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Author SHA1 Message Date
Ricardo Wurmus
ef5e0d7c3c
gnu: r-ensembldb: Disable tests. 
* gnu/packages/bioconductor.scm (r-ensembldb)[arguments]: Disable tests.

Change-Id: Ib12523a7f901f2a37aac9117d008de8bc147385c
 2024-12-03 16:58:39 +01:00
Ricardo Wurmus
722c1b5723
gnu: r-scran: Add test inputs. 
* gnu/packages/bioconductor.scm (r-scran)[native-inputs]: Add
r-delayedmatrixstats, r-hdf5array, and r-testthat.

Change-Id: Icb577c29b7fb27e18beeaf8befb90d39e0491d43
 2024-12-03 16:58:39 +01:00
Ricardo Wurmus
39d92a480b
gnu: r-delayedmatrixstats: Add test inputs. 
* gnu/packages/bioconductor.scm (r-delayedmatrixstats)[native-inputs]: Add
r-hdf5array and r-testthat.

Change-Id: Iefe02c438aa9d52a3206462e41485eea47ff4557
 2024-12-03 16:58:39 +01:00
Ricardo Wurmus
0e66aa3579
gnu: r-genomicfeatures: Disable tests. 
* gnu/packages/bioconductor.scm (r-genomicfeatures)[arguments]: Disable tests.

Change-Id: Ic0513f2736e1100510a365ba1cd78873d8a6436f
 2024-12-03 16:58:39 +01:00
Ricardo Wurmus
edc3eb4d46
gnu: r-biocsingular: Add test inputs. 
* gnu/packages/bioconductor.scm (r-biocsingular)[arguments]: Add phase
'delete-bad-tests.
[native-inputs]: Add r-testthat.

Change-Id: I86eb742c061e21d92ee702494cc11725439c4a7f
 2024-12-03 16:58:39 +01:00
Ricardo Wurmus
28d888832f
gnu: r-beachmat: Add test inputs. 
* gnu/packages/bioconductor.scm (r-beachmat)[arguments]: Add phase
'delete-bad-test.
[native-inputs]: Add r-biocparallel, r-hdf5array, and r-testthat.

Change-Id: I872a0a5329e9a3cbc324a5468f129de96df9b722
 2024-12-03 16:58:39 +01:00
Ricardo Wurmus
890600a029
gnu: r-hdf5array: Add test inputs. 
* gnu/packages/bioconductor.scm (r-hdf5array)[inputs]: Remove empty list.
[arguments]: Add phase 'delete-bad-tests.
[native-inputs]: Add r-biocparallel, r-runit, and r-singlecellexperiment.

Change-Id: Ib51a83a9c1e58d7ce079fd0ed03fd1c55a2f9871
 2024-12-03 16:58:39 +01:00
Ricardo Wurmus
b48924c5c4
gnu: r-zellkonverter: Disable tests. 
* gnu/packages/bioconductor.scm (r-zellkonverter)[arguments]: Disable tests.

Change-Id: Ib40cb7e71d1bf0f627848c9a94334365d4a09bf6
 2024-12-03 16:58:39 +01:00
Ricardo Wurmus
d511971198
gnu: r-rhdf5: Add test inputs. 
* gnu/packages/bioconductor.scm (r-rhdf5)[native-inputs]: Add r-bit64 and
r-testthat.
[arguments]: Add phase 'delete-bad-tests.

Change-Id: Icc44fb7838b397b6777d306c1ee2ddc6bb46d202
 2024-12-03 16:58:39 +01:00
Ricardo Wurmus
b091142af3
gnu: r-limma: Add test inputs. 
* gnu/packages/bioconductor.scm (r-limma)[native-inputs]: Add r-go-db,
r-locfit, r-mass, and r-org-hs-eg-db.

Change-Id: Id279ca7dbe2a55037ba0d6fd63c5260a07325d26
 2024-12-03 16:58:39 +01:00
Ricardo Wurmus
cc08aa837c
gnu: r-graph: Add test inputs. 
* gnu/packages/bioconductor.scm (r-graph)[native-inputs]: Add r-runit and
r-xml.
[arguments]: Add phase 'disable-bad-test.

