me
/
guix
Archived
1
0
Fork 0
Code
62,546 Commits
1 Branch
0 Tags
410 MiB
Commit Graph

55138 Commits (838ac881ec98cb71d4a4e4b20773573f99ecbf25)

Author SHA1 Message Date
Ricardo Wurmus a84abf434d
gnu: r-quasr: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-quasr): Update to 1.28.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:56 +02:00
Ricardo Wurmus 2aff2724ef
gnu: r-rhisat2: Update to 1.4.0. 
* gnu/packages/bioconductor.scm (r-rhisat2): Update to 1.4.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:56 +02:00
Ricardo Wurmus 201902bc05
gnu: r-sgseq: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-sgseq): Update to 1.22.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:56 +02:00
Ricardo Wurmus 568c3929b6
gnu: r-rbowtie: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-rbowtie): Update to 1.28.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:56 +02:00
Ricardo Wurmus ca8d80c90c
gnu: r-iclusterplus: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-iclusterplus): Update to 1.24.0.
 2020-06-13 01:19:56 +02:00
Ricardo Wurmus 173844fc75
gnu: r-biocfilecache: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-biocfilecache): Update to 1.12.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:56 +02:00
Ricardo Wurmus 989b7bb625
gnu: r-arrmnormalization: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-arrmnormalization): Update to 1.28.0.
 2020-06-13 01:19:56 +02:00
Ricardo Wurmus 8e5933a8e4
gnu: r-progeny: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-progeny): Update to 1.10.0.
[propagated-inputs]: Add r-dplyr, r-ggplot2, r-ggrepel, r-gridextra, and
r-tidyr.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:56 +02:00
Ricardo Wurmus 297854e682
gnu: r-rbowtie2: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-rbowtie2): Update to 1.10.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:56 +02:00
Ricardo Wurmus 8fdca89b56
gnu: r-zfpkm: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-zfpkm): Update to 1.10.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:56 +02:00
Ricardo Wurmus 620cc4d976
gnu: r-webbioc: Update to 1.60.0. 
* gnu/packages/bioconductor.scm (r-webbioc): Update to 1.60.0.
 2020-06-13 01:19:56 +02:00
Ricardo Wurmus 08c4d31400
gnu: r-widgettools: Update to 1.66.0. 
* gnu/packages/bioconductor.scm (r-widgettools): Update to 1.66.0.
 2020-06-13 01:19:56 +02:00
Ricardo Wurmus ee0f746088
gnu: r-wiggleplotr: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-wiggleplotr): Update to 1.12.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:55 +02:00
Ricardo Wurmus 996f07b591
gnu: r-wrench: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-wrench): Update to 1.6.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:55 +02:00
Ricardo Wurmus ff9f179a0c
gnu: r-xcms: Update to 3.10.1. 
* gnu/packages/bioconductor.scm (r-xcms): Update to 3.10.1.
[propagated-inputs]: Remove r-multtest; add r-summarizedexperiment.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:55 +02:00
Ricardo Wurmus 11cf2d7bb7
gnu: r-massspecwavelet: Update to 1.54.0. 
* gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.54.0.
 2020-06-13 01:19:55 +02:00
Ricardo Wurmus bcd06bdbff
gnu: r-xbseq: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-xbseq): Update to 1.20.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:55 +02:00
Ricardo Wurmus 1ec10e1987
gnu: r-roar: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-roar): Update to 1.24.0.
 2020-06-13 01:19:55 +02:00
Ricardo Wurmus a37a6ffb2d
gnu: r-yarn: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-yarn): Update to 1.14.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:55 +02:00
Ricardo Wurmus 70d90ae76d
gnu: r-quantro: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-quantro): Update to 1.22.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:55 +02:00
Ricardo Wurmus 761c9427bc
gnu: r-yaqcaffy: Update to 1.48.0. 
* gnu/packages/bioconductor.scm (r-yaqcaffy): Update to 1.48.0.
 2020-06-13 01:19:55 +02:00
Ricardo Wurmus 9ce80f9356
gnu: r-simpleaffy: Update to 2.64.0. 
* gnu/packages/bioconductor.scm (r-simpleaffy): Update to 2.64.0.
 2020-06-13 01:19:55 +02:00
Ricardo Wurmus f0439a1767
gnu: r-gcrma: Update to 2.60.0. 
* gnu/packages/bioconductor.scm (r-gcrma): Update to 2.60.0.
 2020-06-13 01:19:55 +02:00
Ricardo Wurmus 8a5abc62d5
gnu: r-yapsa: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-yapsa): Update to 1.14.0.
[propagated-inputs]: Add r-biostrings, r-bsgenome-hsapiens-ucsc-hg19,
r-doparallel, r-dplyr, r-ggbeeswarm, r-magrittr, and r-pracma.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:55 +02:00
Ricardo Wurmus 63c14717e3
gnu: r-somaticsignatures: Update to 2.24.0. 
* gnu/packages/bioconductor.scm (r-somaticsignatures): Update to 2.24.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:55 +02:00
Ricardo Wurmus a471def062
gnu: r-gtrellis: Update to 1.20.1. 
