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Author SHA1 Message Date
Ricardo Wurmus
eb85e6430a
gnu: Add r-anvilgcp. 
* gnu/packages/bioconductor.scm (r-anvilgcp): New variable.

Change-Id: I82bcd1a276c8d6290b870fe81ac743e8ab0b1184
 2025-04-16 11:00:42 +02:00
Ricardo Wurmus
4b4b58b79a
gnu: Add r-txdb-dmelanogaster-ucsc-dm3-ensgene. 
* gnu/packages/bioconductor.scm (r-txdb-dmelanogaster-ucsc-dm3-ensgene): New variable.

Change-Id: I5555a99f9849106c0741121320e5e90b37bae752
 2025-04-16 11:00:42 +02:00
Ricardo Wurmus
21ce2b4086
gnu: r-bisquerna: Add test input. 
* gnu/packages/bioconductor.scm (r-bisquerna)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-plyr.

Change-Id: Ic490076e7a34e5e81b6c83ee82566c4197faaffe
 2025-04-16 11:00:30 +02:00
Ricardo Wurmus
6144fe944a
gnu: r-cytolib: Update to 2.18.2. 
* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.18.2.
[inputs]: Remove openblas and zlib.

Change-Id: I09471134262fcbbe364dd90ca3500a596953eb3c
 2025-04-16 11:00:30 +02:00
Ricardo Wurmus
0c3c8a67c4
gnu: r-densvis: Disable tests. 
* gnu/packages/bioconductor.scm (r-densvis)[arguments]: Disable tests.

Change-Id: Iceee314fcb63566854886be13dd91bdd7acf8e1b
 2025-04-16 11:00:30 +02:00
Ricardo Wurmus
9c0ca928d3
gnu: r-msigdb: Disable tests. 
* gnu/packages/bioconductor.scm (r-msigdb)[arguments]: Disable tests.

Change-Id: Id58ad75c7a6e37b3ad60e9be3288cf0163f31fc4
 2025-04-16 11:00:30 +02:00
Ricardo Wurmus
3b47971382
gnu: r-dose: Disable tests. 
* gnu/packages/bioconductor.scm (r-dose)[arguments]: Disable tests.

Change-Id: I1776b50523925f2fb2250538409a9d1ddbd3e246
 2025-04-16 11:00:30 +02:00
Ricardo Wurmus
a4e2a0d583
gnu: r-gosemsim: Add test input. 
* gnu/packages/bioconductor.scm (r-gosemsim)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-org-hs-eg-db.

Change-Id: I1d15da54ed1581535d77e880ad08c634221c2df7
 2025-04-16 11:00:30 +02:00
Ricardo Wurmus
e03a93db85
gnu: r-biocdockermanager: Disable tests. 
* gnu/packages/bioconductor.scm (r-biocdockermanager)[arguments]: Disable
tests.

Change-Id: Ie006490f2894995d4c06927dd14355b283993a72
 2025-04-16 11:00:30 +02:00
Ricardo Wurmus
4240add223
gnu: r-curatedtcgadata: Disable tests. 
* gnu/packages/bioconductor.scm (r-curatedtcgadata)[arguments]:
Disable tests.

Change-Id: I37fe309b5d23ce113428254bc7e5a364c39c77f5
 2025-04-16 11:00:29 +02:00
Ricardo Wurmus
34802a98ae
gnu: r-qfeatures: Add test inputs. 
* gnu/packages/bioconductor.scm (r-qfeatures)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-impute, r-preprocesscore, r-singlecellexperiment, and
r-vsn.

Change-Id: If167d6a5a092b0c7e5c90db758585e8118c2d8bd
 2025-04-16 11:00:29 +02:00
Ricardo Wurmus
1f2fecadd3
gnu: r-metabocoreutils: Add test input. 
* gnu/packages/bioconductor.scm (r-metabocoreutils)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-robustbase.

Change-Id: I7382fa9cfdb171e14152a3de3766a9adcaa2bad6
 2025-04-16 11:00:29 +02:00
Ricardo Wurmus
6c8f2c68eb
gnu: r-mscoreutils: Add test inputs. 
* gnu/packages/bioconductor.scm (r-mscoreutils)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-impute, r-imputelcmd, r-matrix, r-missforest, r-norm,
r-pcamethods, r-preprocesscore, and r-vsn.