Change-Id: I5b079ea2eea6df051aae50c9e32e4e1c93f7abf2
 2024-12-03 16:58:38 +01:00
Ricardo Wurmus
e8a7e55313
gnu: Add r-sift-hsapiens-dbsnp132. 
* gnu/packages/bioconductor.scm (r-sift-hsapiens-dbsnp132): New variable.

Change-Id: Iab5456515fd017136b0fa463292c686179f64bd4
 2024-12-03 16:58:19 +01:00
Ricardo Wurmus
d50e73b69c
gnu: Add r-bsgenome-drerio-ucsc-danrer7. 
* gnu/packages/bioconductor.scm (r-bsgenome-drerio-ucsc-danrer7): New variable.

Change-Id: I259d56594ba5ac9dc3191b19333fbc4cbf8e1e7b
 2024-12-03 16:58:18 +01:00
Ricardo Wurmus
f78f547f5f
gnu: Add r-beachmat-hdf5. 
* gnu/packages/bioconductor.scm (r-beachmat-hdf5): New variable.

Change-Id: I77b9f2346ea405bb2c799472ed3cfeeb8c729448
 2024-12-03 16:58:18 +01:00
Ricardo Wurmus
7778981bea
gnu: r-s4vectors: Disable tests. 
* gnu/packages/bioconductor.scm (r-s4vectors)[arguments]: Disable tests.

Change-Id: I0978cd8843046c9da94e58fe155e3370f192caf9
 2024-12-03 16:58:08 +01:00
Ricardo Wurmus
331c853821
gnu: r-rtracklayer: Disable tests. 
* gnu/packages/bioconductor.scm (r-rtracklayer)[arguments]: Disable tests.

Change-Id: I1b6659a3e9d15c91d040c8dbd69bfe32a4d46f87
 2024-12-03 16:58:08 +01:00
Ricardo Wurmus
e0e339ac8c
gnu: r-keggrest: Disable tests. 
* gnu/packages/bioconductor.scm (r-keggrest)[arguments]: Disable tests.

Change-Id: If3a78ec33bbb461c597d9d485b5960400b555383
 2024-12-03 16:58:08 +01:00
Ricardo Wurmus
1b599c691e
gnu: r-genomeinfodb: Disable tests. 
* gnu/packages/bioconductor.scm (r-genomeinfodb)[arguments]: Disable tests.

Change-Id: I0a58cfc91c7ab0cb343c70987a1b4f926b5c05a7
 2024-12-03 16:58:08 +01:00
Ricardo Wurmus
f66f27c16a
gnu: r-biobase: Disable tests. 
* gnu/packages/bioconductor.scm (r-biobase)[arguments]: Disable tests.

Change-Id: Ib8549c0a3dd87e54f5ba52455013d1c373f3ac1c
 2024-12-03 16:58:08 +01:00
Ricardo Wurmus
7397a52214
gnu: r-annotationdbi: Disable tests. 
* gnu/packages/bioconductor.scm (r-annotationdbi)[arguments]: Disable tests.

Change-Id: I09e9e2dce9d8991a70f1272ddffabef132426745
 2024-12-03 16:58:08 +01:00
Ricardo Wurmus
aaf7927c49
gnu: r-annotate: Disable tests. 
* gnu/packages/bioconductor.scm (r-annotate)[arguments]: Disable tests.

Change-Id: I0bb26f7f53743df35282280fc47ac853ed97de5c
 2024-12-03 16:58:08 +01:00
Ricardo Wurmus
0970955ed6
gnu: r-iranges: Disable tests. 
* gnu/packages/bioconductor.scm (r-iranges)[arguments]: Disable tests.

Change-Id: Id9d8e27e1871ab1c7832c1e25a6ab831e5c4aae8
 2024-12-03 16:58:08 +01:00
Ricardo Wurmus
ad8dadc1a0
gnu: r-delayedarray: Disable tests. 
* gnu/packages/bioconductor.scm (r-delayedarray)[arguments]: Disable tests.

Change-Id: Iade075addc7e4f9c80ef0e61618c4a4a7720b5b5
 2024-12-03 16:58:08 +01:00
Ricardo Wurmus
845fa70612
gnu: r-biocgenerics: Disable tests. 
* gnu/packages/bioconductor.scm (r-biocgenerics)[arguments]: Disable tests.