* gnu/packages/bioconductor.scm (r-gtrellis): Update to 1.20.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:54 +02:00
Ricardo Wurmus 6e397aad32
gnu: r-yamss: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-yamss): Update to 1.14.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:54 +02:00
Ricardo Wurmus 4eccf8e5e5
gnu: r-ebimage: Update to 4.30.0. 
* gnu/packages/bioconductor.scm (r-ebimage): Update to 4.30.0.
 2020-06-13 01:19:54 +02:00
Ricardo Wurmus e059ab2503
gnu: r-aucell: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-aucell): Update to 1.10.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:54 +02:00
Ricardo Wurmus 6314938884
gnu: r-allelicimbalance: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-allelicimbalance): Update to 1.26.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:54 +02:00
Ricardo Wurmus 231898d5b9
gnu: r-annotationtools: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-annotationtools): Update to 1.62.0.
 2020-06-13 01:19:54 +02:00
Ricardo Wurmus 7866994c03
gnu: r-annotationfuncs: Update to 1.38.0. 
* gnu/packages/bioconductor.scm (r-annotationfuncs): Update to 1.38.0.
 2020-06-13 01:19:54 +02:00
Ricardo Wurmus 6a65ac1537
gnu: r-abaenrichment: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-abaenrichment): Update to 1.18.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:54 +02:00
Ricardo Wurmus 19b39ac579
gnu: r-gofuncr: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-gofuncr): Update to 1.8.0.
 2020-06-13 01:19:54 +02:00
Ricardo Wurmus a007de81e5
gnu: r-atacseqqc: Update to 1.12.3. 
* gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.12.3.
 2020-06-13 01:19:54 +02:00
Ricardo Wurmus 785c759617
gnu: r-genomicscores: Update to 2.0.0. 
* gnu/packages/bioconductor.scm (r-genomicscores): Update to 2.0.0.
[propagated-inputs]: Remove r-bsgenome; add r-delayedarray, r-hdf5array, and r-rhdf5.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:54 +02:00
Ricardo Wurmus e6fbaf0cc7
gnu: r-motifstack: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-motifstack): Update to 1.32.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:54 +02:00
Ricardo Wurmus e65783e032
gnu: r-motifbreakr: Update to 2.2.0. 
* gnu/packages/bioconductor.scm (r-motifbreakr): Update to 2.2.0.
[propagated-inputs]: Add r-summarizedexperiment.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:54 +02:00
Ricardo Wurmus da6a75fe00
gnu: r-motifdb: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-motifdb): Update to 1.30.0.
[propagated-inputs]: Add r-genomicranges.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:53 +02:00
Ricardo Wurmus 352cfa3434
gnu: r-motiv: Update to 1.43.0. 
* gnu/packages/bioconductor.scm (r-motiv): Update to 1.43.0.
 2020-06-13 01:19:53 +02:00
Ricardo Wurmus 6d02e17139
gnu: r-rgadem: Update to 2.36.0. 
* gnu/packages/bioconductor.scm (r-rgadem): Update to 2.36.0.
 2020-06-13 01:19:53 +02:00
Ricardo Wurmus 7450edca0d
gnu: r-bacon: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-bacon): Update to 1.16.0.
 2020-06-13 01:19:53 +02:00
Ricardo Wurmus 35bcfaefae
gnu: r-abseqr: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-abseqr): Update to 1.6.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:53 +02:00
Ricardo Wurmus b391b1e47c
gnu: r-a4: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-a4): Update to 1.36.0.
 2020-06-13 01:19:53 +02:00
Ricardo Wurmus 2a91c987fd
gnu: r-a4base: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-a4base): Update to 1.36.0.
 2020-06-13 01:19:53 +02:00
Ricardo Wurmus e47f9f48d4
gnu: r-a4reporting: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-a4reporting): Update to 1.36.0.
 2020-06-13 01:19:53 +02:00
Ricardo Wurmus 6afea4ea93
gnu: r-a4preproc: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-a4preproc): Update to 1.36.0.
 2020-06-13 01:19:53 +02:00
Ricardo Wurmus 33c9c8563d
gnu: r-a4classif: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-a4classif): Update to 1.36.0.
 2020-06-13 01:19:53 +02:00
Ricardo Wurmus 4f2112add9
gnu: r-a4core: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-a4core): Update to 1.36.0.
 2020-06-13 01:19:53 +02:00
Ricardo Wurmus d200b4dc48
gnu: r-annaffy: Update to 1.60.0. 
* gnu/packages/bioconductor.scm (r-annaffy): Update to 1.60.0.
 2020-06-13 01:19:53 +02:00
Ricardo Wurmus 500f7df840
gnu: r-mlinterfaces: Update to 1.68.0. 
* gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.68.0.
[propagated-inputs]: Add r-rcpp.
 2020-06-13 01:19:53 +02:00
Ricardo Wurmus 63c8323ae9
gnu: r-clusterprofiler: Update to 3.16.0. 
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 3.16.0.
