jackhill/guix/guix.git
5 years agognu: opencv: Loosen test suite failures.
Efraim Flashner [Mon, 14 Jan 2019 09:32:02 +0000 (11:32 +0200)]
gnu: opencv: Loosen test suite failures.

* gnu/packages/image-processing.scm (opencv)[native-inputs]: Add patch
to opencv-contrib.
[arguments]: Update 'unpack-submodule-sources phase.
* gnu/packages/patches/opencv-rgbd-aarch64-test-fix.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.

5 years agognu: opencv: Update configure flags.
Efraim Flashner [Mon, 14 Jan 2019 08:03:41 +0000 (10:03 +0200)]
gnu: opencv: Update configure flags.

* gnu/packages/image-processing.scm (opencv)[arguments]: Don't use
precompiled headers. Enable all available CPU optimizations.

5 years agognu: opencv: Don't hardcode build directories.
Efraim Flashner [Mon, 14 Jan 2019 08:01:52 +0000 (10:01 +0200)]
gnu: opencv: Don't hardcode build directories.

* gnu/packages/image-processing.scm (opencv)[arguments]: Change
OPENCV_EXTRA_MODULES_PATH and OPENCV_TEST_DATA_PATH to use 'getcwd'
instead of hardcoding the build path.

5 years agognu: opencv: Fix building on non-x86_64 systems.
Efraim Flashner [Sun, 13 Jan 2019 20:26:40 +0000 (22:26 +0200)]
gnu: opencv: Fix building on non-x86_64 systems.

* gnu/packages/image-processing.scm (opencv)[arguments]: Add
configure-flag to disable carotene. Don't require x86_64 CPU
except on x86_64. Fix typo.

5 years agognu: gnurl: Update to 7.63.0.
Efraim Flashner [Mon, 14 Jan 2019 11:57:49 +0000 (13:57 +0200)]
gnu: gnurl: Update to 7.63.0.

* gnu/packages/gnunet.scm (gnurl): Update to 7.63.0.

5 years agognu: emacs-pass: Update to 1.8.
Clément Lassieur [Mon, 14 Jan 2019 10:45:23 +0000 (11:45 +0100)]
gnu: emacs-pass: Update to 1.8.

* gnu/packages/emacs.scm (emacs-pass): Update to 1.8.

5 years agognu: dosbox: Update to 0.74-2.
Rutger Helling [Mon, 14 Jan 2019 08:04:23 +0000 (09:04 +0100)]
gnu: dosbox: Update to 0.74-2.

* gnu/packages/emulators.scm (dosbox): Update to 0.74-2.
[arguments]: Use invoke in 'autogen.sh phase.

5 years agognu: linux-libre: Update to 4.20.2.
Mark H Weaver [Mon, 14 Jan 2019 06:29:47 +0000 (01:29 -0500)]
gnu: linux-libre: Update to 4.20.2.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.20.2.
(%linux-libre-hash): Update hash.

5 years agognu: linux-libre@4.19: Update to 4.19.15.
Mark H Weaver [Mon, 14 Jan 2019 06:28:02 +0000 (01:28 -0500)]
gnu: linux-libre@4.19: Update to 4.19.15.

* gnu/packages/linux.scm (%linux-libre-4.19-version): Update to 4.19.15.
(%linux-libre-4.19-hash): Update hash.

5 years agognu: linux-libre@4.14: Update to 4.14.93.
Mark H Weaver [Mon, 14 Jan 2019 06:26:21 +0000 (01:26 -0500)]
gnu: linux-libre@4.14: Update to 4.14.93.

* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.93.
(%linux-libre-4.14-hash): Update hash.

5 years agognu: linux-libre@4.9: Update to 4.9.150.
Mark H Weaver [Mon, 14 Jan 2019 06:25:28 +0000 (01:25 -0500)]
gnu: linux-libre@4.9: Update to 4.9.150.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.150.

