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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
67a289e5bd
gnu: Add r-dot.
...
* gnu/packages/cran.scm (r-dot): New variable.
2020-06-13 01:19:39 +02:00
06ceac32e6
gnu: Add r-v8.
...
* gnu/packages/cran.scm (r-v8): New variable.
2020-06-13 01:19:39 +02:00
e6aacef67e
gnu: Add r-scatterpie.
...
* gnu/packages/cran.scm (r-scatterpie): New variable.
2020-06-13 01:19:39 +02:00
45f54b418b
gnu: Add r-gprofiler2.
...
* gnu/packages/cran.scm (r-gprofiler2): New variable.
2020-06-13 01:19:39 +02:00
f9311eaa7c
gnu: node: Build shared library.
...
* gnu/packages/node.scm (node)[arguments]: Build shared library.
2020-06-13 01:19:39 +02:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
53bf76c574
gnu: r-systemfonts: Update to 0.2.3.
...
* gnu/packages/cran.scm (r-systemfonts): Update to 0.2.3.
2020-06-11 17:03:47 +02:00
897ed4a76f
gnu: r-rhpcblasctl: Update to 0.20-137.
...
* gnu/packages/cran.scm (r-rhpcblasctl): Update to 0.20-137.
2020-06-11 17:03:47 +02:00
4c4c34a154
gnu: r-ggraph: Update to 2.0.3.
...
* gnu/packages/cran.scm (r-ggraph): Update to 2.0.3.
2020-06-11 17:03:47 +02:00
ed7fa0af07
gnu: r-europepmc: Update to 0.4.
...
* gnu/packages/cran.scm (r-europepmc): Update to 0.4.
[propagated-inputs]: Add r-rlang, r-tibble, and r-tidyr.
[native-inputs]: Add r-knitr.
2020-06-11 17:03:47 +02:00
93043ba337
gnu: r-msigdbr: Update to 7.1.1.
...
* gnu/packages/cran.scm (r-msigdbr): Update to 7.1.1.
[native-inputs]: Add r-knitr.
2020-06-11 17:03:47 +02:00
a50246f455
gnu: r-bookdown: Update to 0.19.
...
* gnu/packages/cran.scm (r-bookdown): Update to 0.19.
2020-06-11 17:03:46 +02:00
5547b4360f
gnu: r-rms: Update to 6.0-0.
...
* gnu/packages/cran.scm (r-rms): Update to 6.0-0.
[propagated-inputs]: Add r-cluster, r-digest, and r-mass.
2020-06-11 17:03:46 +02:00
d263b2d67b
gnu: r-polspline: Update to 1.1.19.
...
* gnu/packages/cran.scm (r-polspline): Update to 1.1.19.
2020-06-11 17:03:46 +02:00
5130c454dd
gnu: r-lemon: Update to 0.4.5.
...
* gnu/packages/cran.scm (r-lemon): Update to 0.4.5.
[native-inputs]: Add r-knitr.
2020-06-11 17:03:46 +02:00
2de55fbab9
gnu: r-picante: Update to 1.8.2.
...
* gnu/packages/cran.scm (r-picante): Update to 1.8.2.
2020-06-11 17:03:46 +02:00
e27fc23b07
gnu: r-lavaan: Update to 0.6-6.
...
* gnu/packages/cran.scm (r-lavaan): Update to 0.6-6.
2020-06-11 17:03:46 +02:00
52d7306100
gnu: r-cmprsk: Update to 2.2-10.
...
* gnu/packages/cran.scm (r-cmprsk): Update to 2.2-10.
2020-06-11 17:03:46 +02:00
4c96ee1c40
gnu: r-gmp: Update to 0.6-0.
...
* gnu/packages/cran.scm (r-gmp): Update to 0.6-0.
2020-06-11 17:03:46 +02:00
d6df7299d3
gnu: r-bigrquery: Update to 1.3.1.
...
* gnu/packages/cran.scm (r-bigrquery): Update to 1.3.1.
2020-06-11 17:03:46 +02:00
f71791c501
gnu: r-iso: Update to 0.0-18.1.
...
* gnu/packages/cran.scm (r-iso): Update to 0.0-18.1.
2020-06-11 17:03:46 +02:00
fc1db3fcf5
gnu: r-sjplot: Update to 2.8.4.
...
* gnu/packages/cran.scm (r-sjplot): Update to 2.8.4.
2020-06-11 17:03:46 +02:00
4a0fbb7799
gnu: r-effectsize: Update to 0.3.1.
...
* gnu/packages/cran.scm (r-effectsize): Update to 0.3.1.
2020-06-11 17:03:46 +02:00
9908ec56cd
gnu: r-bayesplot: Update to 1.7.2.
...
* gnu/packages/cran.scm (r-bayesplot): Update to 1.7.2.
[native-inputs]: Add r-knitr.
2020-06-11 17:03:46 +02:00
a4a34d3ea8
gnu: r-emmeans: Update to 1.4.7.
...
* gnu/packages/cran.scm (r-emmeans): Update to 1.4.7.
2020-06-11 17:03:45 +02:00
0220c89e96
gnu: r-mosaicdata: Update to 0.18.0.
...
* gnu/packages/cran.scm (r-mosaicdata): Update to 0.18.0.
2020-06-11 17:03:45 +02:00
4223df8af1
gnu: r-doby: Update to 4.6.6.
...
* gnu/packages/cran.scm (r-doby): Update to 4.6.6.
[propagated-inputs]: Remove r-dplyr and r-plyr.
[native-inputs]: Add r-knitr.
2020-06-11 17:03:45 +02:00
Ricardo Wurmus
Ludovic Courtès
Katherine Cox-Buday
Ryan Desfosses
Efraim Flashner
Mathieu Othacehe
Pierre Neidhardt
Ekaitz Zarraga
Jakub Kądziołka
Mark H Weaver