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45565 Commits (217b4a1587e8b9af6526915a10e648f58234ebf0)

Author SHA1 Message Date
Brett Gilio b425426236
gnu: emacs-async: Update to 1.9.4. 
* gnu/packages/emacs-xyz.scm (emacs-async): Update to 1.9.4.
 2019-12-15 13:50:19 -06:00
Brett Gilio 9a27551b39
gnu: emacs-doom-modeline: Update to 2.8.2. 
* gnu/packages/emacs-xyz.scm (emacs-doom-modeline): Update to 2.8.2.
 2019-12-15 13:43:46 -06:00
Vagrant Cascadian 6a65185ee4
gnu: diffoscope: Update to 133. 
* gnu/packages/diffoscope (diffoscope): Update to 133.
 2019-12-15 10:19:04 -08:00
Carlo Zancanaro 514001e9ce
gnu: abcl: Update to 1.6.0. 
* gnu/packages/java.scm (abcl): Update to 1.6.0.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2019-12-15 18:44:43 +02:00
Mathieu Othacehe a13116b60c
gnu: texinfo: Add missing include. 
* gnu/packages/texinfo.scm (info-reader): Fix missing include, introduced by
f5d670606354728a453b8cc962c4f85516007d13.
 2019-12-15 17:11:18 +01:00
Pierre Neidhardt 97115892b9
gnu: Add theorafile. 
* gnu/packages/video.scm (theorafile): New variable.
 2019-12-15 16:21:19 +01:00
Mathieu Othacehe 614a1e3fa2
gnu: info-reader: Fix cross-compilation. 
* gnu/packages/texinfo.scm (info-reader)[arguments]: Add keep-only-info-reader
phase to inherited texinfo package phases, so that fix-cross-configure phase
is preserved.
 2019-12-15 15:48:15 +01:00
Ricardo Wurmus 6e10ac0780
gnu: r-destiny: Update to 3.0.0. 
* gnu/packages/bioconductor.scm (r-destiny): Update to 3.0.0.
[propagated-inputs]: Add r-ggplot-multistats, r-irlba, r-knn-covertree,
r-pcamethods, r-rcpphnsw, r-rspectra, r-singlecellexperiment, r-tidyr, and
r-tidyselect; remove r-igraph.
 2019-12-15 15:39:13 +01:00
Ricardo Wurmus b4ee414880
gnu: r-siggenes: Update to 1.60.0. 
* gnu/packages/bioconductor.scm (r-siggenes): Update to 1.60.0.
 2019-12-15 15:39:13 +01:00
Ricardo Wurmus 4efdac562b
gnu: r-bumphunter: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-bumphunter): Update to 1.28.0.
 2019-12-15 15:39:13 +01:00
Ricardo Wurmus dfd4287cba
gnu: r-minfi: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-minfi): Update to 1.32.0.
 2019-12-15 15:39:13 +01:00
Ricardo Wurmus b57cffb974
gnu: r-methylumi: Update to 2.32.0. 
* gnu/packages/bioconductor.scm (r-methylumi): Update to 2.32.0.
 2019-12-15 15:39:13 +01:00
Ricardo Wurmus 8f7bc872e1
gnu: r-lumi: Update to 2.38.0. 
* gnu/packages/bioconductor.scm (r-lumi): Update to 2.38.0.
 2019-12-15 15:39:13 +01:00
Ricardo Wurmus a2877d6970
gnu: r-linnorm: Update to 2.10.0. 
* gnu/packages/bioconductor.scm (r-linnorm): Update to 2.10.0.
 2019-12-15 15:39:12 +01:00
Ricardo Wurmus 1b890c3231
gnu: r-ioniser: Update to 2.10.0. 
* gnu/packages/bioconductor.scm (r-ioniser): Update to 2.10.0.
 2019-12-15 15:39:12 +01:00
Ricardo Wurmus a18f325e0a
gnu: r-triform: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-triform): Update to 1.28.0.
 2019-12-15 15:39:12 +01:00
Ricardo Wurmus 9b72bbf784
gnu: r-varianttools: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-varianttools): Update to 1.28.0.
 2019-12-15 15:39:12 +01:00
Ricardo Wurmus 9f218627d6
gnu: r-heatplus: Update to 2.32.0. 
* gnu/packages/bioconductor.scm (r-heatplus): Update to 2.32.0.