5 years agognu: linux-libre@4.4: Update to 4.4.170.
Mark H Weaver [Mon, 14 Jan 2019 06:24:40 +0000 (01:24 -0500)]
gnu: linux-libre@4.4: Update to 4.4.170.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.170.

5 years agognu: Add ocaml-merlin.
Gabriel Hondet [Thu, 27 Dec 2018 09:54:34 +0000 (10:54 +0100)]
gnu: Add ocaml-merlin.

* gnu/packages/ocaml.scm (ocaml-merlin): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
5 years agognu: Add emacs-tldr.
Gabriel Hondet [Wed, 2 Jan 2019 16:03:32 +0000 (17:03 +0100)]
gnu: Add emacs-tldr.

* gnu/packages/emacs.scm (emacs-tldr): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
5 years agosystem: Add sudoedit to %setuid-programs.
Meiyo Peng [Sat, 5 Jan 2019 13:06:47 +0000 (21:06 +0800)]
system: Add sudoedit to %setuid-programs.

* gnu/system.scm (%setuid-programs): Add sudoedit.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
5 years agognu: Add python-miniboa.
Christopher Baines [Thu, 3 Jan 2019 20:42:38 +0000 (20:42 +0000)]
gnu: Add python-miniboa.

python2-miniboa is required for the linkchecker testsuite.

* gnu/packages/python.scm (python-miniboa, python2-miniboa): New variable.

5 years agognu: python-pillow: Update to 5.4.1.
Christopher Baines [Sun, 13 Jan 2019 17:09:52 +0000 (17:09 +0000)]
gnu: python-pillow: Update to 5.4.1.

I'm looking at this, as this release fixes an issue with the Django testsuite:

https://github.com/python-pillow/Pillow/pull/3525

* gnu/packages/python.scm (python-pillow): Update to 5.4.1.

5 years agognu: r-biocgenerics: Move to bioconductor.
Ricardo Wurmus [Sun, 13 Jan 2019 12:01:35 +0000 (13:01 +0100)]
gnu: r-biocgenerics: Move to bioconductor.

* gnu/packages/bioinformatics.scm (r-biocgenerics): Move from here...
* gnu/packages/bioconductor.scm (r-biocgenerics): ...to here.

5 years agognu: r-annotate: Move to bioconductor.
Ricardo Wurmus [Sun, 13 Jan 2019 11:55:46 +0000 (12:55 +0100)]
gnu: r-annotate: Move to bioconductor.

* gnu/packages/bioinformatics.scm (r-annotate): Move from here...
* gnu/packages/bioconductor.scm (r-annotate): ...to here.

5 years agognu: r-vegan: Move from bioinformatics to cran.
Ricardo Wurmus [Sun, 13 Jan 2019 11:14:32 +0000 (12:14 +0100)]
gnu: r-vegan: Move from bioinformatics to cran.

* gnu/packages/bioinformatics.scm (r-vegan): Move from here...
* gnu/packages/cran.scm (r-vegan): ...to here.

5 years agognu: conda: Use 'invoke'.
Efraim Flashner [Sun, 13 Jan 2019 10:38:17 +0000 (12:38 +0200)]
gnu: conda: Use 'invoke'.

* gnu/packages/package-management.scm (conda)[arguments]: Use 'invoke'.

5 years agognu: python-conda: All phases return #t.
Efraim Flashner [Sun, 13 Jan 2019 10:30:51 +0000 (12:30 +0200)]
gnu: python-conda: All phases return #t.

* gnu/packages/package-management.scm (python-conda)[arguments]: Use
'invoke'.

5 years agognu: python-conda: Fix test suite.
Efraim Flashner [Sun, 13 Jan 2019 10:29:35 +0000 (12:29 +0200)]
gnu: python-conda: Fix test suite.

* gnu/packages/package-management.scm (python-conda)[native-inputs]: Add
python-cytoolz.

5 years agognu: Add r-raster.
Ricardo Wurmus [Sun, 13 Jan 2019 10:11:52 +0000 (11:11 +0100)]
gnu: Add r-raster.

* gnu/packages/cran.scm (r-raster): New variable.