Change-Id: Id3566a7598cf05728b6f9842da2375f5e9033278
 2025-04-16 11:00:29 +02:00
Ricardo Wurmus
7a0d041472
gnu: r-genie3: Add test inputs. 
* gnu/packages/bioconductor.scm (r-genie3)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-biobase and r-summarizedexperiment.

Change-Id: I6c46d8decf383ace85a0fa5c053753e9ed008ead
 2025-04-16 11:00:28 +02:00
Ricardo Wurmus
8859980639
gnu: r-beclear: Add test input. 
* gnu/packages/bioconductor.scm (r-beclear)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-seewave.

Change-Id: Ibba2ccd27930582269a794be61841a221b6148e8
 2025-04-16 11:00:28 +02:00
Ricardo Wurmus
d9b188b00a
gnu: r-bigmemoryextras: Disable tests. 
* gnu/packages/bioconductor.scm (r-bigmemoryextras)[arguments]: Disable tests.

Change-Id: I4e104437f8952eb3f411bfd881c0c8e0225d4fb7
 2025-04-16 11:00:28 +02:00
Ricardo Wurmus
8c8bb7aa20
gnu: r-bsseq: Add test input. 
* gnu/packages/bioconductor.scm (r-bsseq)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-batchtools.

Change-Id: Iaea22f0ea5edb6f8cda9cac106d6805f61dbc735
 2025-04-16 11:00:28 +02:00
Ricardo Wurmus
a56318df98
gnu: r-dexseq: Disable tests. 
* gnu/packages/bioconductor.scm (r-dexseq)[arguments]: Disable tests.

Change-Id: Ica5451100fe261f401dc68dc526546425a1c7505
 2025-04-16 11:00:28 +02:00
Ricardo Wurmus
cb0352c27b
gnu: r-awst: Add test input. 
* gnu/packages/bioconductor.scm (r-awst)[native-inputs]: Add r-edaseq.
[properties]: Record updater-extra-native-inputs.

Change-Id: Id785bac10cc783de9d863f8e1cc97644ea7dc5fc
 2025-04-16 11:00:28 +02:00
Ricardo Wurmus
7d2e0a653d
gnu: r-decoupler: Add test inputs. 
* gnu/packages/bioconductor.scm (r-decoupler)[properties]: Record
updater-extra-native-inputs.
[arguments]: Add phase 'disable-bad-tests.
[native-inputs]: Add r-aucell, r-fgsea, r-gsva, r-omnipathr, r-ranger, and
r-rpart.

Change-Id: I592a34dc911c113ddf44539dc3033f555bfb415d
 2025-04-16 11:00:27 +02:00
Ricardo Wurmus
9c3fffb966
gnu: r-fgsea: Update to 1.32.2. 
* gnu/packages/bioconductor.scm (r-fgsea): Update to 1.32.2.

Change-Id: I89b790d713ed59d0ec5d5ebcbcd60e5065df69c3
 2025-04-16 11:00:27 +02:00
Ricardo Wurmus
d19e2971b3
gnu: r-preprocesscore: Disable threading. 
Since we use OpenBLAS we cannot use threading.  See
https://github.com/Bioconductor/bioconductor_docker/issues/22 for details.

* gnu/packages/bioconductor.scm (r-preprocesscore)[arguments]: Enable tests;
disable threading; add phase 'disable-threading.

Change-Id: I6ceeeddfe713ffd7dc2ef65c2a808a2b3d0ea7c1
 2025-04-16 10:59:56 +02:00
Ricardo Wurmus
fde63a41ff
gnu: r-valr: Update to 0.8.3. 
* gnu/packages/bioconductor.scm (r-valr): Update to 0.8.3.
[propagated-inputs]: Add r-cpp11bigwig; remove r-rtracklayer.
[native-inputs]: Add r-vdiffr.

Change-Id: I5ce361a8e0525257c22b5ef06c70ba42752992ad
 2025-04-16 10:59:54 +02:00
Ricardo Wurmus
635e3b8881
gnu: r-tximeta: Disable tests. 
* gnu/packages/bioconductor.scm (r-tximeta)[arguments]: Disable tests.

Change-Id: I1e22647d10715b4deb2dafd2a00f0582b201a01b
 2025-04-16 10:59:54 +02:00
Ricardo Wurmus
c02443448c
gnu: r-spatialexperiment: Disable tests. 
* gnu/packages/bioconductor.scm (r-spatialexperiment)[arguments]: Disable
tests.