 2019-12-15 15:39:12 +01:00
Ricardo Wurmus c245ec3d49
gnu: r-gosemsim: Update to 2.12.0. 
* gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.12.0.
 2019-12-15 15:39:12 +01:00
Ricardo Wurmus 5ed767521c
gnu: r-anota: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-anota): Update to 1.34.0.
 2019-12-15 15:39:12 +01:00
Ricardo Wurmus 869965df1c
gnu: r-sigpathway: Update to 1.54.0. 
* gnu/packages/bioconductor.scm (r-sigpathway): Update to 1.54.0.
 2019-12-15 15:39:12 +01:00
Ricardo Wurmus b4e1268c7b
gnu: r-fgsea: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-fgsea): Update to 1.12.0.
 2019-12-15 15:39:12 +01:00
Ricardo Wurmus 166b3c2da6
gnu: r-dose: Update to 3.12.0. 
* gnu/packages/bioconductor.scm (r-dose): Update to 3.12.0.
 2019-12-15 15:39:12 +01:00
Ricardo Wurmus 0654a9bc3b
gnu: r-enrichplot: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.6.0.
[propagated-inputs]: Remove r-upsetr.
 2019-12-15 15:39:11 +01:00
Ricardo Wurmus 08c01b7e0e
gnu: r-clusterprofiler: Update to 3.14.0. 
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 3.14.0.
 2019-12-15 15:39:11 +01:00
Ricardo Wurmus 6374984a20
gnu: r-mlinterfaces: Update to 1.66.0. 
* gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.66.0.
 2019-12-15 15:39:11 +01:00
Ricardo Wurmus fc4a9dd579
gnu: r-annaffy: Update to 1.58.0. 
* gnu/packages/bioconductor.scm (r-annaffy): Update to 1.58.0.
 2019-12-15 15:39:11 +01:00
Ricardo Wurmus 4ed18ddc0f
gnu: r-a4core: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-a4core): Update to 1.34.0.
 2019-12-15 15:39:11 +01:00
Ricardo Wurmus 102b982cbe
gnu: r-a4classif: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-a4classif): Update to 1.34.0.
 2019-12-15 15:39:11 +01:00
Ricardo Wurmus d6859c7c9b
gnu: r-a4preproc: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-a4preproc): Update to 1.34.0.
 2019-12-15 15:39:11 +01:00
Ricardo Wurmus 977a7802c1
gnu: r-a4reporting: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-a4reporting): Update to 1.34.0.
 2019-12-15 15:39:11 +01:00
Ricardo Wurmus 85c945aa97
gnu: r-a4base: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-a4base): Update to 1.34.0.
 2019-12-15 15:39:11 +01:00
Ricardo Wurmus 344eb4c404
gnu: r-a4: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-a4): Update to 1.34.0.
 2019-12-15 15:39:11 +01:00
Ricardo Wurmus aef4b34669
gnu: r-abseqr: Update to 1.4.0. 
* gnu/packages/bioconductor.scm (r-abseqr): Update to 1.4.0.
 2019-12-15 15:39:10 +01:00
Ricardo Wurmus 32b471f4a7
gnu: r-bacon: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-bacon): Update to 1.14.0.
 2019-12-15 15:39:10 +01:00
Ricardo Wurmus 6dfe5056c9
gnu: r-rgadem: Update to 2.34.0. 
* gnu/packages/bioconductor.scm (r-rgadem): Update to 2.34.0.
 2019-12-15 15:39:10 +01:00
Ricardo Wurmus 35a1b3ec4c
gnu: r-motiv: Update to 1.42.0. 
* gnu/packages/bioconductor.scm (r-motiv): Update to 1.42.0.
[propagated-inputs]: Add r-genomicranges.
 2019-12-15 15:39:10 +01:00
Ricardo Wurmus dda936ca9a
gnu: r-motifstack: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-motifstack): Update to 1.30.0.
[propagated-inputs]: Add r-ggplot2.
 2019-12-15 15:39:10 +01:00
Ricardo Wurmus e89f16e646
gnu: r-genomicscores: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-genomicscores): Update to 1.10.0.
 2019-12-15 15:39:10 +01:00
Ricardo Wurmus 36aecb2105
gnu: r-atacseqqc: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.10.1.
 2019-12-15 15:39:10 +01:00
Ricardo Wurmus 4997e0254a
gnu: r-gofuncr: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-gofuncr): Update to 1.6.0.
