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4122 Commits (de33bed5c4fc0c951030ed502e1985996f7561c6)

Author SHA1 Message Date
Ricardo Wurmus ef3ce37eeb
gnu: r-genefilter: Update to 1.82.1. 
* gnu/packages/bioconductor.scm (r-genefilter): Update to 1.82.1.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus 56524dc465
gnu: r-edger: Update to 3.42.2. 
* gnu/packages/bioconductor.scm (r-edger): Update to 3.42.2.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus d9d920403a
gnu: r-deseq2: Update to 1.40.1. 
* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.40.1.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus 7a9e68f103
gnu: r-biocparallel: Update to 1.34.1. 
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.34.1.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus 69e954bb0a
gnu: r-annotationdbi: Update to 1.62.1. 
* gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.62.1.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus 931ac0735f
gnu: r-densvis: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-densvis): Update to 1.10.1.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus 06b903963c
gnu: r-delayedarray: Update to 0.26.2. 
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.26.2.
[propagated-inputs]: Add r-s4arrays.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus 01faf51999
gnu: r-bandits: Update to 1.16.1. 
* gnu/packages/bioconductor.scm (r-bandits): Update to 1.16.1.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus 13dde61328
gnu: r-bambu: Update to 3.2.2. 
* gnu/packages/bioconductor.scm (r-bambu): Update to 3.2.2.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus 6401f048cf
gnu: r-amplican: Update to 1.22.1. 
* gnu/packages/bioconductor.scm (r-amplican): Update to 1.22.1.
[propagated-inputs]: Remove r-clustercrit; add r-cluster.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus 0861bca905
gnu: r-affyplm: Update to 1.76.1. 
* gnu/packages/bioconductor.scm (r-affyplm): Update to 1.76.1.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus 7a58dc01d3
gnu: Add r-s4arrays. 
* gnu/packages/bioconductor.scm (r-s4arrays): New variable.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus 6aa299aa1c
gnu: r-ggpicrust2: Update to 1.6.3. 
* gnu/packages/bioconductor.scm (r-ggpicrust2): Update to 1.6.3.
 2023-05-09 15:24:13 +02:00
Ricardo Wurmus bd3ef47877
gnu: r-biomartr: Update to 1.0.3. 
* gnu/packages/bioconductor.scm (r-biomartr): Update to 1.0.3.
 2023-05-09 15:24:13 +02:00
Mădălin Ionel Patrașcu 0e09e8ab15
gnu: Add r-multibac. 
* gnu/packages/bioconductor.scm (r-multibac): New variable.
 2023-05-08 10:34:06 +02:00
Ricardo Wurmus 3f8c4899a9
gnu: Add r-ggpicrust2. 
* gnu/packages/bioconductor.scm (r-ggpicrust2): New variable.
 2023-05-02 10:14:37 +02:00
Ricardo Wurmus 9bb428ad68
gnu: Add r-microbiomestat. 
* gnu/packages/bioconductor.scm (r-microbiomestat): New variable.
 2023-05-02 10:14:37 +02:00
Ricardo Wurmus 62ed97c07d
gnu: Add r-lefser. 
* gnu/packages/bioconductor.scm (r-lefser): New variable.
 2023-05-02 10:14:37 +02:00
Ricardo Wurmus 85c137adde
gnu: r-motifstack: Update to 1.44.1. 
* gnu/packages/bioconductor.scm (r-motifstack): Update to 1.44.1.
 2023-04-29 23:52:00 +02:00
Ricardo Wurmus f2ad160acd
gnu: r-chippeakanno: Update to 3.34.1. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.34.1.
 2023-04-29 23:52:00 +02:00
Ricardo Wurmus 46d78bf045
gnu: r-hpar: Avoid internet access. 
ExperimentHub::createHubAccessors needs internet access.  When R tests if the
package can be loaded it runs zzz.R, which contains the call to
createHubAccessors.  We set the variable GUIX_BUILD to conditionally disable
this call.

* gnu/packages/bioconductor.scm (r-hpar)[arguments]: Add two build phases:
'set-HOME and 'avoid-internet-access.
 2023-04-29 20:28:08 +02:00
Ricardo Wurmus 6cb123b190
gnu: r-phyloseq: Update to 1.44.0. 
* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.44.0.
 2023-04-29 20:28:08 +02:00
Ricardo Wurmus e0c28e52e4
gnu: r-tximeta: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.18.0.
 2023-04-29 20:28:08 +02:00
Ricardo Wurmus a605826139
gnu: r-tricycle: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-tricycle): Update to 1.8.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus c33697b714
gnu: r-biscuiteer: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-biscuiteer): Update to 1.14.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 04978d4592
gnu: r-omnipathr: Update to 3.8.0. 
* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.8.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus b2a3e274ec
gnu: r-omicade4: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-omicade4): Update to 1.40.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 15f364a933
gnu: r-dmrseq: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.20.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 3862877bb2
gnu: r-dada2: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-dada2): Update to 1.28.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 56586f9b9e
gnu: r-bsseq: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-bsseq): Update to 1.36.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 096133af16
gnu: r-biotmle: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-biotmle): Update to 1.24.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 0f594abe26
gnu: r-biotip: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-biotip): Update to 1.14.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 5a5d466e15
gnu: r-bioqc: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-bioqc): Update to 1.28.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus cb91d8ff79
gnu: r-bionet: Update to 1.60.0. 
* gnu/packages/bioconductor.scm (r-bionet): Update to 1.60.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus e1292069fc
gnu: r-bionero: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-bionero): Update to 1.8.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 26c76918cb
gnu: r-biomvcclass: Update to 1.68.0. 
* gnu/packages/bioconductor.scm (r-biomvcclass): Update to 1.68.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus ce9ee69644
gnu: r-mvcclass: Update to 1.74.0. 
* gnu/packages/bioconductor.scm (r-mvcclass): Update to 1.74.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 3d49b388a5
gnu: r-biomformat: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-biomformat): Update to 1.28.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus c10979dcbe
gnu: r-biodb: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-biodb): Update to 1.8.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 4eb1e7e542
gnu: r-biocdockermanager: Update to 1.11.0. 
* gnu/packages/bioconductor.scm (r-biocdockermanager): Update to 1.11.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 4684b0d333
gnu: r-biocthis: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.10.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus fbd4e9195f
gnu: r-basilisk: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-basilisk): Update to 1.12.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus d91cc19ee9
gnu: r-basilisk-utils: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.12.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus ad0efa110e
gnu: r-dir-expiry: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-dir-expiry): Update to 1.8.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 1b80b39aa7
gnu: r-genetclassifier: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-genetclassifier): Update to 1.40.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 939155e312
gnu: r-minet: Update to 3.58.0. 
* gnu/packages/bioconductor.scm (r-minet): Update to 3.58.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus d297d24edb
gnu: r-biobtreer: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-biobtreer): Update to 1.12.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 1ff662c8e2
gnu: r-bgeedb: Update to 2.26.0. 
* gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.26.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 189f9d805e
gnu: r-bgeecall: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-bgeecall): Update to 1.16.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 4dd9fdb68f
gnu: r-beclear: Update to 2.16.0. 
* gnu/packages/bioconductor.scm (r-beclear): Update to 2.16.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 0d879deae1
gnu: r-megadepth: Update to 1.9.0. 
* gnu/packages/bioconductor.scm (r-megadepth): Update to 1.9.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus c09a9bc427
gnu: r-ballgown: Update to 2.32.0. 
* gnu/packages/bioconductor.scm (r-ballgown): Update to 2.32.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus e5e7089db5
gnu: r-guitar: Update to 2.16.0. 
* gnu/packages/bioconductor.scm (r-guitar): Update to 2.16.0.
 2023-04-29 20:28:07 +02:00
Ricardo Wurmus 3616dd923f
gnu: r-chromstar: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-chromstar): Update to 1.26.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus 1b3be92024
gnu: r-snpstats: Update to 1.50.0. 
* gnu/packages/bioconductor.scm (r-snpstats): Update to 1.50.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus 72288df46a
gnu: r-snapcgh: Update to 1.70.0. 
* gnu/packages/bioconductor.scm (r-snapcgh): Update to 1.70.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus 61432d53ff
gnu: r-pathview: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-pathview): Update to 1.40.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus ef6059cf27
gnu: r-ldblock: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-ldblock): Update to 1.30.0.
[propagated-inputs]: Remove r-ensdb-hsapiens-v75, r-ensembldb, r-genomeinfodb,
r-genomicfiles, r-rsamtools, r-snpstats, and r-variantannotation; add
r-rlang.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus c00d4a394d
gnu: r-kegggraph: Update to 1.60.0. 
* gnu/packages/bioconductor.scm (r-kegggraph): Update to 1.60.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus 70514e0281
gnu: r-gwascat: Update to 2.32.0. 
* gnu/packages/bioconductor.scm (r-gwascat): Update to 2.32.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus e8a52e54f7
gnu: r-gviz: Update to 1.44.0. 
* gnu/packages/bioconductor.scm (r-gviz): Update to 1.44.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus 311339801e
gnu: r-ggbio: Update to 1.48.0. 
* gnu/packages/bioconductor.scm (r-ggbio): Update to 1.48.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus 764220f848
gnu: r-erma: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-erma): Update to 1.16.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus bc7db31ceb
gnu: r-catalyst: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-catalyst): Update to 1.24.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus d1e16723dd
gnu: r-msmstests: Update to 1.38.0. 
* gnu/packages/bioconductor.scm (r-msmstests): Update to 1.38.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus 0d854ac754
gnu: r-msmseda: Update to 1.38.0. 
* gnu/packages/bioconductor.scm (r-msmseda): Update to 1.38.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus bca0afda01
gnu: r-biocio: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-biocio): Update to 1.10.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus 6459537f90
gnu: r-msfeatures: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-msfeatures): Update to 1.8.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus f4c4bc5473
gnu: r-mscoreutils: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.12.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus 643e63ef61
gnu: r-delayedmatrixstats: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.22.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus 4b4df8d533
gnu: r-sparsematrixstats: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-sparsematrixstats): Update to 1.12.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus 1435a289dd
gnu: r-scran: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-scran): Update to 1.28.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus c3056799b3
gnu: r-scater: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-scater): Update to 1.28.0.
