Commit Graph

31254 Commits

Author SHA1 Message Date
Ricardo Wurmus b58d9e4aa2
gnu: metabat: Fetch sources from git.
* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
Ricardo Wurmus 5c1f35e71b
gnu: mash: Update to 2.1.
* gnu/packages/bioinformatics.scm (mash): Update to 2.1.
2018-11-07 21:41:55 +01:00
Ricardo Wurmus 497fc04d8f
gnu: mash: Fetch sources from git.
* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
Marius Bakke b31e156161
gnu: fio: Update to 3.11.
* gnu/packages/benchmark.scm (fio): Update to 3.11.
[source]: Use bz2 compressed tarball.
2018-11-07 21:09:00 +01:00
Ricardo Wurmus 2dc28391f3
gnu: kaiju: Update to 1.6.3.
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
2018-11-07 20:47:22 +01:00
Ricardo Wurmus 6fe323bf2e
gnu: kaiju: Fetch sources from git.
* gnu/packages/bioinformatics.scm (kaiju)[source]: Fetch from git.
[arguments]: Remove redundant installation step.
2018-11-07 20:46:36 +01:00
Ricardo Wurmus f0731591a5
gnu: idr: Fetch sources from git.
* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
2018-11-07 20:41:58 +01:00
Ricardo Wurmus b8a6230df3
gnu: java-htsjdk: Fetch sources from git.
* gnu/packages/bioinformatics.scm (java-htsjdk)[source]: Fetch from git.
2018-11-07 20:36:07 +01:00
Ricardo Wurmus 57be690d91
gnu: hisat2: Use versioned source URL.
* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
2018-11-07 20:32:29 +01:00
Ricardo Wurmus c8f02c1dcb
gnu: grit: Update to 2.0.5.
* gnu/packages/bioinformatics.scm (grit): Update to 2.0.5.
[arguments]: Simplify.
2018-11-07 20:30:44 +01:00
Ricardo Wurmus 8d75adbf03
gnu: grit: Fetch sources from git.
* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
2018-11-07 20:27:10 +01:00
Ricardo Wurmus 152bebd9e0
gnu: gemma: Update to 0.98.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/gemma-intel-compat.patch: Remove file.
* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.
[source]: Remove patch.
[inputs]: Add eigen, gfortran:lib, and openblas.
[arguments]: Add phase "find-eigen".
2018-11-07 20:26:46 +01:00
Ricardo Wurmus b113f39019
gnu: gemma: Fetch sources from git.
* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
2018-11-07 20:26:45 +01:00
Pierre Langlois f09e8abc5e
gnu: clementine: Build with sqlite-with-column-metadata.
* gnu/packages/music.scm (clementine)[inputs]: Use sqlite-with-column-metadata.

Signed-off-by: Leo Famulari <leo@famulari.name>
2018-11-07 14:25:07 -05:00
Ricardo Wurmus 91b71cfbba
gnu: fxtract: Fetch sources from git.
* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
2018-11-07 19:55:50 +01:00
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 dcb45127e0
services: cuirass: Add 'ttl' configuration field.
* gnu/services/cuirass.scm (<cuirass-configuration>)[ttl]: New field.
(cuirass-shepherd-service): Honor it.
2018-11-07 16:06:42 +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
Ludovic Courtès 970c9993f1
linux-initrd: Make sure 'build-initrd' can delete files.
Fixes <https://bugs.gnu.org/33297>.
Reported by Mark H Weaver <mhw@netris.org>.

This fixes a regression introduced in
72dc64f8f7, which made files read-only.

* gnu/build/linux-initrd.scm (build-initrd): Call 'make-file-writable'
on all the files under contents/.
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 2d9dace8c2
services: kmscon: Add an auto-login option.
Add an auto-login option that behaves as the one of mingetty-service.

* gnu/services/base.scm (kmscon-configuration)[auto-login]: New field.
(kmscon-service-type): Pass it to kmscon command.
* doc/guix.texi (Base Services): Document it.
2018-11-07 18:21:42 +09:00
Mathieu Othacehe f4e8bc5f25
services: kmscon: Do not switch to vt at start.
* gnu/services/base.scm (kmscon-service-type): Add "--no-switchvt" to kmscon
command.
2018-11-07 18:15:00 +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
Ludovic Courtès c5ce2db569
install: Add 'install-database-and-gc-roots'.
* gnu/build/install.scm (%root-profile): New variable.
(install-database-and-gc-roots): New procedure.
(populate-single-profile-directory): Replace inline code with a call to
'install-database-and-gc-roots'.
2018-11-06 23:21:24 +01:00
Ludovic Courtès b27ef1d46c
pack: Import (guix store database) only when '--localstatedir' is passed.
This is another way to address <https://bugs.gnu.org/32184>, which was
previously addressed in commit 19c924af4f.