 2019-12-15 15:39:10 +01:00
Ricardo Wurmus 307667c4ef
gnu: r-abaenrichment: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-abaenrichment): Update to 1.16.0.
 2019-12-15 15:39:10 +01:00
Ricardo Wurmus 3a731c8334
gnu: r-annotationfuncs: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-annotationfuncs): Update to 1.36.0.
 2019-12-15 15:39:10 +01:00
Ricardo Wurmus eda4908556
gnu: r-annotationtools: Update to 1.60.0. 
* gnu/packages/bioconductor.scm (r-annotationtools): Update to 1.60.0.
 2019-12-15 15:39:10 +01:00
Ricardo Wurmus 50e6f76278
gnu: r-allelicimbalance: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-allelicimbalance): Update to 1.24.0.
 2019-12-15 15:39:10 +01:00
Ricardo Wurmus 3a35d27450
gnu: r-aucell: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-aucell): Update to 1.8.0.
[propagated-inputs]: Add r-biocgenerics and r-s4vectors.
 2019-12-15 15:39:09 +01:00
Ricardo Wurmus ca7192a1c9
gnu: r-ebimage: Update to 4.28.1. 
* gnu/packages/bioconductor.scm (r-ebimage): Update to 4.28.1.
 2019-12-15 15:39:09 +01:00
Ricardo Wurmus 3796e2442b
gnu: r-yamss: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-yamss): Update to 1.12.0.
 2019-12-15 15:39:09 +01:00
Ricardo Wurmus cf0a1cb3b4
gnu: r-gtrellis: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-gtrellis): Update to 1.18.0.
 2019-12-15 15:39:09 +01:00
Ricardo Wurmus 4f8e0487fc
gnu: r-somaticsignatures: Update to 2.22.0. 
* gnu/packages/bioconductor.scm (r-somaticsignatures): Update to 2.22.0.
 2019-12-15 15:39:09 +01:00
Ricardo Wurmus 580e434267
gnu: r-yapsa: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-yapsa): Update to 1.12.0.
 2019-12-15 15:39:09 +01:00
Ricardo Wurmus 2f90bab8d1
gnu: r-gcrma: Update to 2.58.0. 
* gnu/packages/bioconductor.scm (r-gcrma): Update to 2.58.0.
 2019-12-15 15:39:09 +01:00
Ricardo Wurmus a87aa2ff5a
gnu: r-simpleaffy: Update to 2.62.0. 
* gnu/packages/bioconductor.scm (r-simpleaffy): Update to 2.62.0.
 2019-12-15 15:39:09 +01:00
Ricardo Wurmus 87942b74c6
gnu: r-yaqcaffy: Update to 1.46.0. 
* gnu/packages/bioconductor.scm (r-yaqcaffy): Update to 1.46.0.
 2019-12-15 15:39:09 +01:00
Ricardo Wurmus eb697ff5bb
gnu: r-quantro: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-quantro): Update to 1.20.0.
 2019-12-15 15:39:09 +01:00
Ricardo Wurmus 94fdea1267
gnu: r-yarn: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-yarn): Update to 1.12.0.
 2019-12-15 15:39:08 +01:00
Ricardo Wurmus f0dd0fec40
gnu: r-roar: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-roar): Update to 1.22.0.
 2019-12-15 15:39:08 +01:00
Ricardo Wurmus 1f0101ae01
gnu: r-xbseq: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-xbseq): Update to 1.18.0.
 2019-12-15 15:39:08 +01:00
Ricardo Wurmus a07ee2584a
gnu: r-massspecwavelet: Update to 1.52.0. 
* gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.52.0.
 2019-12-15 15:39:08 +01:00
Ricardo Wurmus 4fb52345b2
gnu: r-xcms: Update to 3.8.1. 
* gnu/packages/bioconductor.scm (r-xcms): Update to 3.8.1.
[propagated-inputs]: Add r-iranges.
 2019-12-15 15:39:08 +01:00
Ricardo Wurmus 92f40538d3
gnu: r-wrench: Update to 1.4.0. 
* gnu/packages/bioconductor.scm (r-wrench): Update to 1.4.0.
 2019-12-15 15:39:08 +01:00
Ricardo Wurmus 25db5611e2
gnu: r-wiggleplotr: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-wiggleplotr): Update to 1.10.1.
 2019-12-15 15:39:08 +01:00
Ricardo Wurmus 1a2569e4cc
gnu: r-widgettools: Update to 1.64.0. 