5 years agognu: r-ggformula: Update to 0.9.1.
Ricardo Wurmus [Sun, 13 Jan 2019 10:11:38 +0000 (11:11 +0100)]
gnu: r-ggformula: Update to 0.9.1.

* gnu/packages/cran.scm (r-ggformula): Update to 0.9.1.

5 years agognu: r-tibble: Update to 2.0.1.
Ricardo Wurmus [Sun, 13 Jan 2019 10:09:01 +0000 (11:09 +0100)]
gnu: r-tibble: Update to 2.0.1.

* gnu/packages/statistics.scm (r-tibble): Update to 2.0.1.

5 years agognu: r-psych: Update to 1.8.12.
Ricardo Wurmus [Sun, 13 Jan 2019 09:11:45 +0000 (10:11 +0100)]
gnu: r-psych: Update to 1.8.12.

* gnu/packages/cran.scm (r-psych): Update to 1.8.12.

5 years agognu: bitshuffle: Fix build on armhf-linux.
Efraim Flashner [Sun, 13 Jan 2019 08:39:31 +0000 (10:39 +0200)]
gnu: bitshuffle: Fix build on armhf-linux.

* gnu/packages/compression.scm (bitshuffle)[arguments]: Add custom phase
to only use NEON on aarch64.

5 years agognu: wine-staging: Update to 4.0-rc6.
Rutger Helling [Sun, 13 Jan 2019 09:13:13 +0000 (10:13 +0100)]
gnu: wine-staging: Update to 4.0-rc6.

* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 4.0-rc6.
* gnu/packages/wine.scm (wine-staging): Update to 4.0-rc6.

5 years agognu: Sort package module references in (gnu packages graphviz).
Ricardo Wurmus [Sun, 13 Jan 2019 09:06:06 +0000 (10:06 +0100)]
gnu: Sort package module references in (gnu packages graphviz).

* gnu/packages/graphviz.scm: Sort package module references; delete
duplicates.

5 years agognu: Add python-pygraphviz.
Ricardo Wurmus [Mon, 31 Dec 2018 13:48:17 +0000 (14:48 +0100)]
gnu: Add python-pygraphviz.

* gnu/packages/graphviz.scm (python-pygraphviz): New variable.

5 years agognu: Add python-doctest-ignore-unicode.
Ricardo Wurmus [Mon, 31 Dec 2018 13:48:16 +0000 (14:48 +0100)]
gnu: Add python-doctest-ignore-unicode.

* gnu/packages/python.scm (python-doctest-ignore-unicode): New variable.

5 years agognu: Add graphviz-2.38.
Ricardo Wurmus [Mon, 31 Dec 2018 13:48:15 +0000 (14:48 +0100)]
gnu: Add graphviz-2.38.

* gnu/packages/graphviz.scm (graphviz-2.38): New variable.

5 years agognu: sudo: Update to 1.8.27.
Marius Bakke [Sat, 12 Jan 2019 21:22:26 +0000 (22:22 +0100)]
gnu: sudo: Update to 1.8.27.

* gnu/packages/admin.scm (sudo): Update to 1.8.27.

5 years agognu: libassuan: Update to 2.5.2.
Marius Bakke [Sat, 12 Jan 2019 20:58:40 +0000 (21:58 +0100)]
gnu: libassuan: Update to 2.5.2.

* gnu/packages/gnupg.scm (libassuan): Update to 2.5.2.

5 years agognu: libgxps: Update to 0.3.1.
Marius Bakke [Sat, 12 Jan 2019 20:58:20 +0000 (21:58 +0100)]
gnu: libgxps: Update to 0.3.1.

* gnu/packages/gnome.scm (libgxps): Update to 0.3.1.

5 years agognu: libqmi: Update to 1.22.0.
Marius Bakke [Sat, 12 Jan 2019 20:57:45 +0000 (21:57 +0100)]
gnu: libqmi: Update to 1.22.0.

* gnu/packages/freedesktop.scm (libqmi): Update to 1.22.0.

