27abca93b1
gnu: r-diffbind: Update to 3.2.1.
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* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.2.1.
2021-06-05 09:12:45 +02:00
737a228702
gnu: r-greylistchip: Update to 1.24.0.
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* gnu/packages/bioconductor.scm (r-greylistchip): Update to 1.24.0.
2021-06-05 09:12:45 +02:00
941a868515
gnu: r-apeglm: Update to 1.14.0.
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* gnu/packages/bioconductor.scm (r-apeglm): Update to 1.14.0.
2021-06-05 09:12:45 +02:00
371149da6f
gnu: r-qvalue: Update to 2.24.0.
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* gnu/packages/bioconductor.scm (r-qvalue): Update to 2.24.0.
2021-06-05 09:12:45 +02:00
359c350c7d
gnu: r-oligo: Update to 1.56.0.
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* gnu/packages/bioconductor.scm (r-oligo): Update to 1.56.0.
2021-06-05 09:12:45 +02:00
2c9c656f47
gnu: r-oligoclasses: Update to 1.54.0.
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* gnu/packages/bioconductor.scm (r-oligoclasses): Update to 1.54.0.
2021-06-05 09:12:45 +02:00
c68607725b
gnu: r-geneplotter: Update to 1.70.0.
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* gnu/packages/bioconductor.scm (r-geneplotter): Update to 1.70.0.
2021-06-05 09:12:45 +02:00
473371dfc1
gnu: r-zlibbioc: Update to 1.38.0.
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* gnu/packages/bioconductor.scm (r-zlibbioc): Update to 1.38.0.
2021-06-05 09:12:45 +02:00
092d2a8d85
gnu: r-xvector: Update to 0.32.0.
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* gnu/packages/bioconductor.scm (r-xvector): Update to 0.32.0.
2021-06-05 09:12:45 +02:00
e4a34df239
gnu: r-vsn: Update to 3.60.0.
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* gnu/packages/bioconductor.scm (r-vsn): Update to 3.60.0.
2021-06-05 09:12:45 +02:00
c73b9d6c66
gnu: r-variantannotation: Update to 1.38.0.
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* gnu/packages/bioconductor.scm (r-variantannotation): Update to 1.38.0.
2021-06-05 09:12:45 +02:00
2817a8f292
gnu: r-tximport: Update to 1.20.0.
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* gnu/packages/bioconductor.scm (r-tximport): Update to 1.20.0.
2021-06-05 09:12:45 +02:00
ad6ba3de65
gnu: r-topgo: Update to 2.44.0.
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* gnu/packages/bioconductor.scm (r-topgo): Update to 2.44.0.
2021-06-05 09:12:45 +02:00
7728c5909f
gnu: r-systempiper: Update to 1.26.2.
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* gnu/packages/bioconductor.scm (r-systempiper): Update to 1.26.2.
[propagated-inputs]: Add r-testthat.
2021-06-05 09:12:45 +02:00
81c55df9a8
gnu: r-sva: Update to 3.40.0.
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* gnu/packages/bioconductor.scm (r-sva): Update to 3.40.0.
2021-06-05 09:12:45 +02:00
6eaa9221d9
gnu: r-summarizedexperiment: Update to 1.22.0.
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* gnu/packages/bioconductor.scm (r-summarizedexperiment): Update to 1.22.0.
2021-06-05 09:12:44 +02:00
8c0f2d9e0a
gnu: r-structuralvariantannotation: Update to 1.8.0.
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* gnu/packages/bioconductor.scm (r-structuralvariantannotation): Update to 1.8.0.
[propagated-inputs]: Add r-rlang.
[native-inputs]: Add r-knitr.
2021-06-05 09:12:44 +02:00
8e0dac09c4
gnu: r-slingshot: Update to 2.0.0.
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* gnu/packages/bioconductor.scm (r-slingshot): Update to 2.0.0.
[propagated-inputs]: Remove r-ape; add r-s4vectors and r-trajectoryutils.
2021-06-05 09:12:44 +02:00
15f371cc89
gnu: r-shortread: Update to 1.50.0.
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* gnu/packages/bioconductor.scm (r-shortread): Update to 1.50.0.
2021-06-05 09:12:44 +02:00
76edc5ae98
gnu: r-seqpattern: Update to 1.24.0.
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* gnu/packages/bioconductor.scm (r-seqpattern): Update to 1.24.0.
2021-06-05 09:12:44 +02:00
58ae27d46c
gnu: r-seqlogo: Update to 1.58.0.
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* gnu/packages/bioconductor.scm (r-seqlogo): Update to 1.58.0.
2021-06-05 09:12:44 +02:00
5ce21e7153
gnu: r-rtracklayer: Update to 1.52.0.
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* gnu/packages/bioconductor.scm (r-rtracklayer): Update to 1.52.0.
[propagated-inputs]: Add r-biocio and r-restfulr.
2021-06-05 09:12:44 +02:00
e22d743aa6
gnu: r-rsamtools: Update to 2.8.0.
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* gnu/packages/bioconductor.scm (r-rsamtools): Update to 2.8.0.
2021-06-05 09:12:44 +02:00
f2f4ca7456
gnu: r-rhdf5filters: Update to 1.4.0.
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* gnu/packages/bioconductor.scm (r-rhdf5filters): Update to 1.4.0.
2021-06-05 09:12:44 +02:00
51bee5c40f
gnu: r-reportingtools: Update to 2.32.0.
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* gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.32.0.
2021-06-05 09:12:44 +02:00
2da4ee4c77
gnu: r-regioner: Update to 1.24.0.
