Ricardo Wurmus
7ca49ab57a
gnu: ribodiff: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
2018-11-07 19:48:21 +01:00
Ricardo Wurmus
239716fb0b
gnu: python-biom-format: Update to 2.1.7.
...
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.7.
[arguments]: Add phases "use-cython", "disable-broken-test", and
"make-files-writable".
[propagated-inputs]: Add python-flake8.
[native-inputs]: Add python-cython, python-pytest, and python-pytest-cov.
2018-11-07 19:47:07 +01:00
Ricardo Wurmus
007a81d5cf
gnu: python-biom-format: Fetch source from git.
...
* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Fetch from
git.
2018-11-07 19:10:36 +01:00
Ricardo Wurmus
383cb7b8e6
gnu: bioawk: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
2018-11-07 19:06:30 +01:00
Ricardo Wurmus
20ee3e8b76
gnu: bedtools-2.18: Fetch sources from stable URL.
...
* gnu/packages/bioinformatics.scm (bedtools-2.18)[source]: Use stable release
tarball instead of generated tag tarball.
2018-11-07 18:52:46 +01:00
Ricardo Wurmus
8e58319c45
gnu: bamtools: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (bamtools)[source]: Fetch from git.
2018-11-07 18:44:30 +01:00
Ricardo Wurmus
21335fdbec
gnu: ngless: Install links to required tools.
...
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools.
[inputs]: Add prodigal, bwa, samtools, and minimap2.
2018-11-07 17:19:53 +01:00
Ricardo Wurmus
fff67cc8a7
gnu: prodigal: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
2018-11-07 17:19:53 +01:00
Ludovic Courtès
08759829cf
gnu: cuirass: Update to 0b40dca.
...
* gnu/packages/ci.scm (cuirass): Update to 0b40dca.
2018-11-07 16:06:42 +01:00
Ricardo Wurmus
9255198423
gnu: r-mzr: Update to 2.16.0.
...
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.0.
[inputs]: Remove netcdf.
[propagated-inputs]: Add r-ncdf4.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
37200dbcc3
gnu: r-rhdf5lib: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.0.
[source]: Add snippet to remove bundled binaries.
[arguments]: Replace references to hdf5 with references to hdf5-1.10.
[native-inputs]: Likewise.
[propagated-inputs]: Replace hdf5 with hdf5-1.10.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
8e48d36f26
gnu: r-hdf5array: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
611a255d2b
gnu: r-rhdf5: Update to 2.26.0.
...
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
a1c2bf8e54
gnu: r-rcas: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.8.0.
[native-inputs]: Remove r-testthat and ghc-pandoc-citeproc.
[propagated-inputs]: Add r-annotationdbi, r-genomeinfodb, and r-genomicranges;
remove r-bsgenome-mmusculus-ucsc-mm9, r-bsgenome-celegans-ucsc-ce10,
r-bsgenome-dmelanogaster-ucsc-dm3, r-org-ce-eg-db, r-org-dm-eg-db, and
r-org-mm-eg-db.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
900ce2bafd
gnu: r-delayedmatrixstats: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.4.0.
[propagated-inputs]: Add r-biocparallel and r-hdf5array.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
70a3a76ba7
gnu: r-scran: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.1.
[propagated-inputs]: Add r-biocneighbors; remove r-dt, r-fnn, r-ggplot2,
r-shiny, and r-viridis.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
48f2791496
gnu: r-scater: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.0.
[propagated-inputs]: Add r-biocparallel; remove r-biobase, r-data-table,
r-edger, r-limma, r-rhdf5, r-rjson, r-shiny, r-shinydashboard, and r-tximport.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
f93ec63ccf
gnu: r-singlecellexperiment: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
3c833608f3
gnu: r-beachmat: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.4.0.
[propagated-inputs]: Add r-biocgenerics.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
edb91244c3
gnu: r-qvalue: Update to 2.14.0.
...
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
d055f199a9
gnu: r-hitc: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.26.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
8023912934
gnu: r-fithic: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.8.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
7468a76480
gnu: r-sushi: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.20.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
85b16c05e8
gnu: r-gwascat: Update to 2.14.0.
...
