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Author SHA1 Message Date
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