[propagated-inputs]: Remove r-ggplot2; add r-downloader and r-dplyr.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:53 +02:00
Ricardo Wurmus 43fb14cedc
gnu: r-enrichplot: Update to 1.8.1. 
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.8.1.
[propagated-inputs]: Add r-plyr and r-scatterpie.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:52 +02:00
Ricardo Wurmus 3a80f1cfae
gnu: r-dose: Update to 3.14.0. 
* gnu/packages/bioconductor.scm (r-dose): Update to 3.14.0.
[propagated-inputs]: Remove r-s4vectors.
 2020-06-13 01:19:52 +02:00
Ricardo Wurmus 1dec455cb8
gnu: r-fgsea: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-fgsea): Update to 1.14.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:52 +02:00
Ricardo Wurmus b1d76ad0ca
gnu: r-sigpathway: Update to 1.56.0. 
* gnu/packages/bioconductor.scm (r-sigpathway): Update to 1.56.0.
 2020-06-13 01:19:52 +02:00
Ricardo Wurmus 8d30d59adf
gnu: r-anota: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-anota): Update to 1.36.0.
 2020-06-13 01:19:52 +02:00
Ricardo Wurmus 621cd90406
gnu: r-gosemsim: Update to 2.14.0. 
* gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.14.0.
 2020-06-13 01:19:52 +02:00
Ricardo Wurmus 65e0a7b181
gnu: r-heatplus: Update to 2.34.0. 
* gnu/packages/bioconductor.scm (r-heatplus): Update to 2.34.0.
 2020-06-13 01:19:52 +02:00
Ricardo Wurmus f2b686f61a
gnu: r-varianttools: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-varianttools): Update to 1.30.0.
 2020-06-13 01:19:52 +02:00
Ricardo Wurmus ecb4e16519
gnu: r-triform: Update to 1.29.0. 
* gnu/packages/bioconductor.scm (r-triform): Update to 1.29.0.
 2020-06-13 01:19:52 +02:00
Ricardo Wurmus 293fb8a147
gnu: r-ioniser: Update to 2.12.0. 
* gnu/packages/bioconductor.scm (r-ioniser): Update to 2.12.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:52 +02:00
Ricardo Wurmus 1465873c6c
gnu: r-linnorm: Update to 2.12.0. 
* gnu/packages/bioconductor.scm (r-linnorm): Update to 2.12.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:52 +02:00
Ricardo Wurmus ae1c51a1c1
gnu: r-lumi: Update to 2.40.0. 
* gnu/packages/bioconductor.scm (r-lumi): Update to 2.40.0.
 2020-06-13 01:19:52 +02:00
Ricardo Wurmus 5f25d5f80d
gnu: r-methylumi: Update to 2.34.0. 
* gnu/packages/bioconductor.scm (r-methylumi): Update to 2.34.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:52 +02:00
Ricardo Wurmus 83e6ffdac1
gnu: r-minfi: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-minfi): Update to 1.34.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:51 +02:00
Ricardo Wurmus e3fbcb28a4
gnu: r-bumphunter: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-bumphunter): Update to 1.30.0.
 2020-06-13 01:19:51 +02:00
Ricardo Wurmus debaa0f3ba
gnu: r-siggenes: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-siggenes): Update to 1.62.0.
 2020-06-13 01:19:51 +02:00
Ricardo Wurmus d784a4784f
gnu: r-illuminaio: Update to 0.30.0. 
* gnu/packages/bioconductor.scm (r-illuminaio): Update to 0.30.0.
 2020-06-13 01:19:51 +02:00
Ricardo Wurmus 159e427c9f
gnu: r-geoquery: Update to 2.56.0. 
* gnu/packages/bioconductor.scm (r-geoquery): Update to 2.56.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:51 +02:00
Ricardo Wurmus 3fc1e03949
gnu: r-scone: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-scone): Update to 1.12.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:51 +02:00
Ricardo Wurmus ce9e19bc9b
gnu: r-scdd: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-scdd): Update to 1.12.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:51 +02:00
Ricardo Wurmus 22c084ba9d
gnu: r-noiseq: Update to 2.31.0. 
* gnu/packages/bioconductor.scm (r-noiseq): Update to 2.31.0.
 2020-06-13 01:19:51 +02:00
Ricardo Wurmus d1f3c37134
gnu: r-monocle: Update to 2.16.0. 
* gnu/packages/bioconductor.scm (r-monocle): Update to 2.16.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:51 +02:00
Ricardo Wurmus 97cba97aa1
gnu: r-mast: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-mast): Update to 1.14.0.
 2020-06-13 01:19:51 +02:00
Ricardo Wurmus ee1e8fee89
gnu: r-icobra: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-icobra): Update to 1.16.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:51 +02:00
Ricardo Wurmus 359a084aa3
gnu: r-ihw: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-ihw): Update to 1.16.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:51 +02:00
Ricardo Wurmus 0653b8b082
gnu: r-lpsymphony: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.16.0.
[inputs]: Remove gfortran.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:51 +02:00
Ricardo Wurmus 6e2dc9e385
gnu: r-karyoploter: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-karyoploter): Update to 1.14.0.