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.14.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
d57445c9b2
gnu: r-gviz: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
ea55326dc7
gnu: r-gqtlstats: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.14.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
da679b5202
gnu: r-ldblock: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.12.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus
4b91335566
gnu: r-erma: Update to 0.14.0.
...
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.14.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
220ac15e3f
gnu: r-snpstats: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.32.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
181a843143
gnu: r-gqtlbase: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.14.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
f20c766413
gnu: r-ggbio: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.30.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
e7a0bc1ccf
gnu: r-biovizbase: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
cdab2dcfea
gnu: r-organismdbi: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.24.0.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
e8e78c4966
gnu: r-ensembldb: Update to 2.6.0.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
0c96e4b290
gnu: r-dirichletmultinomial: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
5ae5a8ebfc
gnu: r-complexheatmap: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.20.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
d78c6aca55
gnu: r-genomicfiles: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.18.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
122e099e72
gnu: r-gage: Update to 2.32.0.
...
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.32.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
4984212786
gnu: r-keggrest: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.22.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
95df764c01
gnu: r-fastseg: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.28.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
147633d4c1
gnu: r-annotationhub: Update to 2.14.1.
...
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.1.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
d7ea34bf99
gnu: r-interactivedisplaybase: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.20.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
b03951f26b
gnu: r-edaseq: Update to 2.16.0.
...
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.16.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
7812e6b82e
gnu: r-deseq: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.34.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
800954eba4
gnu: r-aroma-light: Update to 3.12.0.
...
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.12.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus
675d91a035
gnu: r-msnid: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.16.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
762aca7270
gnu: r-msnbase: Update to 2.8.0.
...
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
73d7475246
gnu: r-pcamethods: Update to 1.74.0.
...
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.74.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
2c4311dc7c
gnu: r-mzid: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.20.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
0e16fc4699
gnu: r-vsn: Update to 3.50.0.
...
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.50.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
2b085484c0
gnu: r-affy: Update to 1.60.0.
...
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.60.0.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
511abd7add
gnu: r-affyio: Update to 1.52.0.
...
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.52.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
691ce09fd3
gnu: r-protgenerics: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.14.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
8af8688339
gnu: r-sva: Update to 3.30.0.
...
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
18604a76e4
gnu: r-methylkit: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
739a856db8
gnu: r-copywriter: Update to 2.14.0.
...
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
2e9d8116fb
gnu: r-chipseq: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.32.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
cec8f0920b
gnu: r-annotationfilter: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.6.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
d2b60be596
gnu: r-tximport: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
ad90921ddc
gnu: r-mutationalpatterns: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.8.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
338f860cc6
gnu: r-bamsignals: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.14.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
48196899cd
gnu: r-rhtslib: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.14.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
7d7c702c03
gnu: r-zlibbioc: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.28.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus
2919fefe12
gnu: r-motifrg: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.26.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
34f1c60c78
gnu: r-seqlogo: Update to 1.48.0.
...
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.48.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
c5b0815c44
gnu: r-genomation: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.14.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
45ba2caedb
gnu: r-seqpattern: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.14.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
d11bc259a8
gnu: r-impute: Update to 1.56.0.
...
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.56.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
78ecdbc00a
gnu: r-bsgenome: Update to 1.50.0.
...
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.50.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
44fa14dfa3
gnu: r-topgo: Update to 2.34.0.
...
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.34.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
8a0d57d26e
gnu: r-genomicfeatures: Update to 1.34.1.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.1.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
c5f1d1ce80
gnu: r-rtracklayer: Update to 1.42.0.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
52b95337e8
gnu: r-genomicalignments: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
9fd4350e5a
gnu: r-summarizedexperiment: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.12.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
de4c38f80b
gnu: r-delayedarray: Update to 0.8.0.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.8.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
7f3778eb06
gnu: r-rsamtools: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.34.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
4804c59227
gnu: r-biostrings: Update to 2.50.0.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
cd8828918f
gnu: r-biocparallel: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
3359d44210
gnu: r-biomart: Update to 2.38.0.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.38.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
3986e0dee5
gnu: r-annotationdbi: Update to 1.44.0.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.44.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
5b82e12a99
gnu: r-biobase: Update to 2.42.0.
...