5 years agognu: libmbim: Update to 1.18.0.
Marius Bakke [Sat, 12 Jan 2019 20:57:16 +0000 (21:57 +0100)]
gnu: libmbim: Update to 1.18.0.

* gnu/packages/freedesktop.scm (libmbim): Update to 1.18.0.

5 years agognu: libsodium: Update to 1.0.17.
Marius Bakke [Sat, 12 Jan 2019 20:56:48 +0000 (21:56 +0100)]
gnu: libsodium: Update to 1.0.17.

* gnu/packages/crypto.scm (libsodium): Update to 1.0.17.

5 years agognu: exempi: Update to 2.5.0.
Marius Bakke [Sat, 12 Jan 2019 20:04:19 +0000 (21:04 +0100)]
gnu: exempi: Update to 2.5.0.

* gnu/packages/freedesktop.scm (exempi): Update to 2.5.0.

5 years agognu: seabios: Update to 1.12.0.
Marius Bakke [Sat, 12 Jan 2019 20:03:47 +0000 (21:03 +0100)]
gnu: seabios: Update to 1.12.0.

* gnu/packages/firmware.scm (seabios): Update to 1.12.0.

5 years agognu: httpd: Update to 2.4.37.
Marius Bakke [Sat, 12 Jan 2019 19:33:52 +0000 (20:33 +0100)]
gnu: httpd: Update to 2.4.37.

* gnu/packages/web.scm (httpd): Update to 2.4.37.

5 years agognu: nasm: Update license.
Marius Bakke [Thu, 3 Jan 2019 01:17:39 +0000 (02:17 +0100)]
gnu: nasm: Update license.

* gnu/packages/assembly.scm (nasm)[license]: Change to BSD-2.

5 years agognu: nasm: Update home page.
Marius Bakke [Thu, 3 Jan 2019 01:16:42 +0000 (02:16 +0100)]
gnu: nasm: Update home page.

* gnu/packages/assembly.scm (nasm)[home-page]: Use HTTPS.

5 years agognu: libgphoto2: Update to 2.5.22.
Marius Bakke [Thu, 3 Jan 2019 00:00:10 +0000 (01:00 +0100)]
gnu: libgphoto2: Update to 2.5.22.

* gnu/packages/photo.scm (libgphoto2): Update to 2.5.22.

5 years agognu: re2: Update to 2019-01-01.
Marius Bakke [Wed, 2 Jan 2019 23:57:52 +0000 (00:57 +0100)]
gnu: re2: Update to 2019-01-01.

* gnu/packages/regex.scm (re2): Update to 2019-01-01.

5 years agognu: libsecret: Update to 0.18.7.
Marius Bakke [Wed, 2 Jan 2019 23:54:35 +0000 (00:54 +0100)]
gnu: libsecret: Update to 0.18.7.

* gnu/packages/gnome.scm (libsecret): Update to 0.18.7.
[native-inputs]: Remove INTLTOOL.  Add GETTEXT-MINIMAL.

5 years agognu: fluidsynth: Update to 2.0.3.
Marius Bakke [Wed, 2 Jan 2019 23:51:34 +0000 (00:51 +0100)]
gnu: fluidsynth: Update to 2.0.3.

* gnu/packages/audio.scm (fluidsynth): Update to 2.0.3.

5 years agognu: rofi: Update to 1.5.2.
Marius Bakke [Wed, 2 Jan 2019 23:47:28 +0000 (00:47 +0100)]
gnu: rofi: Update to 1.5.2.

* gnu/packages/xdisorg.scm (rofi): Update to 1.5.2.

5 years agognu: xscreensaver: Update to 5.42.
Marius Bakke [Wed, 2 Jan 2019 23:43:04 +0000 (00:43 +0100)]
gnu: xscreensaver: Update to 5.42.

* gnu/packages/xdisorg.scm (xscreensaver): Update to 5.42.
[arguments]: Add "CFLAGS=-std=c99" to #:make-flags.