[propagated-inputs]: Add r-genomicfeatures.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:50 +02:00
Ricardo Wurmus 1e37caca52
gnu: r-ebseq: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-ebseq): Update to 1.28.0.
 2020-06-13 01:19:50 +02:00
Ricardo Wurmus 6a7cfd5f1f
gnu: r-dnacopy: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.62.0.
 2020-06-13 01:19:50 +02:00
Ricardo Wurmus 866939b76d
gnu: r-copynumber: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-copynumber): Update to 1.28.0.
 2020-06-13 01:19:50 +02:00
Ricardo Wurmus 9697afb10e
gnu: r-chipexoqual: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-chipexoqual): Update to 1.12.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:50 +02:00
Ricardo Wurmus 784d1670b7
gnu: r-savr: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-savr): Update to 1.26.0.
 2020-06-13 01:19:50 +02:00
Ricardo Wurmus 265b645075
gnu: r-destiny: Update to 3.2.0. 
* gnu/packages/bioconductor.scm (r-destiny): Update to 3.2.0.
[propagated-inputs]: Add r-nbconvertr.
 2020-06-13 01:19:50 +02:00
Ricardo Wurmus a8351d467c
gnu: r-biocsingular: Update to 1.4.0. 
* gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.4.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:50 +02:00
Ricardo Wurmus f5864c11a4
gnu: r-biocneighbors: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-biocneighbors): Update to 1.6.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:50 +02:00
Ricardo Wurmus ae0fcaa6fd
gnu: r-ruvseq: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.22.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:50 +02:00
Ricardo Wurmus 14f40ae830
gnu: r-dnabarcodes: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-dnabarcodes): Update to 1.18.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:50 +02:00
Ricardo Wurmus 437bc4dda9
gnu: r-inspect: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-inspect): Update to 1.18.0.
[propagated-inputs]: Add r-rtracklayer.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:50 +02:00
Ricardo Wurmus 46a973bc24
gnu: r-plgem: Update to 1.60.0. 
* gnu/packages/bioconductor.scm (r-plgem): Update to 1.60.0.
 2020-06-13 01:19:50 +02:00
Ricardo Wurmus ee73dea61b
gnu: r-rots: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-rots): Update to 1.16.0.
 2020-06-13 01:19:49 +02:00
Ricardo Wurmus a6251d6e8b
gnu: r-glimma: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-glimma): Update to 1.16.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:49 +02:00
Ricardo Wurmus 7fbd97745b
gnu: r-goseq: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-goseq): Update to 1.40.0.
 2020-06-13 01:19:49 +02:00
Ricardo Wurmus c7be592fb4
gnu: r-ctc: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-ctc): Update to 1.62.0.
 2020-06-13 01:19:49 +02:00
Ricardo Wurmus 76dd036e16
gnu: r-genomicinteractions: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.22.0.
 2020-06-13 01:19:49 +02:00
Ricardo Wurmus 861a903f14
gnu: r-interactionset: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.16.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:49 +02:00
Ricardo Wurmus 6b78a91b75
gnu: r-riboseqr: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-riboseqr): Update to 1.22.0.
 2020-06-13 01:19:49 +02:00
Ricardo Wurmus 7aae05a953
gnu: r-riboprofiling: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-riboprofiling): Update to 1.18.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:49 +02:00
Ricardo Wurmus ef1d3231c3
gnu: r-chipcomp: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.18.0.
 2020-06-13 01:19:49 +02:00
Ricardo Wurmus 9834c36724
gnu: r-bayseq: Update to 2.22.0. 
* gnu/packages/bioconductor.scm (r-bayseq): Update to 2.22.0.
 2020-06-13 01:19:49 +02:00
Ricardo Wurmus f4ef564595
gnu: r-qdnaseq: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.24.0.
 2020-06-13 01:19:49 +02:00
Ricardo Wurmus de4a352e8a
gnu: r-cghcall: Update to 2.50.0. 
* gnu/packages/bioconductor.scm (r-cghcall): Update to 2.50.0.
 2020-06-13 01:19:49 +02:00
Ricardo Wurmus bd93ec4cf0
gnu: r-cghbase: Update to 1.48.0. 
* gnu/packages/bioconductor.scm (r-cghbase): Update to 1.48.0.
 2020-06-13 01:19:49 +02:00
Ricardo Wurmus 49d589e530
gnu: r-marray: Update to 1.66.0. 
* gnu/packages/bioconductor.scm (r-marray): Update to 1.66.0.
 2020-06-13 01:19:49 +02:00
Ricardo Wurmus dc24de46ad
gnu: r-chippeakanno: Update to 3.22.2. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.22.2.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:48 +02:00
Ricardo Wurmus 7d37c6d914
gnu: r-graph: Update to 1.66.0. 
* gnu/packages/bioconductor.scm (r-graph): Update to 1.66.0.
 2020-06-13 01:19:48 +02:00
Ricardo Wurmus 8cadf253c3
gnu: r-multtest: Update to 2.44.0. 