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.42.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus
8d3906a95f
gnu: r-genomicranges: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.34.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
fb10fb72ba
gnu: r-xvector: Update to 0.22.0.
...
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.22.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
78d2ffdc73
gnu: r-limma: Update to 3.38.2.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.2.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
ca2945c316
gnu: r-variantannotation: Update to 1.28.1.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.1.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
08cd2d5b59
gnu: r-edger: Update to 3.24.0.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.24.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
12871693fe
gnu: r-genomeinfodb: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
9a8dd51979
gnu: r-iranges: Update to 2.16.0.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.16.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
a037453554
gnu: r-s4vectors: Update to 0.20.0.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
70f2758f71
gnu: r-dnacopy: Update to 1.56.0.
...
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.56.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
a127d3522a
gnu: r-bioccheck: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.18.0.
[propagated-inputs]: Add r-knitr and r-biocmanager; remove r-biocinstaller.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
6087f5ce37
gnu: r-biocstyle: Update to 2.10.0.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.10.0.
[propagated-inputs]: Add biocmanager.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
c8dbb5fa7f
gnu: r-biocviews: Update to 1.50.1.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.1.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
36d7d823a4
gnu: r-biocinstaller: Update to 1.32.1.
...
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.32.1.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
2f28ffd81d
gnu: r-biocgenerics: Update to 0.28.0.
...
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.28.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
5c996cab4c
gnu: r-grohmm: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.16.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
bf25930cf6
gnu: r-systempiper: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.16.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
9adf78c21e
gnu: r-shortread: Update to 1.40.0.
...
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.40.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
4a4b5b8537
gnu: r-gostats: Update to 2.48.0.
...
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.48.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus
95ae5acc89
gnu: r-category: Update to 2.48.0.
...
* gnu/packages/bioinformatics.scm (r-category): Update to 2.48.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
6dfb0b25ae
gnu: r-gseabase: Update to 1.44.0.
...
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.44.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
19a6149190
gnu: r-rbgl: Update to 1.58.0.
...
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
2ff6604a53
gnu: r-annotationforge: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.24.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
856444a0a1
gnu: r-dexseq: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
b5c552e654
gnu: r-deseq2: Update to 1.22.1.
...
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.1.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
85fb33a051
gnu: r-genefilter: Update to 1.64.0.
...
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.64.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
f4a95a0d15
gnu: r-geneplotter: Update to 1.60.0.
...
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.60.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
dadd682c53
gnu: r-copynumber: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-copynumber): Update to 1.22.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
090d4c0159
gnu: r-annotate: Update to 1.60.0.
...
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.60.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
00281ea3cd
gnu: r-modelmetrics: Update to 1.2.2.
...
* gnu/packages/statistics.scm (r-modelmetrics): Update to 1.2.2.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
9bd78484a2
gnu: r-preprocesscore: Update to 1.44.0.
...
* gnu/packages/statistics.scm (r-preprocesscore): Update to 1.44.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
1b3552310d
gnu: r-tidyr: Update to 0.8.2.
...
* gnu/packages/statistics.scm (r-tidyr): Update to 0.8.2.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
466397c35b
gnu: r-dt: Update to 0.5.
...
* gnu/packages/statistics.scm (r-dt): Update to 0.5.
[propagated-inputs]: Add r-promises.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
9094eb892c
gnu: r-roxygen2: Update to 6.1.1.
...
* gnu/packages/statistics.scm (r-roxygen2): Update to 6.1.1.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
0de3ebb099
gnu: r-survival: Update to 2.43-1.
...
* gnu/packages/statistics.scm (r-survival): Update to 2.43-1.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
83ca17d8e8
gnu: r-matrix: Update to 1.2-15.
...
* gnu/packages/statistics.scm (r-matrix): Update to 1.2-15.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
1966d8ffc7
gnu: r-lattice: Update to 0.20-38.
...
* gnu/packages/statistics.scm (r-lattice): Update to 0.20-38.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus
600a25eb04
gnu: r-mass: Update to 7.3-51.1.
...
* gnu/packages/statistics.scm (r-mass): Update to 7.3-51.1.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
a44f8b00fe
gnu: r-pander: Update to 0.6.3.
...