* gnu/packages/bioconductor.scm (r-widgettools): Update to 1.64.0.
 2019-12-15 15:39:08 +01:00
Ricardo Wurmus 316bcd07a8
gnu: r-webbioc: Update to 1.58.0. 
* gnu/packages/bioconductor.scm (r-webbioc): Update to 1.58.0.
 2019-12-15 15:39:08 +01:00
Ricardo Wurmus 18b93e0350
gnu: r-zfpkm: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-zfpkm): Update to 1.8.0.
 2019-12-15 15:39:08 +01:00
Ricardo Wurmus c5a4c5a1ce
gnu: r-rbowtie2: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-rbowtie2): Update to 1.8.0.
 2019-12-15 15:39:08 +01:00
Ricardo Wurmus 82d87ce02a
gnu: r-progeny: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-progeny): Update to 1.8.0.
 2019-12-15 15:39:08 +01:00
Ricardo Wurmus 4f0d858841
gnu: r-arrmnormalization: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-arrmnormalization): Update to 1.26.0.
 2019-12-15 15:39:07 +01:00
Ricardo Wurmus 97e317007c
gnu: r-biocfilecache: Update to 1.10.2. 
* gnu/packages/bioconductor.scm (r-biocfilecache): Update to 1.10.2.
 2019-12-15 15:39:07 +01:00
Ricardo Wurmus 049de95de7
gnu: r-iclusterplus: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-iclusterplus): Update to 1.22.0.
 2019-12-15 15:39:07 +01:00
Ricardo Wurmus 02684becc9
gnu: r-rbowtie: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-rbowtie): Update to 1.26.0.
 2019-12-15 15:39:07 +01:00
Ricardo Wurmus 2cebc5d135
gnu: r-sgseq: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-sgseq): Update to 1.20.0.
 2019-12-15 15:39:07 +01:00
Ricardo Wurmus 3dd2450e65
gnu: r-rhisat2: Update to 1.2.0. 
* gnu/packages/bioconductor.scm (r-rhisat2): Update to 1.2.0.
[arguments]: Add phase to make package reproducible and to avoid shelling out
to 'which'.
[native-inputs]: Remove which.
 2019-12-15 15:39:07 +01:00
Ricardo Wurmus a15e52ec78
gnu: r-quasr: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-quasr): Update to 1.26.0.
 2019-12-15 15:39:07 +01:00
Ricardo Wurmus 11db82b07c
gnu: r-rqc: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-rqc): Update to 1.20.0.
 2019-12-15 15:39:07 +01:00
Ricardo Wurmus a9e5145c32
gnu: r-birewire: Update to 3.18.0. 
* gnu/packages/bioconductor.scm (r-birewire): Update to 3.18.0.
 2019-12-15 15:39:07 +01:00
Ricardo Wurmus 8d766270c4
gnu: r-birta: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-birta): Update to 1.30.0.
 2019-12-15 15:39:07 +01:00
Ricardo Wurmus 643aaf7eaf
gnu: r-ropls: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-ropls): Update to 1.18.0.
[propagated-inputs]: Add r-multidataset.
 2019-12-15 15:39:06 +01:00
Ricardo Wurmus 7d29dc9c7b
gnu: r-biosigner: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-biosigner): Update to 1.14.0.
[propagated-inputs]: Add r-multidataset.
 2019-12-15 15:39:06 +01:00
Ricardo Wurmus 700072565f
gnu: r-annotatr: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-annotatr): Update to 1.12.1.
 2019-12-15 15:39:06 +01:00
Ricardo Wurmus 4390788ea2
gnu: r-rsubread: Update to 2.0.0. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.0.0.
 2019-12-15 15:39:06 +01:00
Ricardo Wurmus 482ba0b3ed
gnu: r-flowutils: Update to 1.50.0. 
* gnu/packages/bioconductor.scm (r-flowutils): Update to 1.50.0.
 2019-12-15 15:39:06 +01:00
Ricardo Wurmus 8ad6b23f68
gnu: r-consensusclusterplus: Update to 1.50.0. 
* gnu/packages/bioconductor.scm (r-consensusclusterplus): Update to 1.50.0.
 2019-12-15 15:39:06 +01:00
Ricardo Wurmus b2a2f32130
gnu: r-flowcore: Update to 1.52.1. 
* gnu/packages/bioconductor.scm (r-flowcore): Update to 1.52.1.