* gnu/packages/bioconductor.scm (r-multtest): Update to 2.44.0.
 2020-06-13 01:19:48 +02:00
Ricardo Wurmus b47b649ae5
gnu: r-diffbind: Update to 2.16.0. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 2.16.0.
 2020-06-13 01:19:48 +02:00
Ricardo Wurmus f9a247590e
gnu: r-qvalue: Update to 2.20.0. 
* gnu/packages/bioconductor.scm (r-qvalue): Update to 2.20.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:48 +02:00
Ricardo Wurmus ace82f805f
gnu: r-oligo: Update to 1.52.0. 
* gnu/packages/bioconductor.scm (r-oligo): Update to 1.52.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:48 +02:00
Ricardo Wurmus b628842f7e
gnu: r-oligoclasses: Update to 1.50.0. 
* gnu/packages/bioconductor.scm (r-oligoclasses): Update to 1.50.0.
 2020-06-13 01:19:48 +02:00
Ricardo Wurmus 53e4201937
gnu: r-geneplotter: Update to 1.66.0. 
* gnu/packages/bioconductor.scm (r-geneplotter): Update to 1.66.0.
 2020-06-13 01:19:48 +02:00
Ricardo Wurmus 7f94cf0184
gnu: r-reportingtools: Update to 2.28.0. 
* gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.28.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:48 +02:00
Ricardo Wurmus 7f34dd58e9
gnu: r-regioner: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.20.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:48 +02:00
Ricardo Wurmus 07bea01092
gnu: r-hpar: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-hpar): Update to 1.30.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:48 +02:00
Ricardo Wurmus c2f4ad96f5
gnu: r-annotate: Update to 1.66.0. 
* gnu/packages/bioconductor.scm (r-annotate): Update to 1.66.0.
 2020-06-13 01:19:48 +02:00
Ricardo Wurmus acaf8a2342
gnu: r-affxparser: Update to 1.60.0. 
* gnu/packages/bioconductor.scm (r-affxparser): Update to 1.60.0.
 2020-06-13 01:19:47 +02:00
Ricardo Wurmus fa61069781
gnu: r-affycoretools: Update to 1.60.1. 
* gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.60.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:47 +02:00
Ricardo Wurmus 36d4ca410d
gnu: r-affycontam: Update to 1.46.0. 
* gnu/packages/bioconductor.scm (r-affycontam): Update to 1.46.0.
 2020-06-13 01:19:47 +02:00
Ricardo Wurmus 251c18f1ed
gnu: r-affycompatible: Update to 1.48.0. 
* gnu/packages/bioconductor.scm (r-affycompatible): Update to 1.48.0.
 2020-06-13 01:19:47 +02:00
Ricardo Wurmus 66aeb1b46d
gnu: r-affycomp: Update to 1.64.0. 
* gnu/packages/bioconductor.scm (r-affycomp): Update to 1.64.0.
 2020-06-13 01:19:47 +02:00
Ricardo Wurmus 2e15c16f1e
gnu: r-biocgenerics: Update to 0.34.0. 
* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.34.0.
 2020-06-13 01:19:47 +02:00
Ricardo Wurmus bc217e4c0c
gnu: r-biocversion: Update to 3.11.1. 
* gnu/packages/bioconductor.scm (r-biocversion): Update to 3.11.1.
 2020-06-13 01:19:47 +02:00
Ricardo Wurmus 1ab0380db9
gnu: r-cummerbund: Update to 2.30.0. 
* gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.30.0.
 2020-06-13 01:19:47 +02:00
Ricardo Wurmus 751fa8ff71
gnu: r-coverageview: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-coverageview): Update to 1.26.0.
 2020-06-13 01:19:47 +02:00
Ricardo Wurmus 725eea00da
gnu: r-ideoviz: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-ideoviz): Update to 1.24.0.
 2020-06-13 01:19:47 +02:00
Ricardo Wurmus a3b55161c7
gnu: r-delayedmatrixstats: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.10.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:47 +02:00
Ricardo Wurmus 47c7670c43
gnu: r-scran: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.16.0.
[propagated-inputs]: Add r-iranges.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:47 +02:00
Ricardo Wurmus 7039b53945
gnu: r-scater: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.16.1.
[propagated-inputs]: Add r-rlang.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus 9e7acf2f14
gnu: r-singlecellexperiment: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.10.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus 16dd6bacaa
gnu: r-beachmat: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 2.4.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus 87d5444d9f
gnu: r-rhdf5lib: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.10.0.
[source]: Update snippet.
[arguments]: Replace ZLIB variables in Makevars.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus cf907680e8
gnu: r-hdf5array: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.16.0.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus 46f188d1df
gnu: r-hitc: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.32.0.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus 6be25cc2db
gnu: r-fithic: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.14.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus a811751f49
gnu: r-sushi: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.26.0.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus ddef43a29d
gnu: r-gwascat: Update to 2.20.1. 
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.20.1.
[propagated-inputs]: Remove r-homo-sapiens; add r-ggplot2.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus 522da60b29
gnu: r-gviz: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.32.0.