* gnu/packages/cran.scm (r-pander): Update to 0.6.3.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
7466c3bb06
gnu: r-rcmdcheck: Update to 1.3.1.
...
* gnu/packages/cran.scm (r-rcmdcheck): Update to 1.3.1.
[propagated-inputs]: Add r-sessioninfo.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
fc532b452f
gnu: r-remotes: Update to 2.0.2.
...
* gnu/packages/cran.scm (r-remotes): Update to 2.0.2.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
3d6fa1a3ad
gnu: r-sessioninfo: Update to 1.1.1.
...
* gnu/packages/cran.scm (r-sessioninfo): Update to 1.1.1.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
244a5c43ec
gnu: r-flextable: Update to 0.4.6.
...
* gnu/packages/cran.scm (r-flextable): Update to 0.4.6.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
84d0d860e1
gnu: r-sjmisc: Update to 2.7.6.
...
* gnu/packages/cran.scm (r-sjmisc): Update to 2.7.6.
[propagated-inputs]: Remove r-pillar, r-tibble, and r-tidyselect.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
cea8a60747
gnu: r-xts: Update to 0.11-2.
...
* gnu/packages/cran.scm (r-xts): Update to 0.11-2.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
5d986a3b41
gnu: r-psych: Update to 1.8.10.
...
* gnu/packages/cran.scm (r-psych): Update to 1.8.10.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
56af171ffd
gnu: r-ipred: Update to 0.9-8.
...
* gnu/packages/cran.scm (r-ipred): Update to 0.9-8.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
ec0ee08576
gnu: r-ffbase: Update to 0.12.7.
...
* gnu/packages/cran.scm (r-ffbase): Update to 0.12.7.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
65dd0e6748
gnu: r-pkgload: Update to 1.0.2.
...
* gnu/packages/cran.scm (r-pkgload): Update to 1.0.2.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
0dd84df121
gnu: r-ps: Update to 1.2.1.
...
* gnu/packages/cran.scm (r-ps): Update to 1.2.1.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
269182b0f1
gnu: r-rgraphviz: Update to 2.26.0.
...
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.26.0.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
bb47aca5e7
gnu: Add hdf5-1.10.
...
* gnu/packages/maths.scm (hdf5-1.10): New variable.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
d639d8884c
gnu: r-regioner: Update to 1.14.0.
...
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.14.0.
[propagated-inputs]: Add r-biostrings.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
ed35d7ca1f
gnu: r-ruvseq: Update to 1.16.0.
...
* gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.16.0.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
286157dc49
gnu: Add r-biocneighbors.
...
* gnu/packages/bioconductor.scm (r-biocneighbors): New variable.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus
318bcbc451
gnu: r-dnabarcodes: Update to 1.12.0.
...
* gnu/packages/bioconductor.scm (r-dnabarcodes): Update to 1.12.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
6f1e1d0f88
gnu: r-inspect: Update to 1.12.0.
...
* gnu/packages/bioconductor.scm (r-inspect): Update to 1.12.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
c348cfed74
gnu: r-rots: Update to 1.10.0.
...
* gnu/packages/bioconductor.scm (r-rots): Update to 1.10.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
016afac30f
gnu: r-glimma: Update to 1.10.0.
...
* gnu/packages/bioconductor.scm (r-glimma): Update to 1.10.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
6ea9ae9c39
gnu: r-goseq: Update to 1.34.0.
...
* gnu/packages/bioconductor.scm (r-goseq): Update to 1.34.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
b858338c76
gnu: r-ctc: Update to 1.56.0.
...
* gnu/packages/bioconductor.scm (r-ctc): Update to 1.56.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
5f2d0e635e
gnu: r-genomicinteractions: Update to 1.16.0.
...
* gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.16.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
bbc4787cf2
gnu: r-interactionset: Update to 1.10.0.
...
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.10.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
c4fed658a9
gnu: r-riboseqr: Update to 1.16.0.
...
* gnu/packages/bioconductor.scm (r-riboseqr): Update to 1.16.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
e22e462b33
gnu: r-riboprofiling: Update to 1.12.0.
...
* gnu/packages/bioconductor.scm (r-riboprofiling): Update to 1.12.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
e9427b2c78
gnu: r-ripseeker: Update to 1.22.0.