* gnu/build/install.scm (register-closure): Move to...
* gnu/build/vm.scm (register-closure): ... here.  New procedure.
* guix/scripts/pack.scm (self-contained-tarball)[build]: Remove
now unneeded 'with-extensions' form and custom (guix config) module.
* tests/guix-pack.sh: Revert the strategy from
commit 19c924af4f.
* tests/pack.scm ("self-contained-tarball"): Likewise.
2018-11-06 23:21:23 +01:00
Ludovic Courtès ec4c81fe32
pack: Move store database creation to a separate derivation.
* guix/scripts/pack.scm (store-database): New procedure.
(self-contained-tarball): Use it when LOCALSTATEDIR? is true.
Remove 'schema' and add 'database'.
[build]: Pass DATABASE to 'populate-single-profile-directory'.
(squashfs-image): Remove #:deduplicate? parameter.
[build]: Remove (gnu build install) and (guix config) from the imported
modules.  Remove 'with-extensions'.
* gnu/build/install.scm (populate-single-profile-directory): Remove
 #:deduplicate?, #:register?, and #:schema; add #:database.  Remove call
to 'register-closure' and simply copy DATABASE instead.
2018-11-06 23:21:23 +01:00
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
Oleg Pykhalov 7f860a8be1
gnu: services: dns: Fix 'ddclient-activation'.
* gnu/services/dns.scm (ddclient-activation): Fix procedure.
2018-11-06 07:16:44 +03:00
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.
* 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.
* 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.
* 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.
* 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.
* 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.
* gnu/packages/monitoring.scm (fswatch): New variable.
2018-11-05 03:01:21 +01:00
Luther Thompson 1417f50317
gnu: python-ilinkedlist: Update to 0.2.0.
* gnu/packages/python.scm (python-ilinkedlist): Update to 0.2.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-05 00:08:47 +01:00
Vagrant Cascadian b6e9514864
gnu: pelican: Update to 3.7.1.
* gnu/packages/python.scm (pelican): Update to 3.7.1.
  [home-page]: Use HTTPS URL.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-05 00:08:47 +01:00
Pkill -9 c834bd3bb2
gnu: xonotic: Add icon and category to desktop files.
* gnu/packages/games.scm (xonotic): Add icon ("xonotic") and category
("Game") to the .desktop files for Xonotic.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-05 00:08:47 +01:00
Ludovic Courtès 688d1a01e4
artwork: Clone over HTTPS.
Suggested by Leo Famulari <leo@famulari.name>
at <https://lists.gnu.org/archive/html/help-guix/2018-11/msg00039.html>.