[propagated-inputs]: Remove r-corpcor, r-graph, r-mass, and r-rrcov; add
r-cytolib.
 2019-12-15 15:39:06 +01:00
Ricardo Wurmus 8042087804
gnu: r-flowmeans: Update to 1.46.0. 
* gnu/packages/bioconductor.scm (r-flowmeans): Update to 1.46.0.
 2019-12-15 15:39:06 +01:00
Ricardo Wurmus ba71567acd
gnu: r-flowsom: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-flowsom): Update to 1.18.0.
[propagated-inputs]: Add r-cytoml, r-flowworkspace, and r-rcolorbrewer; remove
r-flowutils.
 2019-12-15 15:39:06 +01:00
Ricardo Wurmus 4930a89ad5
gnu: r-mixomics: Update to 6.10.6. 
* gnu/packages/bioconductor.scm (r-mixomics): Update to 6.10.6.
 2019-12-15 15:39:06 +01:00
Ricardo Wurmus 51ffac455e
gnu: r-rcistarget: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-rcistarget): Update to 1.6.0.
 2019-12-15 15:39:06 +01:00
Ricardo Wurmus 42b06298ef
gnu: r-cicero: Update to 1.4.0. 
* gnu/packages/bioconductor.scm (r-cicero): Update to 1.4.0.
 2019-12-15 15:39:06 +01:00
Ricardo Wurmus 33ce50e322
gnu: r-genie3: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-genie3): Update to 1.8.0.
 2019-12-15 15:39:06 +01:00
Ricardo Wurmus 3672b74f6f
gnu: r-roc: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-roc): Update to 1.62.0.
[propagated-inputs]: Add r-knitr.
 2019-12-15 15:39:05 +01:00
Ricardo Wurmus 9eade2294e
gnu: r-watermelon: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-watermelon): Update to 1.30.0.
 2019-12-15 15:39:05 +01:00
Ricardo Wurmus f5ef7dd6b7
gnu: r-gdsfmt: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.22.0.
 2019-12-15 15:39:05 +01:00
Ricardo Wurmus 8b941a50ef
gnu: r-bigmelon: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-bigmelon): Update to 1.12.0.
 2019-12-15 15:39:05 +01:00
Ricardo Wurmus 2223bbc726
gnu: r-seqbias: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-seqbias): Update to 1.34.0.
 2019-12-15 15:39:05 +01:00
Ricardo Wurmus 02c18abe62
gnu: r-reqon: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-reqon): Update to 1.32.0.
 2019-12-15 15:39:05 +01:00
Ricardo Wurmus c0cba4b542
gnu: r-wavcluster: Update to 2.20.0. 
* gnu/packages/bioconductor.scm (r-wavcluster): Update to 2.20.0.
 2019-12-15 15:39:05 +01:00
Ricardo Wurmus cb734c60dc
gnu: r-timeseriesexperiment: Update to 1.4.0. 
* gnu/packages/bioconductor.scm (r-timeseriesexperiment): Update to 1.4.0.
 2019-12-15 15:39:05 +01:00
Ricardo Wurmus 6f5415d5f6
gnu: r-variantfiltering: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-variantfiltering): Update to 1.22.0.
 2019-12-15 15:39:05 +01:00
Ricardo Wurmus 053a2127bc
gnu: r-genomegraphs: Update to 1.46.0. 
* gnu/packages/bioconductor.scm (r-genomegraphs): Update to 1.46.0.
 2019-12-15 15:39:05 +01:00
Ricardo Wurmus e13f977312
gnu: r-wavetiling: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-wavetiling): Update to 1.28.0.
 2019-12-15 15:39:05 +01:00
Ricardo Wurmus e2f481dad0
gnu: r-variancepartition: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.16.0.
 2019-12-15 15:39:05 +01:00
Ricardo Wurmus 0b0906c845
gnu: r-htqpcr: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-htqpcr): Update to 1.40.0.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus 989be6df99
gnu: r-unifiedwmwqpcr: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): Update to 1.22.0.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus 0726645eca
gnu: r-genefilter: Update to 1.68.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.68.0.
[propagated-inputs]: Remove r-s4vectors and add r-biocgenerics.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus 867018e138
gnu: r-deseq2: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.26.0.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus ebc81e300c
gnu: r-dexseq: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.32.0.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus 12c4555d44
gnu: r-annotationforge: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.28.0.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus 33a2acb757
gnu: r-rbgl: Update to 1.62.1. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.62.1.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus d2661841be
gnu: r-gseabase: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.48.0.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus 4afcf941d2
gnu: r-category: Update to 2.52.1. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.52.1.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus 545730891e
gnu: r-gostats: Update to 2.52.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.52.0.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus f29c9f0d33
gnu: r-shortread: Update to 1.44.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.0.