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* gnu/packages/bioconductor.scm (r-regioner): Update to 1.24.0.
2021-06-05 09:12:44 +02:00
38fa99c1d0
gnu: r-rcas: Update to 1.18.0.
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* gnu/packages/bioconductor.scm (r-rcas): Update to 1.18.0.
[propagated-inputs]: Add r-knitr.
2021-06-05 09:12:44 +02:00
7c45bc9391
gnu: r-rbgl: Update to 1.68.0.
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* gnu/packages/bioconductor.scm (r-rbgl): Update to 1.68.0.
2021-06-05 09:12:44 +02:00
dc67525ae6
gnu: r-protgenerics: Update to 1.24.0.
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* gnu/packages/bioconductor.scm (r-protgenerics): Update to 1.24.0.
2021-06-05 09:12:44 +02:00
0ec6177cc1
gnu: r-pcamethods: Update to 1.84.0.
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* gnu/packages/bioconductor.scm (r-pcamethods): Update to 1.84.0.
2021-06-05 09:12:44 +02:00
5d37cee6c1
gnu: r-organismdbi: Update to 1.34.0.
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* gnu/packages/bioconductor.scm (r-organismdbi): Update to 1.34.0.
2021-06-05 09:12:44 +02:00
00b2174930
gnu: r-mzid: Update to 1.30.0.
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* gnu/packages/bioconductor.scm (r-mzid): Update to 1.30.0.
2021-06-05 09:12:44 +02:00
d647eb090b
gnu: r-msnbase: Update to 2.18.0.
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* gnu/packages/bioconductor.scm (r-msnbase): Update to 2.18.0.
[propagated-inputs]: Remove r-preprocesscore; add r-mscoreutils.
2021-06-05 09:12:43 +02:00
c966cef2b4
gnu: r-mutationalpatterns: Update to 3.2.0.
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* gnu/packages/bioconductor.scm (r-mutationalpatterns): Update to 3.2.0.
2021-06-05 09:12:43 +02:00
0b3fd7e89a
gnu: r-methylkit: Update to 1.18.0.
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* gnu/packages/bioconductor.scm (r-methylkit): Update to 1.18.0.
2021-06-05 09:12:43 +02:00
595b75e05c
gnu: r-limma: Update to 3.48.0.
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* gnu/packages/bioconductor.scm (r-limma): Update to 3.48.0.
2021-06-05 09:12:43 +02:00
60b598ee16
gnu: r-keggrest: Update to 1.32.0.
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* gnu/packages/bioconductor.scm (r-keggrest): Update to 1.32.0.
2021-06-05 09:12:43 +02:00
2cbb8e19af
gnu: r-interactivedisplaybase: Update to 1.30.0.
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* gnu/packages/bioconductor.scm (r-interactivedisplaybase): Update to 1.30.0.
2021-06-05 09:12:43 +02:00
94b4e64fd0
gnu: r-impute: Update to 1.66.0.
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* gnu/packages/bioconductor.scm (r-impute): Update to 1.66.0.
2021-06-05 09:12:43 +02:00
76fc8a53b2
gnu: r-rhtslib: Update to 1.24.0.
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* gnu/packages/bioconductor.scm (r-rhtslib): Update to 1.24.0.
2021-06-05 09:12:43 +02:00
78eb1fdf3e
gnu: r-hpar: Update to 1.34.0.
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* gnu/packages/bioconductor.scm (r-hpar): Update to 1.34.0.
2021-06-05 09:12:43 +02:00
330a7fe3b1
gnu: r-gseabase: Update to 1.54.0.
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* gnu/packages/bioconductor.scm (r-gseabase): Update to 1.54.0.
2021-06-05 09:12:43 +02:00
214e784b57
gnu: r-gostats: Update to 2.58.0.
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* gnu/packages/bioconductor.scm (r-gostats): Update to 2.58.0.
2021-06-05 09:12:43 +02:00
1b44202e20
gnu: r-genomicranges: Update to 1.44.0.
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* gnu/packages/bioconductor.scm (r-genomicranges): Update to 1.44.0.
2021-06-05 09:12:43 +02:00
d491b7eb1a
gnu: r-genomicfiles: Update to 1.28.0.
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* gnu/packages/bioconductor.scm (r-genomicfiles): Update to 1.28.0.
2021-06-05 09:12:43 +02:00
62889b9915
gnu: r-genomicfeatures: Update to 1.44.0.
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* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.44.0.
[propagated-inputs]: Add r-biocio.
2021-06-05 09:12:43 +02:00
570e80d62f
gnu: r-genomicalignments: Update to 1.28.0.
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* gnu/packages/bioconductor.scm (r-genomicalignments): Update to 1.28.0.
2021-06-05 09:12:43 +02:00
f88ab81fc7
gnu: r-genomeinfodb: Update to 1.28.0.
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* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.28.0.
2021-06-05 09:12:43 +02:00
ef7bbc40de
gnu: r-genomation: Update to 1.24.0.
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* gnu/packages/bioconductor.scm (r-genomation): Update to 1.24.0.
[propagated-inputs]: Remove r-runit.
2021-06-05 09:12:43 +02:00
3c024e9e96
gnu: r-geneoverlap: Update to 1.28.0.
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* gnu/packages/bioconductor.scm (r-geneoverlap): Update to 1.28.0.
2021-06-05 09:12:42 +02:00
389ce4e42b
gnu: r-genefilter: Update to 1.74.0.
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* gnu/packages/bioconductor.scm (r-genefilter): Update to 1.74.0.