[propagated-inputs]: Add r-ensembldb.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus a97897bc3d
gnu: r-gqtlstats: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.20.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus 6caad43c18
gnu: r-ldblock: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.18.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus 87772ab4dd
gnu: r-erma: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.4.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus aab0e28fc1
gnu: r-snpstats: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.38.0.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus 42d8cd9f97
gnu: r-gqtlbase: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.20.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus 7038aeb210
gnu: r-ggbio: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.36.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus 07518c3a34
gnu: r-biovizbase: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.36.0.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus 7c26687871
gnu: r-organismdbi: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.30.0.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus 39da6fbc40
gnu: r-ensembldb: Update to 2.12.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.12.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus 7a9e7e4844
gnu: r-dirichletmultinomial: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.30.0.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus ca5c92c0c7
gnu: r-complexheatmap: Update to 2.4.2. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.4.2.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus 8323ff3376
gnu: r-genomicfiles: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.24.0.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus 817e4c8b68
gnu: r-gage: Update to 2.37.0. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.37.0.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus d80a6cacaf
gnu: r-keggrest: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.28.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus 3422533bd9
gnu: r-fastseg: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.34.0.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus 5fce232977
gnu: r-annotationhub: Update to 2.20.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.20.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus 334e8d7b79
gnu: r-interactivedisplaybase: Update to 1.26.3. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to
1.26.3.
[propagated-inputs]: Add r-dt.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus 15990617eb
gnu: r-edaseq: Update to 2.22.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.22.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus c9059a3b0e
gnu: r-deseq: Update to 1.39.0. 
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.39.0.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus 019bc36732
gnu: r-aroma-light: Update to 3.18.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.18.0.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus f6ddf20891
gnu: r-msnid: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.22.0.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus 10a7ee2609
gnu: r-msnbase: Update to 2.14.2. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.14.2.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus 7b4fc6ae0a
gnu: r-pcamethods: Update to 1.80.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.80.0.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus 8eb579883d
gnu: r-mzid: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.26.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus 8e0d11d88b
gnu: r-vsn: Update to 3.56.0. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.56.0.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus 736f6cfe66
gnu: r-affy: Update to 1.66.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.66.0.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus d93af7d632
gnu: r-affyio: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.58.0.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus 157eb89707
gnu: r-protgenerics: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.20.0.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus d95a1cb10e
gnu: r-sva: Update to 3.36.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.36.0.
[propagated-inputs]: Add r-edger.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus c336d54d5f
gnu: r-methylkit: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.14.2.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus 3475ad075b
gnu: r-copywriter: Update to 2.20.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.20.0.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus 6a25fb9b6c
gnu: r-chipseq: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.38.0.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus 43dec928d2
gnu: r-annotationfilter: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.12.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus 05716c1b1c
gnu: r-rhdf5: Update to 2.32.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus 876e05bfce
gnu: r-tximport: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.16.1.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus 40a4772f09
gnu: r-mutationalpatterns: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 2.0.0.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus 3c53617efc
gnu: r-rcas: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.14.0.
[propagated-inputs]: Remove r-annotationdbi, r-biomart, r-dbi, r-knitr,
r-motifrg, r-org-hs-eg-db, and r-topgo; add r-bsgenome, r-gprofiler2,
r-iranges, and r-ranger.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus 261d931406
gnu: r-bamsignals: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.20.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus 8f08457f05
gnu: r-rhtslib: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.20.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus 52ce0d299d
gnu: r-zlibbioc: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.34.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus 239ca0f3bd
gnu: r-motifrg: Update to 1.31.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.31.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus 40ba4e8466
gnu: r-seqlogo: Update to 1.54.3. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.54.3.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus 837e7634d9
gnu: r-genomation: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.20.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus 2d537b5afc
gnu: r-seqpattern: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.20.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus e6df69a84d
gnu: r-impute: Update to 1.62.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.62.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus d9b23ec47c
gnu: r-bsgenome: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.56.0.
[propagated-inputs]: Add r-matrixstats.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus 543fd63c2e
gnu: r-topgo: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.40.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus a285314e29
gnu: r-genomicfeatures: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.40.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus f85794edb8
gnu: r-rtracklayer: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.48.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus 58613ca1e5
gnu: r-genomicalignments: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.24.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus 87c98cf701
gnu: r-summarizedexperiment: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.18.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus 46e103a1b5
gnu: r-delayedarray: Update to 0.14.0. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.14.0.
[propagated-inputs]: Remove r-biocparallel.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus 1f9c87a442
gnu: r-rsamtools: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.4.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus d3491d4dad
gnu: r-biostrings: Update to 2.56.0. 
* gnu/packages/bioinformatics.scm ( r-biostrings): Update to 2.56.0.