Change-Id: I4c079ec846fa743e664998572bac8c0fec547fa5
 2024-12-03 16:58:08 +01:00
Ricardo Wurmus
6bb5835a54
gnu: r-adacgh2: Keep extra input. 
* gnu/packages/bioconductor.scm (r-adacgh2)[properties]: Tell updater to keep
python-wrapper as extra input.

Change-Id: I3d35a76abced47d842629aa529b8da0a144da436
 2024-12-03 16:58:07 +01:00
Ricardo Wurmus
f3950e65bb
gnu: Add r-pasillabamsubset. 
* gnu/packages/bioconductor.scm (r-pasillabamsubset): New variable.

Change-Id: Ifca1677e6c162799db2bb8f428eb844ba4c6660a
 2024-12-03 16:58:07 +01:00
Ricardo Wurmus
12f819f564
gnu: Add r-hgu95av2-db. 
* gnu/packages/bioconductor.scm (r-hgu95av2-db): New variable.

Change-Id: I59b617db5bab4fb529f29cb12232784fcf692e5f
 2024-12-03 16:58:07 +01:00
Ricardo Wurmus
33eb8fd7c6
gnu: Add r-golubesets. 
* gnu/packages/bioconductor.scm (r-golubesets): New variable.

Change-Id: I31a3bb20e2709f4e694c26cb6b04bb52f5a38ed4
 2024-12-03 16:58:06 +01:00
Ricardo Wurmus
ac7d8e8d93
gnu: r-destiny: Skip examples. 
* gnu/packages/bioconductor.scm (r-destiny)[arguments]: Override 'check phase.
[native-inputs]: Add r-testthat.

Change-Id: I3122f2f033e3b544223a1cc939f5971074e6e3a2
 2024-12-03 16:58:06 +01:00
Ricardo Wurmus
fc7a9a47c0
gnu: r-singlecellexperiment: Update to 1.28.1. 
* gnu/packages/bioconductor.scm (r-singlecellexperiment): Update to 1.28.1.

Change-Id: I0019c76b7907ea518fe87e3a0b79c38a1c16fc60
 2024-12-03 16:58:03 +01:00
Ricardo Wurmus
37a1afab30
gnu: r-universalmotif: Update to 1.24.2. 
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.24.2.

Change-Id: I1d1ead7f3530c9b6fabac88f0d5d085feb6b2e62
 2024-12-03 16:58:03 +01:00
Ricardo Wurmus
6eb9de85a9
gnu: r-ucell: Update to 2.10.1. 
* gnu/packages/bioconductor.scm (r-ucell): Update to 2.10.1.

Change-Id: Id9a7a54371382b3630e77323741f4db3554af0ab
 2024-12-03 16:58:03 +01:00
Ricardo Wurmus
991df15cd6
gnu: r-variancepartition: Update to 1.36.2. 
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.36.2.

Change-Id: I65d4fedf59a5242dbab303b18c9bddf4aa186ecd
 2024-12-03 16:58:03 +01:00
Ricardo Wurmus
f3f5f08652
gnu: r-flames: Update to 2.0.1. 
* gnu/packages/bioconductor.scm (r-flames): Update to 2.0.1.

Change-Id: I63fd65f2a8fb5caa8d97e1ae605f9d6c6a1278d4
 2024-12-03 16:58:03 +01:00
Ricardo Wurmus
a76d9ed4f7
gnu: r-clusterprofiler: Update to 4.14.3. 
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.14.3.

Change-Id: Ic21e53c8fe6f8834d0ff174b87f578a146e9806f
 2024-12-03 16:58:02 +01:00
Ricardo Wurmus
b8930d9d14
gnu: r-enrichplot: Update to 1.26.2. 
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.26.2.

Change-Id: Ib3b4b1fbc3af68d17a5d2a919c249c2efa041893
 2024-12-03 16:58:02 +01:00
Ricardo Wurmus
6ada0f4b6c
gnu: r-structstrings: Update to 1.22.1. 
* gnu/packages/bioconductor.scm (r-structstrings): Update to 1.22.1.