2021-06-05 09:12:42 +02:00
f22f4caa69
gnu: r-gage: Update to 2.42.0.
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* gnu/packages/bioconductor.scm (r-gage): Update to 2.42.0.
2021-06-05 09:12:42 +02:00
ff59b34dc3
gnu: r-fastseg: Update to 1.38.0.
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* gnu/packages/bioconductor.scm (r-fastseg): Update to 1.38.0.
2021-06-05 09:12:42 +02:00
6abbb53c3e
gnu: r-ensembldb: Update to 2.16.0.
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* gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.16.0.
2021-06-05 09:12:42 +02:00
bdc1b908d3
gnu: r-edger: Update to 3.34.0.
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* gnu/packages/bioconductor.scm (r-edger): Update to 3.34.0.
2021-06-05 09:12:42 +02:00
f998c95d60
gnu: r-edaseq: Update to 2.26.0.
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* gnu/packages/bioconductor.scm (r-edaseq): Update to 2.26.0.
2021-06-05 09:12:42 +02:00
30ce1f9b66
gnu: r-dirichletmultinomial: Update to 1.34.0.
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* gnu/packages/bioconductor.scm (r-dirichletmultinomial): Update to 1.34.0.
2021-06-05 09:12:42 +02:00
e9445cdd78
gnu: r-dexseq: Update to 1.38.0.
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* gnu/packages/bioconductor.scm (r-dexseq): Update to 1.38.0.
2021-06-05 09:12:42 +02:00
45225c60cc
gnu: r-deseq2: Update to 1.32.0.
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* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.32.0.
2021-06-05 09:12:42 +02:00
2835e7c0be
gnu: r-copywriter: Update to 2.24.0.
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* gnu/packages/bioconductor.scm (r-copywriter): Update to 2.24.0.
2021-06-05 09:12:42 +02:00
a8cfce4852
gnu: r-complexheatmap: Update to 2.8.0.
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* gnu/packages/bioconductor.scm (r-complexheatmap): Update to 2.8.0.
[propagated-inputs]: Remove r-s4vectors; add r-doparallel and r-foreach.
2021-06-05 09:12:42 +02:00
d296ac9cde
gnu: r-chipseq: Update to 1.42.0.
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* gnu/packages/bioconductor.scm (r-chipseq): Update to 1.42.0.
2021-06-05 09:12:42 +02:00
ca10bafc65
gnu: r-chipseeker: Update to 1.28.3.
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* gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.28.3.
[inputs]: Remove r-knitr.
[native-inputs]: Add r-knitr.
2021-06-05 09:12:42 +02:00
336107c13d
gnu: r-category: Update to 2.58.0.
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* gnu/packages/bioconductor.scm (r-category): Update to 2.58.0.
2021-06-05 09:12:42 +02:00
e039d07bf8
gnu: r-bsgenome: Update to 1.60.0.
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* gnu/packages/bioconductor.scm (r-bsgenome): Update to 1.60.0.
2021-06-05 09:12:42 +02:00
98f3c55999
gnu: r-biovizbase: Update to 1.40.0.
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* gnu/packages/bioconductor.scm (r-biovizbase): Update to 1.40.0.
2021-06-05 09:12:42 +02:00
16fe6abd27
gnu: r-biostrings: Update to 2.60.0.
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* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.60.0.
[propagated-inputs]: Add r-genomeinfodb.
2021-06-05 09:12:42 +02:00
3eedef80e4
gnu: r-biocparallel: Update to 1.26.0.
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* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.26.0.
2021-06-05 09:12:41 +02:00
f9ae0a4102
gnu: r-biomart: Update to 2.48.0.
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* gnu/packages/bioconductor.scm (r-biomart): Update to 2.48.0.
[propagated-inputs]: Remove r-openssl and r-xml2; add r-digest.
2021-06-05 09:12:41 +02:00
8be5d4f6fc
gnu: r-biobase: Update to 2.52.0.
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* gnu/packages/bioconductor.scm (r-biobase): Update to 2.52.0.
2021-06-05 09:12:41 +02:00
baaed6fd68
gnu: r-bamsignals: Update to 1.24.0.
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* gnu/packages/bioconductor.scm (r-bamsignals): Update to 1.24.0.
2021-06-05 09:12:41 +02:00
3e290768c6
gnu: r-aroma-light: Update to 3.22.0.
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* gnu/packages/bioconductor.scm (r-aroma-light): Update to 3.22.0.
2021-06-05 09:12:41 +02:00
2071ed58d5
gnu: r-annotationhub: Update to 3.0.0.
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* gnu/packages/bioconductor.scm (r-annotationhub): Update to 3.0.0.
2021-06-05 09:12:41 +02:00
4d13cf066d
gnu: r-annotationforge: Update to 1.34.0.
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* gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.34.0.
2021-06-05 09:12:41 +02:00
361f2f647a
gnu: r-annotationfilter: Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-annotationfilter): Update to 1.16.0.
2021-06-05 09:12:41 +02:00
c7811ed4bf
gnu: r-annotationdbi: Update to 1.54.0.
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* gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.54.0.
[propagated-inputs]: Add r-keggrest.
2021-06-05 09:12:41 +02:00
1bb87755b8
gnu: r-annotate: Update to 1.70.0.
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* gnu/packages/bioconductor.scm (r-annotate): Update to 1.70.0.
2021-06-05 09:12:41 +02:00
308067c09c
gnu: r-affxparser: Update to 1.64.0.
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* gnu/packages/bioconductor.scm (r-affxparser): Update to 1.64.0.