 2019-12-15 15:39:04 +01:00
Ricardo Wurmus 58fd68b299
gnu: r-systempiper: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.20.0.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus f8f815667d
gnu: r-grohmm: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.20.0.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus 74d59b6748
gnu: r-biocviews: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.54.0.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus ef96154433
gnu: r-biocstyle: Update to 2.14.2. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.14.2.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus 7758d5205c
gnu: r-bioccheck: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.22.0.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus d37daf8929
gnu: r-s4vectors: Update to 0.24.1. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.1.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus d2723484f6
gnu: r-iranges: Update to 2.20.1. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.20.1.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus 937f3a46eb
gnu: r-genomeinfodb: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.22.0.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus da03fa3c90
gnu: r-edger: Update to 3.28.0. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.0.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus 8f5d2c3abc
gnu: r-variantannotation: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.32.0.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus eea491e5c6
gnu: r-limma: Update to 3.42.0. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.42.0.
 2019-12-15 15:39:03 +01:00
Ricardo Wurmus da6edb199d
gnu: r-xvector: Update to 0.26.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.26.0.
 2019-12-15 15:39:02 +01:00
Ricardo Wurmus 0202b13e8b
gnu: r-genomicranges: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.38.0.
 2019-12-15 15:39:02 +01:00
Ricardo Wurmus 8d1c3666d7
gnu: r-biobase: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.46.0.
 2019-12-15 15:39:02 +01:00
Ricardo Wurmus de9ae3e7b1
gnu: r-annotationdbi: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.48.0.
 2019-12-15 15:39:02 +01:00
Ricardo Wurmus 68a9d9f26a
gnu: r-biomart: Update to 2.42.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.42.0.
[propagated-inputs]: Add r-biocfilecache, r-openssl, and r-rappdirs; remove
r-rcurl.
 2019-12-15 15:39:02 +01:00
Ricardo Wurmus 5854a4a265
gnu: r-biocparallel: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.20.0.
 2019-12-15 15:39:02 +01:00
Ricardo Wurmus 15cd3f6ef5
gnu: r-biostrings: Update to 2.54.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.54.0.
 2019-12-15 15:39:02 +01:00
Ricardo Wurmus e1d681e2af
gnu: r-rsamtools: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.1.
 2019-12-15 15:39:02 +01:00
Ricardo Wurmus 4ada4fb745
gnu: r-delayedarray: Update to 0.12.0. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.0.
 2019-12-15 15:39:02 +01:00
Ricardo Wurmus 264db038c6
gnu: r-summarizedexperiment: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.16.0.
 2019-12-15 15:39:02 +01:00
Ricardo Wurmus 55e515d206
gnu: r-genomicalignments: Update to 1.22.1. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.22.1.
 2019-12-15 15:39:01 +01:00
Ricardo Wurmus 15187da9e7
gnu: r-rtracklayer: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.46.0.
 2019-12-15 15:39:01 +01:00
Ricardo Wurmus 9fec340391
gnu: r-genomicfeatures: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.0.
 2019-12-15 15:39:01 +01:00
Ricardo Wurmus 323f42b2ca
gnu: r-topgo: Update to 2.37.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.37.0.
 2019-12-15 15:39:01 +01:00
Ricardo Wurmus e3a2b96c80
gnu: r-bsgenome: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.54.0.
 2019-12-15 15:39:01 +01:00
Ricardo Wurmus bca1c45e4e
gnu: r-impute: Update to 1.60.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.60.0.
 2019-12-15 15:39:01 +01:00
Ricardo Wurmus b590742362
gnu: r-seqpattern: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.18.0.
 2019-12-15 15:39:01 +01:00
Ricardo Wurmus e06b34e8c6
gnu: r-genomation: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.18.0.
 2019-12-15 15:39:01 +01:00
Ricardo Wurmus a9790190d1
gnu: r-seqlogo: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.52.0.
 2019-12-15 15:39:01 +01:00
Ricardo Wurmus a5f9b30338
gnu: r-motifrg: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.30.0.
 2019-12-15 15:39:01 +01:00
Ricardo Wurmus 2f15045400
gnu: r-zlibbioc: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.32.0.
