locales,
r-dplyr, r-hms, r-lubridate, r-stringr, r-tibble, and tzdata-for-tests.
[arguments]: Add phases 'delete-bad-tests, 'set-test-locale, and
'set-timezone.

Change-Id: Iece4e463ebe73d41a42594eff7850f2efa96b26f
 2024-12-03 16:59:51 +01:00
Ricardo Wurmus
527598ca24
gnu: r-annotatr: Disable tests. 
* gnu/packages/bioconductor.scm (r-annotatr)[arguments]: Disable tests.

Change-Id: I819fe4bc651c39315ba6d42e34d36b505979003d
 2024-12-03 16:59:51 +01:00
Ricardo Wurmus
4860cad2d6
gnu: r-lpsymphony: Add missing input. 
* gnu/packages/bioconductor.scm (r-lpsymphony)[native-inputs]: Add gfortran.

Change-Id: Id5bcbdb1bf19364fc8cbee905efb18698893f771
 2024-12-03 16:59:51 +01:00
Ricardo Wurmus
641d197db5
gnu: r-multiassayexperiment: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-multiassayexperiment)[native-inputs]: Add
r-hdf5array, r-raggedexperiment, and r-reshape2.
[arguments]: Add phase 'set-HOME.

Change-Id: Ifafc630ebd32cc255a4d7fd1c190a885e2f7020f
 2024-12-03 16:59:51 +01:00
Ricardo Wurmus
404ce6d28b
gnu: r-phylogram: Add missing input. 
* gnu/packages/cran.scm (r-phylogram)[native-inputs]: Add r-knitr.

Change-Id: Ib2e4816c516cc5af9f9495c925e9e244453d30c9
 2024-12-03 16:59:51 +01:00
Ricardo Wurmus
6dfbabc8e9
gnu: r-dicekriging: Add missing inputs. 
* gnu/packages/cran.scm (r-dicekriging)[native-inputs]: Add r-numderiv.

Change-Id: Ie5ac8b8e7d9c809ee06d26988c582d91d78fdfe6
 2024-12-03 16:59:51 +01:00
Ricardo Wurmus
8b01aff62e
gnu: r-mvnfast: Disable tests. 
* gnu/packages/cran.scm (r-mvnfast)[arguments]: Disable tests.

Change-Id: I2c4ad28984200081faa328fbd606aff22c2bd0cb
 2024-12-03 16:59:51 +01:00
Ricardo Wurmus
f73d165d7a
gnu: r-janitor: Fix tests. 
* gnu/packages/cran.scm (r-janitor)[native-inputs]: Add tzdata-for-tests.
[arguments]: Add phases 'set-timezone and 'delete-bad-tests.

Change-Id: Ibbea9ef585d6697e93c31d46b1ff7cc4e23e0e17
 2024-12-03 16:59:51 +01:00
Ricardo Wurmus
82c028588d
gnu: r-trajectoryutils: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-trajectoryutils)[native-inputs]: Add
r-biocneighbors and r-delayedmatrixstats.

Change-Id: Id49b6e481ebae657f40aba4692dda4de4e2d5bd1
 2024-12-03 16:59:51 +01:00
Ricardo Wurmus
915cf0626d
gnu: r-reinforcelearn: Add missing inputs. 
* gnu/packages/cran.scm (r-reinforcelearn)[native-inputs]: Add r-knitr and
r-testthat.

Change-Id: I71965722253610030cce43e34d299891760cdc9f
 2024-12-03 16:59:51 +01:00
Ricardo Wurmus
e4a8fb8078
gnu: r-bigmemoryextras: Add missing input. 
* gnu/packages/bioconductor.scm (r-bigmemoryextras)[native-inputs]: Add
r-testthat.

Change-Id: Iafc29855c30e74c055f157303e3c2f351f0e7aeb
 2024-12-03 16:59:51 +01:00
Ricardo Wurmus
5fc92ca9e3
gnu: r-leidenbase: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-leidenbase)[native-inputs]: Add r-knitr and
r-testthat.

Change-Id: I35e5aebbe6a5e44dea1743f011e4a3a362f6efb1
 2024-12-03 16:59:51 +01:00