...
* gnu/packages/bioconductor.scm (r-ripseeker): Update to 1.22.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
aa802eafb6
gnu: r-chipcomp: Update to 1.12.0.
...
* gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.12.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
4728e27511
gnu: r-bayseq: Update to 2.16.0.
...
* gnu/packages/bioconductor.scm (r-bayseq): Update to 2.16.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
57d2fcd9ee
gnu: r-chippeakanno: Update to 3.16.0.
...
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.16.0.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
14520b640e
gnu: r-graph: Update to 1.60.0.
...
* gnu/packages/bioconductor.scm (r-graph): Update to 1.60.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
95ee4a466b
gnu: r-multtest: Update to 2.38.0.
...
* gnu/packages/bioconductor.scm (r-multtest): Update to 2.38.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
a92f523026
gnu: r-qdnaseq: Update to 1.18.0.
...
* gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.18.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
9add0933d0
gnu: r-cghcall: Update to 2.44.0.
...
* gnu/packages/bioconductor.scm (r-cghcall): Update to 2.44.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
46cdceef4c
gnu: r-cghbase: Update to 1.42.0.
...
* gnu/packages/bioconductor.scm (r-cghbase): Update to 1.42.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
f1c606ce8c
gnu: r-marray: Update to 1.60.0.
...
* gnu/packages/bioconductor.scm (r-marray): Update to 1.60.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus
98652568a4
gnu: r-diffbind: Update to 2.10.0.
...
* gnu/packages/bioconductor.scm (r-diffbind): Update to 2.10.0.
2018-11-07 12:26:31 +01:00
Ricardo Wurmus
6168692159
gnu: r-hpar: Update to 1.24.0.
...
* gnu/packages/bioconductor.scm (r-hpar): Update to 1.24.0.
2018-11-07 12:26:31 +01:00
Ricardo Wurmus
1e605c030f
gnu: Add r-biocmanager.
...
* gnu/packages/cran.scm (r-biocmanager): New variable.
2018-11-07 12:26:31 +01:00
Ricardo Wurmus
b58940cb03
gnu: Add r-ncdf4.
...
* gnu/packages/cran.scm (r-ncdf4): New variable.
2018-11-07 12:26:31 +01:00
Ricardo Wurmus
bfa5662e38
gnu: Add r-rcppannoy.
...
* gnu/packages/cran.scm (r-rcppannoy): New variable.
2018-11-07 12:26:31 +01:00
Mathieu Othacehe
8243f4e55a
gnu: slang: Use a correct location for terminfo dirs.
...
As termcap is disabled and no terminfo directory is given, slang is not able
to query terminal capabilities. Specifying a correct path for terminfo will
automatically disable termcap support in the configuration.
* gnu/packages/slang.scm (slang)[source]: Remove the snippet disabling
termcap.
[arguments]: Set MISC_TERMINFO_DIRS to a correct location.
2018-11-07 18:39:19 +09:00
Mathieu Othacehe
a7903ca150
gnu: terminals: Change libtsm and kmscon repositories.
...
Those two packages (from the same author) are no longer maintained and do not
even compile. Switch to a fork that is maintained even if it does not have any
release yet.
* gnu/packages/terminals.scm (libtsm)[origin]: Use
"https://github.com/Aetf/libtsm " as new origin and switch to git-fetch method.
(kmscon)[origin]: Use "https://github.com/Aetf/kmscon " as new origin and
switch to git-fetch method.
2018-11-07 18:27:01 +09:00
Mathieu Othacehe
581720bc74
gnu: Add guile-newt.
...
* gnu/packages/guile.scm (guile-newt): New variable.
2018-11-07 18:09:30 +09:00
Efraim Flashner
cbb5d2e145
gnu: kodi: Fix typo.
...
This is a follow-up to 2c17bd7b29
.
* gnu/packages/kodi.scm (kodi)[arguments]: Remove unwanted symbols.
2018-11-07 10:38:13 +02:00
Leo Famulari
02e2133bd2
gnu: LibreOffice: Update to 6.1.3.2.
...
* gnu/packages/libreoffice.scm (libreoffice): Update to 6.1.3.2.