 2019-12-15 15:39:01 +01:00
Ricardo Wurmus 108c03a8eb
gnu: r-rhtslib: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.18.0.
[propagated-inputs]: Add curl.
 2019-12-15 15:39:01 +01:00
Ricardo Wurmus 7b6c008960
gnu: r-bamsignals: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.18.0.
 2019-12-15 15:39:00 +01:00
Ricardo Wurmus f375d74072
gnu: r-rcas: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.12.0.
 2019-12-15 15:39:00 +01:00
Ricardo Wurmus 3964f2c24e
gnu: r-mutationalpatterns: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.12.0.
 2019-12-15 15:39:00 +01:00
Ricardo Wurmus 3a0229eba0
gnu: r-tximport: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.14.0.
 2019-12-15 15:39:00 +01:00
Ricardo Wurmus 126539d1ae
gnu: r-rhdf5: Update to 2.30.1. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.30.1.
 2019-12-15 15:39:00 +01:00
Ricardo Wurmus 4e5c217684
gnu: r-pcamethods: Update to 1.78.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.78.0.
 2019-12-15 15:39:00 +01:00
Ricardo Wurmus 589939937d
gnu: r-msnbase: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.12.0.
 2019-12-15 15:39:00 +01:00
Ricardo Wurmus 597aeb8a34
gnu: r-msnid: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.20.0.
 2019-12-15 15:39:00 +01:00
Ricardo Wurmus 3ccf1e3c20
gnu: r-aroma-light: Update to 3.16.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.16.0.
 2019-12-15 15:39:00 +01:00
Ricardo Wurmus 783bbe3ace
gnu: r-deseq: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.38.0.
 2019-12-15 15:39:00 +01:00
Ricardo Wurmus 0a6704e226
gnu: r-edaseq: Update to 2.20.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.20.0.
 2019-12-15 15:38:59 +01:00
Ricardo Wurmus 2beffcb558
gnu: r-interactivedisplaybase: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.24.0.
 2019-12-15 15:38:59 +01:00
Ricardo Wurmus 6339ea22f1
gnu: r-annotationhub: Update to 2.18.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.18.0.
[propagated-inputs]: Add r-biocversion.
 2019-12-15 15:38:59 +01:00
Ricardo Wurmus c21bf901e2
gnu: r-fastseg: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.32.0.
 2019-12-15 15:38:59 +01:00
Ricardo Wurmus fedba48bb5
gnu: r-keggrest: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.26.1.
 2019-12-15 15:38:59 +01:00
Ricardo Wurmus b342b20a24
gnu: r-gage: Update to 2.36.0. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.36.0.
 2019-12-15 15:38:59 +01:00
Ricardo Wurmus 48c7ee93b7
gnu: r-genomicfiles: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.22.0.
 2019-12-15 15:38:59 +01:00
Ricardo Wurmus dac706c322
gnu: r-complexheatmap: Update to 2.2.0. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.2.0.
 2019-12-15 15:38:59 +01:00
Ricardo Wurmus 2edb116c1c
gnu: r-dirichletmultinomial: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.28.0.
 2019-12-15 15:38:59 +01:00
Ricardo Wurmus e107f3df54
gnu: r-ensembldb: Update to 2.10.2. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.10.2.
 2019-12-15 15:38:59 +01:00
Ricardo Wurmus e89032667d
gnu: r-organismdbi: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.28.0.
 2019-12-15 15:38:59 +01:00
Ricardo Wurmus 866810e686
gnu: r-biovizbase: Update to 1.34.1. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.34.1.
 2019-12-15 15:38:59 +01:00
Ricardo Wurmus 81600df302
gnu: r-ggbio: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.34.0.
 2019-12-15 15:38:58 +01:00
Ricardo Wurmus 89a41696ab
gnu: r-gqtlbase: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.18.0.
 2019-12-15 15:38:58 +01:00
Ricardo Wurmus 67d4fd523d
gnu: r-erma: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.2.0.
 2019-12-15 15:38:58 +01:00
Ricardo Wurmus 14eb0978a8
gnu: r-snpstats: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.36.0.
 2019-12-15 15:38:58 +01:00
Ricardo Wurmus 6fff104191
gnu: r-ldblock: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.16.0.
[propagated-inputs]: Remove r-go-db and r-homo-sapiens.