2021-06-05 09:12:41 +02:00
dfeb135ef0
gnu: r-affyio: Update to 1.62.0.
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* gnu/packages/bioconductor.scm (r-affyio): Update to 1.62.0.
2021-06-05 09:12:41 +02:00
a9083169c6
gnu: r-affycoretools: Update to 1.64.0.
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* gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.64.0.
2021-06-05 09:12:41 +02:00
3abb0b6523
gnu: r-affycontam: Update to 1.50.0.
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* gnu/packages/bioconductor.scm (r-affycontam): Update to 1.50.0.
2021-06-05 09:12:41 +02:00
bd17befeb1
gnu: r-affycompatible: Update to 1.52.0.
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* gnu/packages/bioconductor.scm (r-affycompatible): Update to 1.52.0.
2021-06-05 09:12:41 +02:00
b045bf2d6f
gnu: r-affycomp: Update to 1.68.0.
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* gnu/packages/bioconductor.scm (r-affycomp): Update to 1.68.0.
2021-06-05 09:12:41 +02:00
af04e2cc12
gnu: r-affy: Update to 1.70.0.
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* gnu/packages/bioconductor.scm (r-affy): Update to 1.70.0.
2021-06-05 09:12:41 +02:00
60b9546472
gnu: r-iranges: Update to 2.26.0.
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* gnu/packages/bioconductor.scm (r-iranges): Update to 2.26.0.
2021-06-05 09:12:41 +02:00
cfd4c05bd4
gnu: r-ideoviz: Update to 1.28.0.
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* gnu/packages/bioconductor.scm (r-ideoviz): Update to 1.28.0.
2021-06-05 09:12:40 +02:00
4075ac7287
gnu: r-bluster: Update to 1.2.1.
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* gnu/packages/bioconductor.scm (r-bluster): Update to 1.2.1.
[propagated-inputs]: Add r-cluster.
2021-06-05 09:12:40 +02:00
8eb0c715e3
gnu: r-delayedarray: Update to 0.18.0.
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* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.18.0.
2021-06-05 09:12:40 +02:00
f0f839c124
gnu: r-deepsnv: Update to 1.38.0.
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* gnu/packages/bioconductor.scm (r-deepsnv): Update to 1.38.0.
[inputs]: Remove zlib.
[native-inputs]: Add r-knitr.
2021-06-05 09:12:40 +02:00
dec096f827
gnu: r-decipher: Update to 2.20.0.
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* gnu/packages/bioconductor.scm (r-decipher): Update to 2.20.0.
[propagated-inputs]: Add r-dbi, r-iranges, r-s4vectors, and r-xvector.
2021-06-05 09:12:40 +02:00
116df58449
gnu: r-cummerbund: Update to 2.34.0.
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* gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.34.0.
2021-06-05 09:12:40 +02:00
e6c5d8ce2c
gnu: r-coverageview: Update to 1.30.0.
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* gnu/packages/bioconductor.scm (r-coverageview): Update to 1.30.0.
2021-06-05 09:12:40 +02:00
7bac473d06
gnu: r-biocgenerics: Update to 0.38.0.
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* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.38.0.
2021-06-05 09:12:40 +02:00
b05761a5a9
gnu: r-biocversion: Update to 3.13.1.
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* gnu/packages/bioconductor.scm (r-biocversion): Update to 3.13.1.
2021-06-05 09:12:40 +02:00
405b386656
gnu: r-aneufinder: Update to 1.20.0.
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* gnu/packages/bioconductor.scm (r-aneufinder): Update to 1.20.0.
2021-06-05 09:12:40 +02:00
75817956c1
gnu: r-hdf5array: Update to 1.20.0.
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* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.20.0.
[arguments]: Remove.
[propagated-inputs]: Add r-rhdf5filters.
2021-06-05 09:12:40 +02:00
bfa23ec526
gnu: r-cytoml: Update to 2.4.0.
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* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.4.0.
[arguments]: Remove.
2021-06-05 09:12:40 +02:00
764e2dba20
gnu: r-flowworkspace: Update to 4.4.0.
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* gnu/packages/bioconductor.scm (r-flowworkspace): Update to 4.4.0.
[arguments]: Remove.
[propagated-inputs]: Add r-delayedarray and r-s4vectors.
2021-06-05 09:12:40 +02:00
b9751b629c
gnu: r-ncdfflow: Update to 2.38.0.
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* gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.38.0.
[arguments]: Remove.
2021-06-05 09:12:40 +02:00
5c37a048bb
gnu: r-cytolib: Update to 2.4.0.
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* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.4.0.
[arguments]: Remove.
[native-inputs]: Remove pkg-config.
2021-06-05 09:12:40 +02:00
782d27f77d
gnu: r-rhdf5: Update to 2.36.0.
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* gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.36.0.
[arguments]: Remove.
2021-06-05 09:12:40 +02:00
87d06a725f
gnu: r-mzr: Update to 2.26.0.
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* gnu/packages/bioconductor.scm (r-mzr): Update to 2.26.0.
[arguments]: Remove obsolute substitution.
2021-06-05 09:12:40 +02:00
5d13aab6ca
gnu: r-msnid: Update to 1.26.0.
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* gnu/packages/bioconductor.scm (r-msnid): Update to 1.26.0.
[arguments]: Set HOME variable.
2021-06-05 09:12:40 +02:00
d0a7dc0cb6
gnu: r-bioccheck: Update to 1.28.0.
...
* gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.28.0.
[arguments]: Remove.
2021-06-05 09:12:39 +02:00
1b0338d76b
gnu: r-rhdf5lib: Update to 1.14.0.
