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52502 commits

Author SHA1 Message Date
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
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
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
Efraim Flashner
4908ba058f
gnu: subversion: Update to 1.14.0. 
* gnu/packages/version-control.scm (subversion): Update to 1.14.0.
[source]: Update source URI.
 2020-06-11 22:41:02 +03:00
Ludovic Courtès
ecf92194a5
gnu: nghttp2: Replace with version 1.41 [fixes CVE-2020-11080]. 
* gnu/packages/web.scm (nghttp2-1.41): New variable.
(nghttp2)[replacement]: New field.
 2020-06-11 19:05:05 +02:00
Ricardo Wurmus
cbd9581acc
gnu: r-with-tests, r-minimal: Update to 4.0.1. 
* gnu/packages/statistics.scm (r-with-tests, r-minimal): Update to 4.0.1.
 2020-06-11 17:03:48 +02:00
Ricardo Wurmus
67ee20fbd2
gnu: r-brms: Update to 2.13.0. 
* gnu/packages/cran.scm (r-brms): Update to 2.13.0.
 2020-06-11 17:03:48 +02:00
Ricardo Wurmus
20702ad9a3
gnu: r-crochet: Update to 2.3.0. 
* gnu/packages/cran.scm (r-crochet): Update to 2.3.0.
[native-inputs]: Add r-knitr.
 2020-06-11 17:03:48 +02:00
Ricardo Wurmus
e5884ce4c7
gnu: r-openmx: Update to 2.17.4. 
* gnu/packages/cran.scm (r-openmx): Update to 2.17.4.
 2020-06-11 17:03:48 +02:00
Ricardo Wurmus
b34ba0649a
gnu: r-stanheaders: Update to 2.21.0-5. 
* gnu/packages/cran.scm (r-stanheaders): Update to 2.21.0-5.
[propagated-inputs]: Add r-rcppeigen and r-rcppparallel.
 2020-06-11 17:03:48 +02:00
Ricardo Wurmus
3a9a695255
gnu: r-semtools: Update to 0.5-3. 
* gnu/packages/cran.scm (r-semtools): Update to 0.5-3.
 2020-06-11 17:03:48 +02:00
Ricardo Wurmus
bd76f9561d
gnu: r-sem: Update to 3.1-11. 
* gnu/packages/cran.scm (r-sem): Update to 3.1-11.
 2020-06-11 17:03:48 +02:00
Ricardo Wurmus
db4d3b2581
gnu: r-emplik: Update to 1.1-1. 
* gnu/packages/cran.scm (r-emplik): Update to 1.1-1.
 2020-06-11 17:03:48 +02:00
Ricardo Wurmus
de26ce7265
gnu: r-rsvg: Update to 2.1. 
* gnu/packages/cran.scm (r-rsvg): Update to 2.1.
[native-inputs]: Add r-knitr.
 2020-06-11 17:03:48 +02:00
Ricardo Wurmus
8ddf3be097
gnu: r-actuar: Update to 3.0-0. 
* gnu/packages/cran.scm (r-actuar): Update to 3.0-0.
 2020-06-11 17:03:48 +02:00
Ricardo Wurmus
8050cce35d
gnu: r-gdina: Update to 2.8.0. 
* gnu/packages/cran.scm (r-gdina): Update to 2.8.0.
 2020-06-11 17:03:48 +02:00
Ricardo Wurmus
242fae8edf
gnu: r-seewave: Update to 2.1.6. 
* gnu/packages/cran.scm (r-seewave): Update to 2.1.6.
[inputs]: Add libsndfile.
 2020-06-11 17:03:47 +02:00
Ricardo Wurmus
30031516d1
gnu: r-elasticnet: Update to 1.3. 
* gnu/packages/cran.scm (r-elasticnet): Update to 1.3.
 2020-06-11 17:03:47 +02:00
Ricardo Wurmus
bb714ae79f
gnu: r-showtext: Update to 0.8-1. 
* gnu/packages/cran.scm (r-showtext): Update to 0.8-1.
 2020-06-11 17:03:47 +02:00
Ricardo Wurmus
8957a336f7
gnu: r-showtextdb: Update to 3.0. 
* gnu/packages/cran.scm (r-showtextdb): Update to 3.0.
 2020-06-11 17:03:47 +02:00
Ricardo Wurmus
b99ed8e6e5
gnu: r-abcrlda: Update to 1.0.3. 
* gnu/packages/cran.scm (r-abcrlda): Update to 1.0.3.
 2020-06-11 17:03:47 +02:00
Ricardo Wurmus
7262c1ff18
gnu: r-rgdal: Update to 1.5-10. 
* gnu/packages/cran.scm (r-rgdal): Update to 1.5-10.
[native-inputs]: Add r-knitr.
 2020-06-11 17:03:47 +02:00
Ricardo Wurmus
dfd0b55f9e
gnu: r-parameters: Update to 0.8.0. 
* gnu/packages/cran.scm (r-parameters): Update to 0.8.0.
 2020-06-11 17:03:47 +02:00