 2019-12-15 15:38:58 +01:00
Ricardo Wurmus cfa93a30b4
gnu: r-gqtlstats: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.18.0.
 2019-12-15 15:38:58 +01:00
Ricardo Wurmus d57b6b4bae
gnu: r-gviz: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.0.
 2019-12-15 15:38:58 +01:00
Ricardo Wurmus 2e13f10e89
gnu: r-sushi: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.24.0.
 2019-12-15 15:38:58 +01:00
Ricardo Wurmus 28329991b0
gnu: r-gwascat: Update to 2.18.0. 
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.18.0.
 2019-12-15 15:38:58 +01:00
Ricardo Wurmus 0a16021241
gnu: r-hitc: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.30.0.
 2019-12-15 15:38:58 +01:00
Ricardo Wurmus 8db2915900
gnu: r-fithic: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.12.0.
 2019-12-15 15:38:58 +01:00
Ricardo Wurmus 7557bd0cce
gnu: r-hdf5array: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.1.
[propagated-inputs]: Add r-matrix.
 2019-12-15 15:38:57 +01:00
Ricardo Wurmus 1f5d262cfd
gnu: r-rhdf5lib: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.8.0.
[arguments]: Update patches.
 2019-12-15 15:38:57 +01:00
Ricardo Wurmus 8804e4b48e
gnu: r-beachmat: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 2.2.1.
[propagated-inputs]: Add r-matrix.
 2019-12-15 15:38:57 +01:00
Ricardo Wurmus 376f2f35b6
gnu: r-singlecellexperiment: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.8.0.
 2019-12-15 15:38:57 +01:00
Ricardo Wurmus bf23416fe1
gnu: r-scater: Update to 1.14.5. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.14.5.
[propagated-inputs]: Remove r-dplyr.
 2019-12-15 15:38:57 +01:00
Ricardo Wurmus 964634fa44
gnu: r-scran: Update to 1.14.5. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.14.5.
[propagated-inputs]: Remove r-dynamictreecut.
 2019-12-15 15:38:57 +01:00
Ricardo Wurmus c81ccd3076
gnu: r-delayedmatrixstats: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.8.0.
 2019-12-15 15:38:57 +01:00
Ricardo Wurmus 758dfc61ee
gnu: r-mzid: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.24.0.
 2019-12-15 15:38:57 +01:00
Ricardo Wurmus dc9d4832b9
gnu: r-vsn: Update to 3.54.0. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.54.0.
 2019-12-15 15:38:57 +01:00
Ricardo Wurmus af87ac3aa7
gnu: r-annotationfilter: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.10.0.
 2019-12-15 15:38:57 +01:00
Ricardo Wurmus 43058ca656
gnu: r-chipseq: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.36.0.
 2019-12-15 15:38:57 +01:00
Ricardo Wurmus 746e1f062e
gnu: r-copywriter: Update to 2.18.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.18.0.
 2019-12-15 15:38:57 +01:00
Ricardo Wurmus 32f6059635
gnu: r-affy: Update to 1.64.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.64.0.
 2019-12-15 15:38:56 +01:00
Ricardo Wurmus 51ca216bdf
gnu: r-affyio: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.56.0.
 2019-12-15 15:38:56 +01:00
Ricardo Wurmus 065c305ca5
gnu: r-methylkit: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.12.0.
 2019-12-15 15:38:56 +01:00
Ricardo Wurmus 2a6ce98b17
gnu: r-sva: Update to 3.34.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.34.0.
 2019-12-15 15:38:56 +01:00
Ricardo Wurmus d12328f9fe
gnu: r-protgenerics: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.18.0.
 2019-12-15 15:38:56 +01:00
Ricardo Wurmus 3381dc4b5c
gnu: r-mzr: Update to 2.20.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.20.0.
 2019-12-15 15:38:56 +01:00
Ricardo Wurmus 418d72142c
gnu: r-illuminaio: Update to 0.28.0. 
* gnu/packages/bioconductor.scm (r-illuminaio): Update to 0.28.0.
 2019-12-15 15:38:56 +01:00
Ricardo Wurmus db85744ef3
gnu: r-geoquery: Update to 2.54.1. 
* gnu/packages/bioconductor.scm (r-geoquery): Update to 2.54.1.
 2019-12-15 15:38:56 +01:00
Ricardo Wurmus 048a43d6a5
gnu: r-scone: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-scone): Update to 1.10.0.
 2019-12-15 15:38:56 +01:00