...
* gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.14.0.
[source]: Update deletions.
[arguments]: Update substitutions.
[inputs]: Move zlib from here...
[propagated-inputs]: ...to here.
2021-06-05 09:12:39 +02:00
53ec97713a
gnu: Add r-metapod.
...
* gnu/packages/bioconductor.scm (r-metapod): New variable.
2021-06-05 09:12:39 +02:00
8caab75883
gnu: Add r-ggtree.
...
* gnu/packages/bioconductor.scm (r-ggtree): New variable.
2021-06-05 09:12:39 +02:00
ab4a91b252
gnu: Add r-treeio.
...
* gnu/packages/bioconductor.scm (r-treeio): New variable.
2021-06-05 09:12:39 +02:00
fd4fa40ac4
gnu: Add r-scaledmatrix.
...
* gnu/packages/bioconductor.scm (r-scaledmatrix): New variable.
2021-06-05 09:12:39 +02:00
efefb2be3a
gnu: Add r-trajectoryutils.
...
* gnu/packages/bioconductor.scm (r-trajectoryutils): New variable.
2021-06-05 09:12:39 +02:00
ce99b4da63
gnu: Add r-restfulr.
...
* gnu/packages/bioconductor.scm (r-restfulr): New variable.
2021-06-05 09:12:39 +02:00
ab66c9a2cd
gnu: Add r-arrow.
...
* gnu/packages/cran.scm (r-arrow): New variable.
2021-06-05 09:12:39 +02:00
b71f21339f
gnu: Add r-ggpointdensity.
...
* gnu/packages/cran.scm (r-ggpointdensity): New variable.
2021-06-05 09:12:39 +02:00
41ea9bed97
gnu: Add r-ggnewscale.
...
* gnu/packages/cran.scm (r-ggnewscale): New variable.
2021-06-05 09:12:39 +02:00
d5c08f11e1
gnu: Add r-aplot.
...
* gnu/packages/cran.scm (r-aplot): New variable.
2021-06-05 09:12:39 +02:00
f98837a6ba
gnu: pigx-rnaseq: Update to 0.0.13.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.13.
[arguments]: Remove obsolete substitutions.
[inputs]: Remove fastqc and trim-galore; add hisat2 and fastp.
2021-06-05 09:12:39 +02:00
7382aa00b8
gnu: python-scanpy: Update to 1.7.2.
...
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
2021-06-04 23:51:35 +02:00
e639da604f
gnu: python-anndata: Update to 0.7.6.
...
* gnu/packages/python-xyz.scm (python-anndata): Update to 0.7.6.
2021-06-04 23:51:24 +02:00
29745d23b8
gnu: Use define-public in (gnu packages xiph).
...
* gnu/pakages/xiph.scm: Replace all manual package #:exports with
define-public.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-06-04 15:08:35 +02:00
bb934ab79d
gnu: python-pydantic: Update to 1.8.2.
...
* gnu/packages/python-xyz.scm (python-pydantic): Update to 1.8.2.
[arguments]: Disable some new tests.
[native-inputs]: Add PYTHON-PYTEST-MOCK.
[propagated-inputs]: Add PYTHON-TYPING-EXTENSIONS.
2021-06-04 14:57:39 +02:00
1ea00cceef
gnu: wfview: Update to 1.0.
...
* gnu/packages/radio.scm (wfview): Update to 1.0.
2021-06-04 13:50:52 +02:00
f50a88c1fa
gnu: smalltalk: Find glibc even when cross-compiling.
...
glibc is named "cross-libc" instead of "libc" when cross-compiling. Smalltalk
still fails to cross-compile though.
* gnu/packages/smalltalk.scm
(smalltalk)[arguments]{phases}<#:fix-libc>: Also search for
"cross-libc" instead of only "libc" in 'inputs'.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-06-04 13:40:02 +02:00
961a8f1302
gnu: smalltalk: Move 'zip' from 'inputs' to 'native-inputs'.
...
The 'zip' package is not in the references of 'smalltalk'.
As such, it probably should be a native input, not a regular
input. This can be confirmed by trying to cross-compile
the 'smalltalk' package, without this commit. The configure
script will ask to install InfoZIP.
* gnu/packages/smalltalk.scm
(smalltalk)[inputs]{zip}: Move to ...
(smalltalk)[native-inputs]{zip} ... here.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-06-04 13:34:58 +02:00
4a600ada5a
gnu: ding: Use 'inputs' in build phases instead of '%build-inputs'.
...
In build phases, the former is preferred.
* gnu/packages/dictionaries.scm
(ding)[arguments]<#:phases>{install}: Use 'inputs' argument instead
of '%build-inputs'.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-06-04 13:34:54 +02:00
156b8f9cd2
gnu: qemacs: Use 'native-inputs' instead of '%build-inputs'.
...
In build phases, the former (or 'inputs', as appropriate) is preferred.
* gnu/packages/text-editors.scm
(qemacs)[arguments]<#:phases>{install-extra-documentation}: Use
'native-inputs' argument instead of '%build-inputs'.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-06-04 13:34:49 +02:00
09be86744f
gnu: neovim: Use 'inputs' in phases instead of '%build-inputs'.
...
In build phases, the former is preferred.
* gnu/packages/vim.scm
(neovim)[arguments]<#:phases>{set-lua-path}: Use 'inputs'
argument instead of '%build-inputs'.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-06-04 13:34:46 +02:00
f5f78d0d02
gnu: smalltalk: Use 'inputs' in phases instead of '%build-inputs'.