5 years agognu: libcmis: Update to 0.5.2.
Marius Bakke [Wed, 2 Jan 2019 23:38:28 +0000 (00:38 +0100)]
gnu: libcmis: Update to 0.5.2.

* gnu/packages/libreoffice.scm (libcmis): Update to 0.5.2.
[source](uri): Use XZ-compressed tarball.
[arguments]: Remove #:phases.  Don't pass "--disable-werror" in #:configure-flags.

5 years agognu: http-parser: Update to 2.9.0.
Marius Bakke [Wed, 2 Jan 2019 22:34:06 +0000 (23:34 +0100)]
gnu: http-parser: Update to 2.9.0.

* gnu/packages/web.scm (http-parser): Update to 2.9.0.

5 years agognu: http-parser: Download from git.
Marius Bakke [Wed, 2 Jan 2019 22:33:12 +0000 (23:33 +0100)]
gnu: http-parser: Download from git.

* gnu/packages/web.scm (http-parser)[source]: Change to GIT-FETCH.

5 years agognu: libetonyek: Adjust inputs.
Marius Bakke [Wed, 2 Jan 2019 22:22:58 +0000 (23:22 +0100)]
gnu: libetonyek: Adjust inputs.

* gnu/packages/libreoffice.scm (libetonyek)[native-inputs]: Remove LIBLANGTAG.
Move GLM and MDDS to ...
[inputs]: ... here.
[propagated-inputs]: Add LIBLANGTAG and ZLIB.

5 years agognu: libetonyek: Update to 0.1.9.
Marius Bakke [Wed, 2 Jan 2019 22:12:16 +0000 (23:12 +0100)]
gnu: libetonyek: Update to 0.1.9.

* gnu/packages/libreoffice.scm (libetonyek): Update to 0.1.9.
[arguments]: Remove #:phases.

5 years agognu: libcdr: Update to 0.1.5.
Marius Bakke [Wed, 2 Jan 2019 22:11:36 +0000 (23:11 +0100)]
gnu: libcdr: Update to 0.1.5.

* gnu/packages/libreoffice.scm (libcdr): Update to 0.1.5.
[source](uri): Download over HTTPS.
[arguments]: Remove.

5 years agognu: tintin++: Update to 2.01.5.
Kei Kebreau [Sat, 12 Jan 2019 23:37:38 +0000 (18:37 -0500)]
gnu: tintin++: Update to 2.01.5.

* gnu/packages/games.scm (tintin++): Update to 2.01.5.

5 years agognu: r-ruvseq: Update to 1.16.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:08:15 +0000 (23:08 +0100)]
gnu: r-ruvseq: Update to 1.16.1.

* gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.16.1.

5 years agognu: r-inspect: Update to 1.12.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:07:38 +0000 (23:07 +0100)]
gnu: r-inspect: Update to 1.12.1.

* gnu/packages/bioconductor.scm (r-inspect): Update to 1.12.1.
[propagated-inputs]: Add r-deseq2, r-plgem, r-shiny, r-summarizedexperiment,
and r-txdb-mmusculus-ucsc-mm9-knowngene.

5 years agognu: Add r-txdb-mmusculus-ucsc-mm9-knowngene.
Ricardo Wurmus [Sat, 12 Jan 2019 22:23:20 +0000 (23:23 +0100)]
gnu: Add r-txdb-mmusculus-ucsc-mm9-knowngene.

* gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm9-knowngene): New
variable.

5 years agognu: Add r-plgem.
Ricardo Wurmus [Sat, 12 Jan 2019 22:07:29 +0000 (23:07 +0100)]
gnu: Add r-plgem.

* gnu/packages/bioconductor.scm (r-plgem): New variable.

5 years agognu: r-rots: Update to 1.10.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:07:18 +0000 (23:07 +0100)]
gnu: r-rots: Update to 1.10.1.

* gnu/packages/bioconductor.scm (r-rots): Update to 1.10.1.

5 years agognu: r-glimma: Update to 1.10.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:07:10 +0000 (23:07 +0100)]
gnu: r-glimma: Update to 1.10.1.