2018-11-06 23:13:50 -05:00
Leo Famulari
b20aef98a0
gnu: GnuPG: Update to 2.2.11.
...
* gnu/packages/gnupg.scm (gnupg): Update to 2.2.11.
2018-11-06 17:26:45 -05:00
Marius Bakke
c6b05bacc0
gnu: nginx: Update to 1.14.1 [security fixes].
...
This fixes CVE-2018-16843, CVE-2018-16844, and CVE-2018-16845.
* gnu/packages/web.scm (nginx): Update to 1.14.1.
2018-11-06 21:34:30 +01:00
Leo Famulari
f25614229b
gnu: Syncthing: Update to 0.14.52.
...
* gnu/packages/syncthing.scm (syncthing): Update to 0.14.52.
2018-11-06 11:16:22 -05:00
Ludovic Courtès
4cceb1432a
gnu: libgit2: Work around test failures on 32-bit platforms.
...
* gnu/packages/patches/libgit2-oom-test.patch: New file.
* gnu/packages/version-control.scm (libgit2)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
2018-11-06 17:08:46 +01:00
Stefan Stefanović
158c02dffa
gnu: Add xcb-util-errors.
...
* gnu/packages/xorg.scm (xcb-util-errors): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-06 17:00:02 +01:00
Ludovic Courtès
3527f600b5
gnu: guile-sqlite3: Update home page.
...
* gnu/packages/guile.scm (guile-sqlite3)[home-page]: Update.
2018-11-06 17:00:01 +01:00
lakshmi
cddc0300b7
gnu: Add r-weights.
...
* gnu/packages/cran.scm (r-weights): New variable.
Signed-off-by: Gábor Boskovits <boskovits@gmail.com>
2018-11-06 16:06:42 +01:00
Tobias Geerinckx-Rice
fe4fb278b8
gnu: youtube-dl: Update to 2018.11.03.
...
* gnu/packages/video.scm (youtube-dl): Update to 2018.11.03.
2018-11-06 15:34:37 +01:00
Tobias Geerinckx-Rice
b1eeeb8dd4
gnu: terraform-docs: Update to 0.5.0.
...
* gnu/packages/terraform.scm (terraform-docs): Update to 0.5.0.
[native-inputs]: Remove them all.
2018-11-06 15:34:36 +01:00
Tobias Geerinckx-Rice
c3b8300af3
gnu: jq: Don't use NAME in source URI.
...
* gnu/packages/web.scm (jq)[source]: Code more hard.
2018-11-06 15:34:36 +01:00
Tobias Geerinckx-Rice
418dd6adb5
gnu: jq: Update to 1.6.
...
* gnu/packages/web.scm (jq): Update to 1.6.
[source]: Remove upstreamed patch.
* gnu/packages/patches/jq-CVE-2015-8863.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-11-06 15:34:36 +01:00
Rutger Helling
c58f3ebaf8
gnu: ffmpeg: Update to 4.1.
...
* gnu/packages/video.scm (ffmpeg): Update to 4.1.
2018-11-06 12:02:59 +01:00
Efraim Flashner
730e5fbc66
Revert "gnu: c-ares: Update to 1.15.0."
...
c-ares has more than 3000 dependant packages.
This reverts commit b588adc96f
.
2018-11-06 12:22:02 +02:00
Efraim Flashner
b588adc96f
gnu: c-ares: Update to 1.15.0.
...
* gnu/packages/adns.scm (c-ares): Update to 1.15.0.
2018-11-06 08:32:56 +02:00
Marius Bakke
adde15186d
gnu: xf86-video-intel: Update to commit 0932a6b37ba6d5c9e916a1cb6ab89c3205b81a0c.
...
* gnu/packages/xorg.scm (xf86-video-intel): Update to 2.99.917-11.0932a6b.
2018-11-05 23:53:30 +01:00
Marius Bakke
208e82297c
gnu: xapian: Update to 1.4.9.
...
* gnu/packages/patches/xapian-revert-5489fb2f8.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/search.scm (xapian): Update to 1.4.9.
[source](patches): Remove.
(python-xapian-bindings): Update to 1.4.9.
2018-11-05 23:46:38 +01:00
Marius Bakke
d79c8148cc
gnu: libssh: Update to 0.7.7.