...
In build phases, the former is preferred.
* gnu/packages/smalltalk.scm
(smalltalk)[arguments]<#:phases>{fix-libc}: Use 'inputs'
argument instead of '%build-inputs'.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-06-04 13:34:42 +02:00
8190f5bb97
gnu: ci: Use 'inputs' in build phases instead of '%build-inputs'.
...
In build phases, the former is preferred.
* gnu/packages/ci.scm
(cuirass)[arguments]<#:phases>{wrap-program}: Use 'inputs'
argument instead of '%build-inputs'.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-06-04 13:34:37 +02:00
d06ae05808
gnu: Add pigx-sars-cov2-ww.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable.
2021-06-04 12:57:08 +02:00
4f773bc22d
gnu: sbcl-nibbles: Update to 0.14-2.dad2524.
...
* gnu/packages/lisp-xyz.scm (sbcl-nibbles): Update to 0.14-2.dad2524.
2021-06-04 10:59:50 +02:00
f1bfd9f194
gnu: remmina: Update to 1.4.18.
...
* gnu/packages/vnc.scm (remmina)[version]: Update to 1.4.18.
2021-06-03 23:46:04 -04:00
6148172c3e
gnu: gajim-omemo: Update to 2.7.14.
...
* gnu/packages/messaging.scm (gajim-omemo)[version]: Update to 2.7.14.
2021-06-03 23:35:12 -04:00
6b6b87f1c3
gnu: linux-libre 4.4: Update to 4.4.271.
...
* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.271.
(linux-libre-4.4-pristine-source): Update hash.
2021-06-03 22:41:01 -04:00
6fa18e48a7
gnu: linux-libre 4.9: Update to 4.9.271.
...
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.271.
(linux-libre-4.9-pristine-source): Update hash.
2021-06-03 22:41:01 -04:00
ba85dff344
gnu: linux-libre 4.14: Update to 4.14.235.
...
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.235.
(linux-libre-4.14-pristine-source): Update hash.
2021-06-03 22:41:01 -04:00
37ec3f3bec
gnu: linux-libre 4.19: Update to 4.19.193.
...
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.193.
(linux-libre-4.19-pristine-source): Update hash.
2021-06-03 22:41:01 -04:00
a75aa36e0a
gnu: linux-libre 5.4: Update to 5.4.124.
...
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.124.
(linux-libre-5.4-pristine-source): Update hash.
2021-06-03 22:41:01 -04:00
f23d5340c2
gnu: linux-libre 5.10: Update to 5.10.42.
...
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.42.
(linux-libre-5.10-pristine-source): Update hash.
(deblob-scripts-5.10): Update hash.
2021-06-03 22:41:00 -04:00
41d73dfba1
gnu: linux-libre: Update to 5.12.9.
...
* gnu/packages/linux.scm (linux-libre-5.12-version): Update to 5.12.9.
(linux-libre-5.12-pristine-source): Update hash.
(deblob-scripts-5.12): Update hash.
2021-06-03 22:40:51 -04:00
bb414c9352
gnu: komikku: Update to 0.29.0.
...
* gnu/packages/gnome.scm (komikku): Update to 0.29.0.
2021-06-03 21:46:48 +02:00
97b4a7e37c
gnu: emacs-calibredb: Update to 2.10.0.
...
* gnu/packages/emacs-xyz.scm (emacs-calibredb): Update to 2.10.0.
2021-06-03 21:13:23 +02:00
9703a51048
gnu: Add rfcat.
...
* gnu/packages/radio.scm (rfcat): New variable.
2021-06-03 19:01:52 +02:00
38adfcd6f5
gnu: rasdaemon: Update to 0.6.7.
...
* gnu/packages/linux.scm (rasdaemon): Update to 0.6.7.
[arguments]: Add a "--with-sysconfdefdir" configure flag.
2021-06-03 18:23:39 +02:00
0e8d650c4f
gnu: php: Update to 7.4.20.
...
* gnu/packages/php.scm (php): Update to 7.4.20.
2021-06-03 18:23:39 +02:00
240cd1a099
gnu: fltk: Update to 1.3.6.
...
* gnu/packages/fltk.scm (fltk): Update to 1.3.6.
2021-06-03 18:23:39 +02:00
0dd2670ad5
gnu: amule: Use HTTPS home page.
...
* gnu/packages/networking.scm (amule)[home-page]: Use HTTPS.
2021-06-03 18:23:39 +02:00
e348436589
gnu: amule: Update to 2.3.3.
...
* gnu/packages/networking.scm (amule): Update to 2.3.3.
[source]: Remove patch.
* gnu/packages/patches/amule-crypto-6.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2021-06-03 18:23:39 +02:00
606b200fe7
gnu: mtools: Update to 4.0.29.
...
* gnu/packages/mtools.scm (mtools): Update to 4.0.29.
2021-06-03 18:23:38 +02:00
cf6be24529
gnu: emacs-epkg: Update to 3.3.0.
...
* gnu/packages/emacs-xyz.scm (emacs-epkg): Update to 3.3.0.
2021-06-03 14:49:15 +02:00
7668c2cbe8
gnu: emacs-closql: Update to 1.0.5.
...
* gnu/packages/emacs-xyz.scm (emacs-closql): Update to 1.0.5.
2021-06-03 14:45:13 +02:00
cc0f152ffd
gnu: emacs-ebdb: Update to 0.6.23.
...
* gnu/packages/emacs-xyz.scm (emacs-ebdb): Update to 0.6.23.
2021-06-03 14:29:08 +02:00
08f1400bec
gnu: monolith: Update to 2.5.0.