[propagated-inputs]: Add r-crayon.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus cb486f16da
gnu: r-biocparallel: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.22.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus e87e6cc89d
gnu: r-biomart: Update to 2.44.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.44.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus 920224771f
gnu: r-annotationdbi: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus 7d91e3bed4
gnu: r-biobase: Update to 2.48.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.48.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus 087a97f8df
gnu: r-genomicranges: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.40.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus e0d40fa275
gnu: r-xvector: Update to 0.28.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.28.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus 49c766d0bb
gnu: r-limma: Update to 3.44.1. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.44.1.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus cdd83b2e22
gnu: r-variantannotation: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.34.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus c14d59d9ad
gnu: r-edger: Update to 3.30.3. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.30.3.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus 506735eea6
gnu: r-genomeinfodb: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.24.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 8a38b676da
gnu: r-iranges: Update to 2.22.2. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.22.2.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus f189f536be
gnu: r-s4vectors: Update to 0.26.1. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.26.1.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 1a9de6cfe8
gnu: r-bioccheck: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.24.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 9f416be83d
gnu: r-biocstyle: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 1ca88fb8e9
gnu: r-biocviews: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 5de96ae98b
gnu: r-grohmm: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.22.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus bb18d11d85
gnu: r-systempiper: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.22.0.
[propagated-inputs]: Add r-assertthat, r-magrittr, r-rsvg, r-dot, and
r-stringr; remove r-biocgenerics.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 681cca95b3
gnu: r-shortread: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.46.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 3d2899dab5
gnu: r-gostats: Update to 2.54.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.54.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus be414286bc
gnu: r-category: Update to 2.54.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.54.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus a8613ff861
gnu: r-gseabase: Update to 1.50.1. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.50.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 7d8b96e24b
gnu: r-rbgl: Update to 1.64.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.64.0.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 397568dbca
gnu: r-annotationforge: Update to 1.30.1. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.30.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus db5addba2c
gnu: r-dexseq: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.34.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 3d7de4ed82
gnu: r-deseq2: Update to 1.28.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.28.1.
[propagated-inputs]: Remove r-hmisc.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 5fdea056c9
gnu: r-genefilter: Update to 1.70.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.70.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus c85e5ac0df
gnu: r-rgraphviz: Update to 2.32.0. 
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.32.0.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 2226a2a8de
gnu: r-preprocesscore: Update to 1.50.0. 
* gnu/packages/statistics.scm (r-preprocesscore): Update to 1.50.0.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 67a289e5bd
gnu: Add r-dot. 
* gnu/packages/cran.scm (r-dot): New variable.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 06ceac32e6
gnu: Add r-v8. 
* gnu/packages/cran.scm (r-v8): New variable.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus e6aacef67e
gnu: Add r-scatterpie. 
* gnu/packages/cran.scm (r-scatterpie): New variable.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 45f54b418b
gnu: Add r-gprofiler2. 
* gnu/packages/cran.scm (r-gprofiler2): New variable.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus f9311eaa7c
gnu: node: Build shared library. 
* gnu/packages/node.scm (node)[arguments]: Build shared library.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus a620d22ea8
gnu: r-gprofiler: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-gprofiler): Move this variable from here...
* gnu/packages/cran.scm (r-gprofiler): ...to here.
 2020-06-13 01:19:38 +02:00
Ludovic Courtès 29e4d3ea06
gnu: guile-sqlite3: Update to 0.1.1. 
* gnu/packages/guile.scm (guile-sqlite3): Update to 0.1.1.
[source]: Remove 'patches', 'modules', and 'snippet'.
* gnu/packages/patches/guile-sqlite3-fix-cross-compilation.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
 2020-06-12 18:56:11 +02:00
Katherine Cox-Buday 7def5056b6
gnu: Add liblogging. 
* gnu/packages/c.scm (liblogging): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-12 18:56:11 +02:00
Katherine Cox-Buday 0aee6e51b4
gnu: Add libfastjson. 
* gnu/packages/c.scm (libfastjson): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-12 18:56:10 +02:00
Katherine Cox-Buday 70a49ef76b
gnu: Add libestr. 
* gnu/packages/c.scm (libestr): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-12 18:56:10 +02:00
Ryan Desfosses 3bec7a356a
gnu: Add emacs-shell-pop. 
* gnu/packages/emacs-xyz.scm (emacs-shell-pop): New variable

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-12 18:56:10 +02:00
Efraim Flashner 9a01efa262
gnu: Fix apache mirror URIs. 
* gnu/packages/web.scm (serf)[source]: Remove redundant part of URI.
* gnu/packages/java.scm (ant-bootstrap, java-commons-httpclient,
java-jakarta-oro)[source]: Same.
* gnu/packages/maven.scm (maven-shared-utils, maven-plugin-annotations,
maven-wagon-provider-api, maven-artifact)[source]: Same.
 2020-06-12 18:23:27 +03:00
Mathieu Othacehe fd1e885236
system: image: Do not produce an HFS tree when building an ISO. 
Use "mbr_only" mode to make sure that no HFS+ tree are generated.

* gnu/system/image.scm (system-image): Set MKRESCUE_SED_MODE to "mbr_only".
 2020-06-12 17:21:18 +02:00
Marius Bakke 8ea91d05b0
gnu: mesa: Ensure replacements are inherited in special variants. 
* gnu/packages/gl.scm (mesa-opencl, mesa-opencl-icd, mesa-headers): Use
PACKAGE/INHERIT instead of regular inheritance.