Change-Id: Ia4434f4330b7f2d79590c5ecbcc99dc38e884d5b
 2025-04-16 10:59:54 +02:00
Ricardo Wurmus
6e390133ce
gnu: r-scran: Add test inputs and delete bad tests. 
* gnu/packages/bioconductor.scm (r-scran)[arguments]: Add phase
'delete-bad-tests.
[native-inputs]: Add r-dynamictreecut and r-residualmatrix.
[properties]: Record updater-extra-native-inputs.

Change-Id: Iaf4b971a2bb7cdb1f8bb34879c1b66e3525196e4
 2025-04-16 10:59:54 +02:00
Ricardo Wurmus
f74b3f6ec0
gnu: r-scater: Add test inputs. 
* gnu/packages/bioconductor.scm (r-scater)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-delayedmatrixstats, r-robustbase, r-scattermore, and
r-sparsematrixstats.

Change-Id: I9f36c9c86a2ded39a6628a4851e36e71cff47626
 2025-04-16 10:59:53 +02:00
Ricardo Wurmus
b557d0d0f6
gnu: r-scuttle: Add test inputs. 
* gnu/packages/bioconductor.scm (r-scuttle)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-delayedmatrixstats and r-sparsematrixstats.

Change-Id: Ie8f095eb5c61bd6ee6e8294ca0bb1a60c2e8790c
 2025-04-16 10:59:53 +02:00
Ricardo Wurmus
f4fbbb0083
gnu: r-s4arrays: Disable tests. 
* gnu/packages/bioconductor.scm (r-s4arrays)[properties]: Record
updater-ignored-native-inputs.
[arguments]: Disable tests.

Change-Id: I51ac55b4c519fd95a5fc6bea1e57f984f59474a5
 2025-04-16 10:59:53 +02:00
Ricardo Wurmus
c96b0f3813
gnu: r-ucsc-utils: Disable tests. 
* gnu/packages/bioconductor.scm (r-ucsc-utils)[arguments]: Disable tests.

Change-Id: Id01c315cdfbca4f8f7816dfca586e44a4688fab9
 2025-04-16 10:59:53 +02:00
Ricardo Wurmus
a7ee9359da
gnu: r-biocneighbors: Add test input. 
* gnu/packages/bioconductor.scm (r-biocneighbors)[native-inputs]: Add
r-biocparallel.

Change-Id: Iae4a0be70263f60e4c8700047f15640760c12d62
 2025-04-16 10:59:53 +02:00
Ricardo Wurmus
6f20da43b3
gnu: r-glmgampoi: Delete bad test. 
* gnu/packages/bioconductor.scm (r-glmgampoi)[arguments]: Add phase
'delete-bad-tests.

Change-Id: I86d6e61d2cf452aae35a76a1535c6ba8e0311899
 2025-04-16 10:59:53 +02:00
Ricardo Wurmus
0ccd8f222a
gnu: r-mbkmeans: Add test input. 
* gnu/packages/bioconductor.scm (r-mbkmeans)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-hdf5array.

Change-Id: I719f38814ce5bd79a509db2b1daf9133501fdb69
 2025-04-16 10:59:53 +02:00
Ricardo Wurmus
a50fedc120
gnu: r-bluster: Add test inputs. 
* gnu/packages/bioconductor.scm (r-bluster)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-apcluster, r-dirichletmultinomial, r-dynamictreecut,
r-kohonen, r-mbkmeans, and r-vegan.

Change-Id: I112c88ade50df7e87b810c0b4049fd97c7de9afc
 2025-04-16 10:59:53 +02:00
Ricardo Wurmus
cfefe006de
gnu: r-biomart: Disable one failing test. 
* gnu/packages/bioconductor.scm (r-biomart)[arguments]: Delete one more test
file.

Change-Id: Idc504762bce251fd54ff92f4ef79e0f47ca9c868
 2025-04-16 10:59:52 +02:00
Ricardo Wurmus
1409b53e84
gnu: r-tximport: Disable test and add build inputs. 
* gnu/packages/bioconductor.scm (r-tximport)[arguments]: Disable tests.
[native-inputs]: Add r-matrix, r-matrixstats, and r-rhdf5.
[properties]: Record updater-extra-native-inputs.

Change-Id: I2880186860423a989741c179206c293c096ac03b
 2025-04-16 10:59:52 +02:00
Ricardo Wurmus
781e9d0594
gnu: r-deseq2: Add test inputs. 
* gnu/packages/bioconductor.scm (r-deseq2)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-apeglm, r-ashr, r-glmgampoi, r-readr, r-tximeta,
r-tximport, and r-tximportdata.