[propagated-inputs]: Remove r-gridextra; add r-densvis.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus febe8360c3
gnu: r-scuttle: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-scuttle): Update to 1.10.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus 8dc03857a6
gnu: r-singler: Update to 2.2.0. 
* gnu/packages/bioconductor.scm (r-singler): Update to 2.2.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus b0a6411b85
gnu: r-singlecellexperiment: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-singlecellexperiment): Update to 1.22.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus 09ada1eb1e
gnu: r-chromvar: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-chromvar): Update to 1.22.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus 0609a92c0b
gnu: r-motifmatchr: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-motifmatchr): Update to 1.22.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus 6263d39069
gnu: r-maftools: Update to 2.16.0. 
* gnu/packages/bioconductor.scm (r-maftools): Update to 2.16.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus 99c001303d
gnu: r-tfbstools: Update to 1.38.0. 
* gnu/packages/bioconductor.scm (r-tfbstools): Update to 1.38.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus 5ab3d66ffc
gnu: r-cner: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-cner): Update to 1.36.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus b9b6c29a75
gnu: r-beadarraysnp: Update to 1.66.0. 
* gnu/packages/bioconductor.scm (r-beadarraysnp): Update to 1.66.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus e76467b72c
gnu: r-beachmat: Update to 2.16.0. 
* gnu/packages/bioconductor.scm (r-beachmat): Update to 2.16.0.
 2023-04-29 20:28:06 +02:00
Ricardo Wurmus f482bb1256
gnu: r-rhdf5lib: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.22.0.
 2023-04-29 20:28:05 +02:00
Ricardo Wurmus 582dac2949
gnu: r-hdf5array: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.28.0.
 2023-04-29 20:28:05 +02:00
Ricardo Wurmus 143b70c92b
gnu: r-hitc: Update to 1.44.0. 
* gnu/packages/bioconductor.scm (r-hitc): Update to 1.44.0.
 2023-04-29 20:28:05 +02:00
Ricardo Wurmus 765b41564a
gnu: r-fithic: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-fithic): Update to 1.26.0.
 2023-04-29 20:28:05 +02:00
Ricardo Wurmus 8866d47bce
gnu: r-fishpond: Update to 2.6.0. 
* gnu/packages/bioconductor.scm (r-fishpond): Update to 2.6.0.
[inputs]: Remove zlib.
 2023-04-29 20:28:05 +02:00
Ricardo Wurmus 85bc989a66
gnu: r-rgraphviz: Update to 2.44.0. 
* gnu/packages/bioconductor.scm (r-rgraphviz): Update to 2.44.0.
 2023-04-29 20:28:05 +02:00
Ricardo Wurmus 2e81140c18
gnu: r-s4vectors: Update to 0.38.0. 
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.38.0.
[native-inputs]: Add r-knitr.
 2023-04-29 20:28:05 +02:00
Ricardo Wurmus ed6d919ef0
gnu: r-preprocesscore: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.62.0.
 2023-04-29 20:28:05 +02:00
Ricardo Wurmus ae8956bbc8
gnu: r-icens: Update to 1.72.0. 
* gnu/packages/bioconductor.scm (r-icens): Update to 1.72.0.
 2023-04-29 20:28:05 +02:00
Ricardo Wurmus ebd0bdd84c
gnu: r-m3c: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-m3c): Update to 1.22.0.
 2023-04-29 20:28:05 +02:00
Ricardo Wurmus aff09ecb05
gnu: r-rgreat: Update to 2.2.0. 
* gnu/packages/bioconductor.scm (r-rgreat): Update to 2.2.0.
 2023-04-29 20:28:05 +02:00
Ricardo Wurmus bd1b41e8d1
gnu: r-pcatools: Update to 2.12.0. 
* gnu/packages/bioconductor.scm (r-pcatools): Update to 2.12.0.
 2023-04-29 20:28:05 +02:00
Ricardo Wurmus f2ce4a037f
gnu: r-biodist: Update to 1.72.0. 
* gnu/packages/bioconductor.scm (r-biodist): Update to 1.72.0.
 2023-04-29 20:28:05 +02:00
Ricardo Wurmus 2f1c5f361f
gnu: r-biocworkflowtools: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-biocworkflowtools): Update to 1.26.0.
 2023-04-29 20:28:05 +02:00
Ricardo Wurmus 37de521f22
gnu: r-biocset: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-biocset): Update to 1.14.0.
 2023-04-29 20:28:05 +02:00
Ricardo Wurmus 72ba2d8f48
gnu: r-biocpkgtools: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.18.0.
 2023-04-29 20:28:05 +02:00
Ricardo Wurmus 8f9bd84fd9
gnu: r-biocor: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-biocor): Update to 1.24.0.
 2023-04-29 20:28:05 +02:00