 2020-06-12 12:57:15 +02:00
Marius Bakke fdd8835093
gnu: mesa: Replace with 20.0.8. 
* gnu/packages/gl.scm (mesa-20.0.8): New variable.
(mesa)[replacement]: New field.
 2020-06-12 12:55:12 +02:00
Pierre Neidhardt cd0f1fbd1a
gnu: xf86-input-libinput: Reduce closure size. 
* gnu/packages/xorg.scm (xf86-input-libinput)[inputs]: Replace libinput by
libinput-minimal.
 2020-06-12 09:00:45 +02:00
Ekaitz Zarraga 9c6ea3cb56
gnu: icecat: Fix WebGL support. 
* gnu/packages/gnuzilla.scm (icecat): Wrap mesa.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2020-06-12 01:29:54 +02:00
Ludovic Courtès 8a02e45d93
shepherd: 'read-pid-file/container' terminates the whole process group. 
This mirrors a change made in the Shepherd 0.8.0.  Previously, upon
startup failure, we could have left processes behind.

* gnu/build/shepherd.scm (read-pid-file/container): Kill (- PID) instead
of PID.
 2020-06-12 00:04:42 +02:00
Ludovic Courtès b6b95685d0
shepherd: Unblock signals in the child process. 
Fixes <https://bugs.gnu.org/41791>.
Reported by Tobias Geerinckx-Rice <me@tobias.gr>.

This change mirrors changes made in the Shepherd 0.8.1, where signals
are blocked in the shepherd process in support of 'signalfd'.  The
regression was introduced with the switch to 0.8.1 in
3f9c62d1a8b345909adaeb22f454ad22554c55a1: child processes would not
receive SIGTERM upon 'herd stop SERVICE'.

* gnu/build/shepherd.scm <top level>: Autoload (shepherd system).
(make-forkexec-constructor/container): Call call to 'sigaction' and
'unblock-signals'.
 2020-06-12 00:04:42 +02:00
Marius Bakke 9b043df740
Merge branch 'master' into staging 2020-06-11 23:30:32 +02:00
Jakub Kądziołka 648ae62112
gnu: Add exercism and dependencies. 
* gnu/packages/education.scm (exercism): New variable.
* gnu/packages/patches/exercism-disable-self-update.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/golang.scm (go-github-com-spf13-afero)
  (go-github-com-spf13-cast)
  (go-github-com-spf13-cobra)
  (go-github-com-spf13-jwalterweatherman)
  (go-github-com-spf13-viper)
  (go-github-com-fsnotify-fsnotify)
  (go-github-com-magiconair-properties)
  (go-github-com-pelletier-go-toml)
  (go-github-com-subosito-gotenv)
  (go-gopkg-in-ini-v1)
  (go-github-com-mitchellh-mapstructure): New variables.
 2020-06-11 22:44:27 +02:00
Mark H Weaver 437e64b7d3
gnu: linux-libre: Update to 5.4.46. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.46.
(linux-libre-5.4-pristine-source): Update hash.
 2020-06-11 16:19:38 -04:00
Mark H Weaver 48f3631b0f
gnu: linux-libre@5.7: Update to 5.7.2. 
* gnu/packages/linux.scm (linux-libre-5.7-version): Update to 5.7.128.
(linux-libre-5.7-pristine-source): Update hash.
 2020-06-11 16:19:36 -04:00
Mark H Weaver 1c02643a06
gnu: linux-libre@5.6: Remove. 
Users of linux-libre-5.6 should migrate to version 5.7.

* gnu/packages/linux.scm (deblob-scripts-5.6, linux-libre-5.6-version)
(linux-libre-5.6-pristine-source, linux-libre-5.6-source)
(linux-libre-headers-5.6, linux-libre-arm-generic-5.6)
(linux-libre-arm64-generic-5.6): Remove variables.
 2020-06-11 16:19:34 -04:00
Mark H Weaver e37aff92e2
gnu: linux-libre@4.19: Update to 4.19.128. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.128.
(linux-libre-4.19-pristine-source): Update hash.
 2020-06-11 16:19:32 -04:00
Mark H Weaver e5630f5d3c
gnu: linux-libre@4.14: Update to 4.14.184. 
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.184.
(linux-libre-4.14-pristine-source): Update hash.
 2020-06-11 16:19:30 -04:00
Mark H Weaver 523d63638a
gnu: linux-libre@4.9: Update to 4.9.227. 
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.227.
(linux-libre-4.9-pristine-source): Update hash.
 2020-06-11 16:19:27 -04:00
Mark H Weaver 59feeb96e4
gnu: linux-libre@4.4: Update to 4.4.227. 
* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.227.
(linux-libre-4.4-pristine-source): Update hash.
 2020-06-11 16:19:25 -04:00
Efraim Flashner e73a016df2
gnu: adns: Update to 1.6.0. 
* gnu/packages/adns.scm (adns): Update to 1.6.0.
[source]: Use https.
[native-inputs]: Add m4.
 2020-06-11 23:13:40 +03:00