* gnu/artwork.scm (%artwork-repository): Switch to HTTPS URL.
2018-11-05 00:08:47 +01:00
Ludovic Courtès ab3c60ace3
install: Parameterize the profile name for 'populate-single-profile-directory'.
* gnu/build/install.scm (populate-single-profile-directory): Add
 #:profile-name.  Replace hard-coded occurrences of "guix-profile" with
PROFILE-NAME.  Make the symlink part under /root a function of
PROFILE-NAME.
2018-11-05 00:08:46 +01:00
Pierre Neidhardt 97b7b96efc
gnu: go-github-com-urfave-cli: Remove duplicate declaration.
* gnu/packages/golang.scm (go-github-com-urfave-cli): Remove duplicate declaration.
2018-11-04 23:33:24 +01:00
Efraim Flashner 30012b7408
gnu: myrepos: Wrap the webcheckout binary.
* gnu/packages/version-control.scm (myrepos)[arguments]: Add a custom
'wrap-webcheckout phase to wrap webcheckout with its perl libraries.
[inputs]: Add perl-encode-locale, perl-html-parser, perl-http-date,
perl-http-message, perl-libwww, perl-try-tiny, perl-uri.
2018-11-04 12:45:27 +02:00
Efraim Flashner f909e21797
gnu: debian-archive-keyring: Update to 2018.1.
* gnu/packages/debian.scm (debian-archive-keyring): Update to 2018.1.
[source]: Download from git repository.
2018-11-04 12:00:13 +02:00
Efraim Flashner 2e77bbed71
gnu: ruby@2.3: Update to 2.3.8.
* gnu/packages/ruby.scm (ruby@2.3): Update to 2.3.8.
2018-11-04 12:00:13 +02:00
Efraim Flashner d4b5e4bb73
gnu: debootstrap: Update to 1.0.109.
* gnu/packages/debian.scm (debootstrap): Update to 1.0.109.
2018-11-04 12:00:10 +02:00
Arun Isaac 3e84ce51fb
gnu: mpop: Update to 1.4.0.
* gnu/packages/mail.scm (mpop): Update to 1.4.0.
2018-11-04 10:36:17 +05:30
Efraim Flashner e9f305a1c8
gnu: sbcl-lift: Don't keep the bundled website.
* gnu/packages/lisp.scm (sbcl-lift)[source]: Remove bundled website.
[arguments]: Remove custom 'make-gzips-writable phase.
2018-11-03 20:43:35 +02:00
Ludovic Courtès 0e091b3e93
gnu: totem: Update to 3.26.2.
* gnu/packages/gnome.scm (totem): Update to 3.26.2.
2018-11-03 15:44:40 +01:00
Ludovic Courtès 504f0cf198
gnu: emacs-debbugs: Update to 0.16.
* gnu/packages/emacs.scm (emacs-debbugs): Update to 0.16.
2018-11-03 15:44:24 +01:00
Ludovic Courtès a7c8574f39
gnu: perl-image-exiftool: Update to 11.11.
* gnu/packages/photo.scm (perl-image-exiftool): Update to 11.11.
2018-11-03 15:16:42 +01:00
Ludovic Courtès 46c8f53ba8
gnu: emacs-dired-du: Update to 0.5.1.
* gnu/packages/emacs.scm (emacs-dired-du): Update to 0.5.1.
2018-11-03 15:16:20 +01:00
Ludovic Courtès 8e5c59868c
gnu: diffoscope: Update to 104.
* gnu/packages/package-management.scm (diffoscope): Update to 104.
2018-11-03 15:16:02 +01:00
Arun Isaac b1c7f5fff9
gnu: emacs-emms: Update to 5.1.
* gnu/packages/emacs.scm (emacs-emms): Update to 5.1.
2018-11-03 19:14:05 +05:30
Tobias Geerinckx-Rice 3995e85462
gnu: tor: Update to 0.3.4.9.
* gnu/packages/tor.scm (tor): Update to 0.3.4.9.
2018-11-02 19:51:12 +01:00
Julien Lepiller ff349415b2
gnu: python-apache-libcloud: Update to 2.3.0.
* gnu/packages/python.scm (python-apache-libcloud)
(python2-apache-libcloud): Update to 2.3.0.
2018-11-02 14:32:24 +01:00
Danny Milosavljevic 722aac1ea1
Merge remote-tracking branch 'origin/wip-rust' into master. 2018-11-02 11:01:45 +01:00
Leo Famulari b3325eb306
gnu: Go 1.11: Avoid unnecessary store references.
This shrinks the closure of Go 1.11 from 1379 MiB to 581 MiB.

Fixes <https://bugs.gnu.org/32949>.

* gnu/packages/golang.scm (go-1.11)[arguments]: Add a 'delete-extraneous-files'
phase.
2018-11-01 23:23:09 -04:00
Leo Famulari 7571ec3576
gnu: MPD: Update to 0.20.23.
* gnu/packages/mpd.scm (mpd): Update to 0.20.23.
2018-11-01 15:30:05 -04:00
Leo Famulari 33279c2a19
gnu: mpd-mpc: Update to 0.31.
* gnu/packages/mpd.scm (mpd-mpc): Update to 0.31.
[native-inputs]: Add python-sphinx.
2018-11-01 15:30:05 -04:00
Leo Famulari 361dd8a556
gnu: icecast: Update to 2.4.4 [fixes CVE-2018-18820].
* gnu/packages/xiph.scm (icecast): Update to 2.4.4.
2018-11-01 12:33:14 -04:00
Rutger Helling d7ca1899aa
gnu: mame: Update to 0.203.
* gnu/packages/emulators.scm (mame): Update to 0.203.
2018-11-01 09:24:52 +01:00
Rutger Helling a769a4d432
gnu: xpra: Update to 2.4.1.
* gnu/packages/xorg.scm (xpra): Update to 2.4.1.
2018-11-01 08:32:45 +01:00