...
* gnu/packages/ssh.scm (libssh): Update to 0.7.7.
2018-11-05 23:46:38 +01:00
Marius Bakke
b5a887637c
gnu: strace: Update to 4.25.
...
* gnu/packages/linux.scm (strace): Update to 4.25.
2018-11-05 23:46:38 +01:00
Marius Bakke
876428dd98
gnu: libmtp: Update to 1.1.16.
...
* gnu/packages/libusb.scm (libmtp): Update to 1.1.16.
2018-11-05 23:46:38 +01:00
Marius Bakke
039241bc96
gnu: libgit2: Update to 0.26.8.
...
* gnu/packages/version-control.scm (libgit2): Update to 0.26.8.
2018-11-05 23:46:38 +01:00
Marius Bakke
c98a7e6b91
gnu: i3-wm: Update to 4.16.
...
* gnu/packages/wm.scm (i3-wm): Update to 4.16.
2018-11-05 23:46:38 +01:00
Marius Bakke
9c415f96ec
gnu: libgphoto2: Update to 2.5.20.
...
* gnu/packages/photo.scm (libgphoto2): Update to 2.5.20.
2018-11-05 23:46:38 +01:00
Marius Bakke
66044a3698
gnu: glm: Update to 0.9.9.3.
...
* gnu/packages/maths.scm (glm): Update to 0.9.9.3.
2018-11-05 23:46:38 +01:00
Marius Bakke
64b60f38e7
gnu: ffmpeg: Update to 4.0.3.
...
* gnu/packages/video.scm (ffmpeg): Update to 4.0.3.
2018-11-05 23:46:38 +01:00
Marius Bakke
c5e5711002
gnu: ffmpeg@3.4: Update to 3.4.5.
...
* gnu/packages/video.scm (ffmpeg-3.4): Update to 3.4.5.
2018-11-05 23:46:37 +01:00
Marius Bakke
196653145a
gnu: feh: Update to 2.28.1.
...
* gnu/packages/image-viewers.scm (feh): Update to 2.28.1.
2018-11-05 23:46:37 +01:00
Marius Bakke
00815eea38
gnu: libsoup: Update to 2.64.2.
...
* gnu/packages/gnome.scm (libsoup): Update to 2.64.2.
2018-11-05 23:46:37 +01:00
Marius Bakke
0a56ffdf1f
gnu: mono: Update home page.
...
* gnu/packages/mono.scm (mono)[home-page]: Use HTTPS.
2018-11-05 23:46:37 +01:00
Leo Famulari
288d24800d
gnu: ruby-rack: Update to 2.0.6 [fixes CVE-2018-{16470,16471}].
...
* gnu/packages/ruby.scm (ruby-rack): Update to 2.0.6.
2018-11-05 16:22:11 -05:00
Pierre Neidhardt
426ffb830a
gnu: emacs-mu4e-conversation: Update to 20181105.
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* gnu/packages/emacs.scm (emacs-mu4e-conversation): Update to 20181105.
2018-11-05 20:22:06 +01:00
Pierre Neidhardt
695db2f98a
gnu: Add emacs-helm-slime.
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* gnu/packages/emacs.scm (emacs-helm-slime): New variable.
2018-11-05 13:58:33 +01:00
Mark H Weaver
c9f3d38be4
gnu: linux-libre: Update to 4.19.1.
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* gnu/packages/linux.scm (%linux-libre-version): Update to 4.19.1.
(%linux-libre-hash): Update hash.
2018-11-05 04:00:45 -05:00
Mark H Weaver
28c717213d
gnu: linux-libre@4.14: Update to 4.14.79.
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* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.79.
(%linux-libre-4.14-hash): Update hash.
2018-11-05 04:00:43 -05:00
Eric Bavier
cddc044ce7
libreoffice: honor '--cores=...' during build.
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* gnu/packages/libreoffice.scm (libreoffice)[configure-flags]: Add
'--with-parallelism' flag.
2018-11-04 21:56:39 -06:00
Danny Milosavljevic
64eb038eef
gnu: Add fswatch.
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* gnu/packages/monitoring.scm (fswatch): New variable.
2018-11-05 03:01:21 +01:00