...
* gnu/packages/web.scm (monolith): Update to 2.5.0.
2021-06-03 14:24:35 +02:00
b7c5f27579
gnu: rust-regex-1: Update to 1.5.4.
...
* gnu/packages/crates-io.scm (rust-regex-1): Update to 1.5.4.
2021-06-03 14:24:35 +02:00
71beab1c1a
gnu: rust-aho-corasick-0.7: Update to 0.7.18.
...
* gnu/packages/crates-io.scm (rust-aho-corasick-0.7): Update to 0.7.18.
2021-06-03 14:24:34 +02:00
a04dd9b01b
gnu: rust-memchr-2: Update to 2.4.0.
...
* gnu/packages/crates-io.scm (rust-memchr-2): Update to 2.4.0.
2021-06-03 14:24:34 +02:00
2282d21fd6
gnu: rust-regex-syntax-0.6: Update to 0.6.25.
...
* gnu/packages/crates-io.scm (rust-regex-syntax-0.6): Update to 0.6.25.
2021-06-03 14:24:34 +02:00
ef0daad211
gnu: rust-reqwest-0.11: Fix build.
...
* gnu/packages/crates-io.scm (rust-reqwest-0.11)[arguments]: Add missing Cargo
development inputs.
2021-06-03 14:24:33 +02:00
c0796540de
gnu: rust-reqwest-0.11: Update to 0.11.3.
...
* gnu/packages/crates-io.scm (rust-reqwest-0.11): Update to 0.11.3.
2021-06-03 14:24:33 +02:00
c695df8c5f
gnu: rust-sha2-0.9: Update to 0.9.5.
...
* gnu/packages/crates-io.scm (rust-sha2-0.9): Update to 0.9.5.
2021-06-03 14:24:33 +02:00
adc7fc093e
gnu: Add rust-cpufeatures-0.1.
...
* gnu/packages/crates-io.scm (rust-cpufeatures-0.1): New variable.
2021-06-03 14:24:32 +02:00
558db7b6e5
gnu: Add rust-sha2-asm-0.6.
...
* gnu/packages/crates-io.scm (rust-sha2-asm-0.6): New variable.
(rust-sha2-asm-0.5): Inherit from above.
2021-06-03 14:24:32 +02:00
11d84f4b7f
gnu: rust-url-2: Update to 2.2.2.
...
* gnu/packages/crates-io.scm (rust-url-2): Update to 2.2.2.
2021-06-03 14:24:32 +02:00
e4283e03a3
gnu: rust-assert-cmd-1: Update to 1.0.4.
...
* gnu/packages/crates-io.scm (rust-assert-cmd-1): Update to 1.0.4.
2021-06-03 14:24:31 +02:00
fe509e017f
machine: ssh: Respect calling convention for monadic procedures.
...
Fixes a regression introduced in
2885c3568e
2021-06-03 13:04:20 +02:00
0928e55266
gnu: Add fit-sne.
...
* gnu/packages/bioinformatics.scm (fit-sne): New variable.
2021-06-03 12:22:29 +02:00
13b737f132
gnu: r-with-tests: Use patched texlive-amsfonts.
...
See commit 75af43162e
2021-06-03 11:18:03 +02:00
f6a979860c
gnu: openshot: Use free font.
...
* gnu/packages/video.scm (openshot)[inputs]: Use font-dejavu.
[patch-font-location]: Adjust accordingly.
2021-06-03 08:49:18 +02:00
a923127d30
gnu: Remove font-ubuntu.
...
The Ubuntu Font License has not been approved by the FSF and is considered
non-free by Debian and Fedora, see <https://bugs.gnu.org/48802 >.
* gnu/packages/fonts.scm (font-ubuntu): Removed variable.
2021-06-03 08:29:04 +02:00
80a6de6b3a
gnu: Add legit.
...
* gnu/packages/lisp-xyz.scm (cl-legit, ecl-legit, sbcl-legit): New variables.
2021-06-03 08:23:28 +02:00
929b72dd58
gnu: Add simple-inferiors.
...
* gnu/packages/lisp-xyz.scm (cl-simple-inferiors, ecl-simple-inferiors,
sbcl-simple-inferiors): New variables.
2021-06-03 08:23:28 +02:00
9e7d93f675
gnu: curl: Update to 7.77.0 [fixes CVE-2021-{22897,22898,22901}].
...
* gnu/packages/curl.scm (curl/fixed): Replace with ...
(curl-7.77.0): ... new variable.
(curl)[replacement]: Use curl-7.77.0.
2021-06-02 23:13:16 -04:00
6d71f6a73c
gnu: expat: Replace with 2.4.1 [fixes CVE-2013-0340].
...
* gnu/packages/xml.scm (expat-2.4.1): New variable.
(expat)[replacement]: New field.
Co-authored-by: Leo Famulari <leo@famulari.name>
2021-06-02 17:07:15 -04:00
f32e6e1e2c
gnu: Add emacs-org-pandoc-import.
...
* gnu/packages/emacs-xyz.scm (emacs-org-pandoc-import): New variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-06-02 21:51:06 +02:00
5be7870a8d
gnu: pioneer: Build with model files.
...
Fixes <https://bugs.gnu.org/48686 >.
* gnu/packages/games.scm (pioneer)[arguments]: Add make-flags for building
with model files.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-06-02 21:38:32 +02:00
b851f38a2f
gnu: r-robustbase: Update to 0.93-8.
...
* gnu/packages/statistics.scm (r-robustbase): Update to 0.93-8.