Change-Id: Ia5857e5337b6ba5f66a05fc4718b13584d730679
 2025-04-16 10:59:52 +02:00
Ricardo Wurmus
2c97b57b73
gnu: r-numbat: Update to 1.4.2. 
* gnu/packages/bioconductor.scm (r-numbat): Update to 1.4.2.
[propagated-inputs]: Add r-hahmmr.

Change-Id: Iffaee79e4e9ab87aaae9866b7995268eeaddb4a6
 2025-04-16 10:59:45 +02:00
Ricardo Wurmus
634a1318b8
gnu: Add r-infusion. 
* gnu/packages/bioconductor.scm (r-infusion): New variable.

Change-Id: I2406097d427606c657b35c4e17f4b80a1e90da1c
 2025-04-16 10:59:44 +02:00
Ricardo Wurmus
a2b452c557
gnu: Add r-xllim. 
* gnu/packages/bioconductor.scm (r-xllim): New variable.

Change-Id: Ie7c6ae8885b855ca329d0955721772e125891344
 2025-04-16 10:59:43 +02:00
Ricardo Wurmus
a47e9e51bd
gnu: Add r-imputelcmd. 
* gnu/packages/bioconductor.scm (r-imputelcmd): New variable.

Change-Id: I02a9d52cee9a3a7deeaf1c1c680b31405f626524
 2025-04-16 10:59:43 +02:00
Ricardo Wurmus
341ddb9594
gnu: Add r-cpp11bigwig. 
* gnu/packages/bioconductor.scm (r-cpp11bigwig): New variable.

Change-Id: I3baf404fea5cdee5d61023a21a93aab52016cfbc
 2025-04-16 10:59:41 +02:00
Ricardo Wurmus
f7008a5b84
gnu: Add r-hahmmr. 
* gnu/packages/bioconductor.scm (r-hahmmr): New variable.

Change-Id: I292e97395d46a693b3f7c208feaf33c9e47325ce
 2025-04-16 10:59:36 +02:00
Ricardo Wurmus
16ed9a2833
gnu: Add r-rnaagecalc. 
* gnu/packages/bioconductor.scm (r-rnaagecalc): New variable.

Change-Id: I7f03b886ce188d9393d7419b616cd96f3f8b8421
 2025-03-21 10:14:36 +01:00
Ricardo Wurmus
0b57a4e27e
gnu: Add r-recount. 
* gnu/packages/bioconductor.scm (r-recount): New variable.

Change-Id: I557062cccaa182eb191f47fbc8c7bd9cfd2808f0
 2025-03-21 10:14:35 +01:00
Efraim Flashner
66daf46b41
gnu: Fix some misspellings. 
Change-Id: I316652aff7418af4b8e83bea24638b1513f8aa97
 2025-02-19 11:21:47 +02:00
Vagrant Cascadian
ddfec2a30e
gnu: Fix typos in bioconductor package descriptions. 
* gnu/packages/bioconductor.scm (r-anvil): Fix spelling of "programmatic".
(r-gypsum): Fix spelling of "administrative".  (r-modstrings): Fix spelling of
"functionality".  (r-enrichedheatmap): Fix spelling of "correspondence".
(r-hybridmtest): Fix spelling of "weight".  (r-sparsearray): Fix spelling of
"support".  (r-basicstarrseq): Fix spelling of "specific".  (r-baynorm): Fix
spelling of "columns".
 2025-02-17 02:16:59 -08:00
Ricardo Wurmus
da259387c3
gnu: r-trackviewer: Fix reference. 
* gnu/packages/bioconductor.scm (r-trackviewer)[arguments]: Use correct label
for reference to origin.

Change-Id: I6c66ab468e19025ee9e912a531c8e6ca458e750b
 2025-01-20 21:38:03 +01:00
Ricardo Wurmus
332a7bb631
gnu: r-motifstack: Fix reference. 
* gnu/packages/bioconductor.scm (r-motifstack)[arguments]: Use correct label
for reference to origin.

Change-Id: Ia9b3222f15c9630bd703713111e79937126e20fd
 2025-01-20 21:38:03 +01:00
Ricardo Wurmus
105f58850b
gnu: r-reportingtools: Fix reference. 
* gnu/packages/bioconductor.scm (r-reportingtools)[arguments]: Use correct
label for reference to origin.

Change-Id: Id3b509c369bd35e12fff2fb2f4822bef4152aff1
 2025-01-20 21:38:03 +01:00