Change-Id: I7eb53a7f0cd9403620f7943e0e4f4ea3d8e40666
 2024-12-03 16:58:02 +01:00
Ricardo Wurmus
e2b7d79196
gnu: r-screpertoire: Update to 2.2.1. 
* gnu/packages/bioconductor.scm (r-screpertoire): Update to 2.2.1.
[propagated-inputs]: Add r-assertthat, r-lifecycle, and r-purrr.

Change-Id: Ibf45b300b192a722920b7e293784af6fa0ccfa94
 2024-12-03 16:58:02 +01:00
Ricardo Wurmus
130e26b84a
gnu: r-muscat: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-muscat): Update to 1.20.0.
[propagated-inputs]: Add r-rlang.

Change-Id: If9b76068b84ce584ffded916b646192716c0b386
 2024-12-03 16:58:02 +01:00
Ricardo Wurmus
9ab1b22e5c
gnu: r-limma: Update to 3.62.1. 
* gnu/packages/bioconductor.scm (r-limma): Update to 3.62.1.

Change-Id: Ie2c1ce64bfcff5c495306311e3562f9fd6da6fe9
 2024-12-03 16:58:02 +01:00
Ricardo Wurmus
d6056b3753
gnu: r-gsva: Update to 2.0.1. 
* gnu/packages/bioconductor.scm (r-gsva): Update to 2.0.1.

Change-Id: Ic8d3e1ee3b9b59bd78e76433d6e77a2bb7b35fb1
 2024-12-03 16:58:02 +01:00
Ricardo Wurmus
bcf75d7cea
gnu: r-alabaster-base: Update to 1.6.1. 
* gnu/packages/bioconductor.scm (r-alabaster-base): Update to 1.6.1.

Change-Id: I60ae24ac892e2547a48fc5f8b35ac23a064880e3
 2024-12-03 16:58:02 +01:00
Ricardo Wurmus
6ae5cd9963
gnu: r-pasilla: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-pasilla): Update to 1.34.0.

Change-Id: I417ef81eee395f92eeea263064d2f7ddb09051e3
 2024-12-03 16:58:02 +01:00
Ricardo Wurmus
6ecb12486c
gnu: r-msigdb: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-msigdb): Update to 1.14.0.

Change-Id: Iee6cf71b97caf4245903886be7dc0953a8fa2015
 2024-12-03 16:58:02 +01:00
Ricardo Wurmus
a977840ab0
gnu: r-msdata: Update to 0.46.0. 
* gnu/packages/bioconductor.scm (r-msdata): Update to 0.46.0.

Change-Id: Idc58f4daba24c9de2a87ae9fd4a2c4e0ed2205ec
 2024-12-03 16:58:02 +01:00
Ricardo Wurmus
e8f70ae16a
gnu: r-mousegastrulationdata: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-mousegastrulationdata): Update to 1.20.0.

Change-Id: I9b298f3de00eee33d27cf1c032a2503aaae338aa
 2024-12-03 16:58:02 +01:00
Ricardo Wurmus
90c74e83f0
gnu: r-escape: Update to 2.2.1. 
* gnu/packages/bioconductor.scm (r-escape): Update to 2.2.1.

Change-Id: Ic39d26698ccd2474e8cef227f215940160708809
 2024-12-03 16:58:02 +01:00
Ricardo Wurmus
21eea9ef43
gnu: r-glimma: Update JavaScript processing. 
* gnu/packages/bioconductor.scm (r-glimma)[arguments]: Use
minify-build-system; update list of JavaScript files to process.
[native-inputs]: Add js-jquery.

Change-Id: I380885b84fe1f6d4d88559c1c2ac01994d070e99
 2024-12-03 16:58:02 +01:00
Ricardo Wurmus
34eed54946
gnu: r-phyloseq: Update to 1.50.0. 
* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.50.0.

Change-Id: I16741509d1bd81e7f887009c53b9ed4cf3267e2d
 2024-12-03 16:58:01 +01:00
Ricardo Wurmus
620d1e268b
gnu: r-tximeta: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.24.0.

Change-Id: I5c28d115ac06e6f0eb17667f6432cb98aec53c8e
 2024-12-03 16:58:01 +01:00