4715d4af17
gnu: raxml: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
5e242b02c3
gnu: pyicoteo: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
b44b1f08f6
gnu: hplip: Remove bundled non-free blobs.
...
This fixes <https://bugs.gnu.org/32184 >.
* gnu/packages/cups.scm (hplip)[source]: Add patch. Update snippet to
remove non-free code and binary blobs.
* gnu/packages/patches/hplip-remove-imageprocessor.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
2018-11-07 23:16:02 +02:00
2b773a9273
gnu: sra-tools: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git.
2018-11-07 21:41:56 +01:00
55698df260
gnu: libgff: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
2018-11-07 21:41:56 +01:00
4257c10ad2
gnu: kentutils: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git.
[arguments]: Add phase "fix-permissions".
2018-11-07 21:41:55 +01:00
1a20bcadf3
gnu: r-seqgl: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
a2b9d6a8d0
gnu: pplacer: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git.
[arguments]: Make files writable; use INVOKE.
2018-11-07 21:41:55 +01:00
6052264b56
gnu: minced: Update to 0.3.2.
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* gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
2018-11-07 21:41:55 +01:00
9d94ca0ebf
gnu: minced: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
b58d9e4aa2
gnu: metabat: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
5c1f35e71b
gnu: mash: Update to 2.1.
...
* gnu/packages/bioinformatics.scm (mash): Update to 2.1.
2018-11-07 21:41:55 +01:00
497fc04d8f
gnu: mash: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
b31e156161
gnu: fio: Update to 3.11.
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* gnu/packages/benchmark.scm (fio): Update to 3.11.
[source]: Use bz2 compressed tarball.
2018-11-07 21:09:00 +01:00
2dc28391f3
gnu: kaiju: Update to 1.6.3.
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* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
2018-11-07 20:47:22 +01:00
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
f0731591a5
gnu: idr: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
2018-11-07 20:41:58 +01:00
b8a6230df3
gnu: java-htsjdk: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (java-htsjdk)[source]: Fetch from git.
2018-11-07 20:36:07 +01:00
57be690d91
gnu: hisat2: Use versioned source URL.
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* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
2018-11-07 20:32:29 +01:00
c8f02c1dcb
gnu: grit: Update to 2.0.5.
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* gnu/packages/bioinformatics.scm (grit): Update to 2.0.5.
[arguments]: Simplify.
2018-11-07 20:30:44 +01:00
8d75adbf03
gnu: grit: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
2018-11-07 20:27:10 +01:00
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
b113f39019
gnu: gemma: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
2018-11-07 20:26:45 +01:00
f09e8abc5e
gnu: clementine: Build with sqlite-with-column-metadata.
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* 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
91b71cfbba
gnu: fxtract: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
2018-11-07 19:55:50 +01:00
7ca49ab57a
gnu: ribodiff: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
2018-11-07 19:48:21 +01:00
239716fb0b
gnu: python-biom-format: Update to 2.1.7.
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* 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
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
383cb7b8e6
gnu: bioawk: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
2018-11-07 19:06:30 +01:00
20ee3e8b76
gnu: bedtools-2.18: Fetch sources from stable URL.
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* 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
8e58319c45
gnu: bamtools: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (bamtools)[source]: Fetch from git.
2018-11-07 18:44:30 +01:00
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
fff67cc8a7
gnu: prodigal: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
2018-11-07 17:19:53 +01:00
08759829cf
gnu: cuirass: Update to 0b40dca.
...
* gnu/packages/ci.scm (cuirass): Update to 0b40dca.
2018-11-07 16:06:42 +01:00
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
37200dbcc3
gnu: r-rhdf5lib: Update to 1.4.0.
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* 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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