2021-06-02 17:27:10 +02:00
02efdd3abf
gnu: r-deoptimr: Update to 1.0-9.
...
* gnu/packages/statistics.scm (r-deoptimr): Update to 1.0-9.
2021-06-02 17:27:10 +02:00
08de5b0689
gnu: r-beeswarm: Update to 0.4.0.
...
* gnu/packages/statistics.scm (r-beeswarm): Update to 0.4.0.
2021-06-02 17:27:10 +02:00
c6be262b78
gnu: r-fastcluster: Update to 1.2.3.
...
* gnu/packages/statistics.scm (r-fastcluster): Update to 1.2.3.
2021-06-02 17:27:10 +02:00
350489b331
gnu: r-matrixstats: Update to 0.59.0.
...
* gnu/packages/statistics.scm (r-matrixstats): Update to 0.59.0.
2021-06-02 17:27:09 +02:00
3319e97c40
gnu: r-e1071: Update to 1.7-7.
...
* gnu/packages/statistics.scm (r-e1071): Update to 1.7-7.
2021-06-02 17:27:09 +02:00
a3268eb598
gnu: r-rcpparmadillo: Update to 0.10.5.0.0.
...
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.10.5.0.0.
2021-06-02 17:27:09 +02:00
a8313bfbae
gnu: r-rversions: Update to 2.1.1.
...
* gnu/packages/statistics.scm (r-rversions): Update to 2.1.1.
2021-06-02 17:27:09 +02:00
80f2d363b8
gnu: r-formatr: Update to 1.11.
...
* gnu/packages/statistics.scm (r-formatr): Update to 1.11.
2021-06-02 17:27:09 +02:00
61d7869e89
gnu: r-mgcv: Update to 1.8-36.
...
* gnu/packages/statistics.scm (r-mgcv): Update to 1.8-36.
2021-06-02 17:27:09 +02:00
fdc6bfa2aa
gnu: r-matrix: Update to 1.3-4.
...
* gnu/packages/statistics.scm (r-matrix): Update to 1.3-4.
2021-06-02 17:27:09 +02:00
72e8eabc3a
gnu: r-textshape: Update to 1.7.3.
...
* gnu/packages/cran.scm (r-textshape): Update to 1.7.3.
2021-06-02 17:27:09 +02:00
0af6a92695
gnu: r-calculus: Update to 0.3.1.
...
* gnu/packages/cran.scm (r-calculus): Update to 0.3.1.
2021-06-02 17:27:09 +02:00
9b9bb2b732
gnu: r-seurat: Update to 4.0.2.
...
* gnu/packages/cran.scm (r-seurat): Update to 4.0.2.
2021-06-02 17:27:09 +02:00
d9d8a1cdc0
gnu: r-parsnip: Update to 0.1.6.
...
* gnu/packages/cran.scm (r-parsnip): Update to 0.1.6.
[propagated-inputs]: Add r-lifecycle.
2021-06-02 17:27:09 +02:00
f6ae19fedc
gnu: r-clusterr: Update to 1.2.5.
...
* gnu/packages/cran.scm (r-clusterr): Update to 1.2.5.
2021-06-02 17:27:09 +02:00
17bd981986
gnu: r-rsconnect: Update to 0.8.18.
...
* gnu/packages/cran.scm (r-rsconnect): Update to 0.8.18.
2021-06-02 17:27:09 +02:00
318808dcdd
gnu: r-forecast: Update to 8.15.
...
* gnu/packages/cran.scm (r-forecast): Update to 8.15.
2021-06-02 17:27:09 +02:00
317267c460
gnu: r-archivist: Update to 2.3.6.
...
* gnu/packages/cran.scm (r-archivist): Update to 2.3.6.
2021-06-02 17:27:09 +02:00
b3aad04bed
gnu: r-biclust: Update to 2.0.3.
...
* gnu/packages/cran.scm (r-biclust): Update to 2.0.3.
2021-06-02 17:27:09 +02:00
83fa31438d
gnu: r-actuar: Update to 3.1-4.
...
* gnu/packages/cran.scm (r-actuar): Update to 3.1-4.
2021-06-02 17:27:08 +02:00
184b3c500c
gnu: r-gdina: Update to 2.8.7.
...
* gnu/packages/cran.scm (r-gdina): Update to 2.8.7.
2021-06-02 17:27:08 +02:00
47cdb9c9a8
gnu: r-parameters: Update to 0.14.0.
...
* gnu/packages/cran.scm (r-parameters): Update to 0.14.0.
2021-06-02 17:27:08 +02:00
8998ed1d8e
gnu: r-leiden: Update to 0.3.8.
...
* gnu/packages/cran.scm (r-leiden): Update to 0.3.8.
2021-06-02 17:27:08 +02:00
81bb987e7e
gnu: r-plot3d: Update to 1.4.
...
* gnu/packages/cran.scm (r-plot3d): Update to 1.4.
2021-06-02 17:27:08 +02:00
509eea0f5d
gnu: r-dalex: Update to 2.2.1.
...
* gnu/packages/cran.scm (r-dalex): Update to 2.2.1.
2021-06-02 17:27:08 +02:00
Ricardo Wurmus
Roel Janssen
Brendan Tildesley
Marius Bakke
Guillaume Le Vaillant
Maxime Devos
Raghav Gururajan
Leo Famulari
Leo Prikler
Nicolas Goaziou
Tobias Geerinckx-Rice
Ludovic Courtès
Lars-Dominik Braun
Pierre Neidhardt
Xinglu Chen
Diego Nicola Barbato