* gnu/packages/bioconductor.scm (r-glimma): Update to 1.10.1.

5 years agognu: r-goseq: Update to 1.34.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:07:01 +0000 (23:07 +0100)]
gnu: r-goseq: Update to 1.34.1.

* gnu/packages/bioconductor.scm (r-goseq): Update to 1.34.1.

5 years agognu: r-chippeakanno: Update to 3.16.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:06:52 +0000 (23:06 +0100)]
gnu: r-chippeakanno: Update to 3.16.1.

* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.16.1.

5 years agognu: r-rtracklayer: Update to 1.42.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:06:31 +0000 (23:06 +0100)]
gnu: r-rtracklayer: Update to 1.42.1.

* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.1.

5 years agognu: r-scater: Update to 1.10.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:06:18 +0000 (23:06 +0100)]
gnu: r-scater: Update to 1.10.1.

* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.1.

5 years agognu: r-singlecellexperiment: Update to 1.4.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:06:08 +0000 (23:06 +0100)]
gnu: r-singlecellexperiment: Update to 1.4.1.

* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.1.

5 years agognu: r-rhdf5lib: Update to 1.4.2.
Ricardo Wurmus [Sat, 12 Jan 2019 22:05:57 +0000 (23:05 +0100)]
gnu: r-rhdf5lib: Update to 1.4.2.

* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.2.

5 years agognu: r-hdf5array: Update to 1.10.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:05:43 +0000 (23:05 +0100)]
gnu: r-hdf5array: Update to 1.10.1.

* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.1.

5 years agognu: r-qvalue: Update to 2.14.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:05:33 +0000 (23:05 +0100)]
gnu: r-qvalue: Update to 2.14.1.

* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.1.

5 years agognu: r-gviz: Update to 1.26.4.
Ricardo Wurmus [Sat, 12 Jan 2019 22:05:23 +0000 (23:05 +0100)]
gnu: r-gviz: Update to 1.26.4.

* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.4.

5 years agognu: r-biovizbase: Update to 1.30.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:05:14 +0000 (23:05 +0100)]
gnu: r-biovizbase: Update to 1.30.1.

* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.1.

5 years agognu: r-ensembldb: Update to 2.6.3.
Ricardo Wurmus [Sat, 12 Jan 2019 22:04:53 +0000 (23:04 +0100)]
gnu: r-ensembldb: Update to 2.6.3.

* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.3.

5 years agognu: r-dirichletmultinomial: Update to 1.24.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:04:43 +0000 (23:04 +0100)]
gnu: r-dirichletmultinomial: Update to 1.24.1.

* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.1.

5 years agognu: r-gage: Update to 2.32.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:04:25 +0000 (23:04 +0100)]
gnu: r-gage: Update to 2.32.1.

* gnu/packages/bioinformatics.scm (r-gage): Update to 2.32.1.

5 years agognu: r-annotationhub: Update to 2.14.2.
Ricardo Wurmus [Sat, 12 Jan 2019 22:04:14 +0000 (23:04 +0100)]
gnu: r-annotationhub: Update to 2.14.2.

* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.2.

5 years agognu: r-edaseq: Update to 2.16.3.
Ricardo Wurmus [Sat, 12 Jan 2019 22:03:53 +0000 (23:03 +0100)]
gnu: r-edaseq: Update to 2.16.3.

* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.16.3.
[propagated-inputs]: Add r-biocmanager.

5 years agognu: r-deseq: Update to 1.34.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:03:34 +0000 (23:03 +0100)]
gnu: r-deseq: Update to 1.34.1.

* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.34.1.

5 years agognu: r-msnid: Update to 1.16.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:03:24 +0000 (23:03 +0100)]
gnu: r-msnid: Update to 1.16.1.

* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.16.1.

5 years agognu: r-msnbase: Update to 2.8.3.
Ricardo Wurmus [Sat, 12 Jan 2019 22:03:12 +0000 (23:03 +0100)]
gnu: r-msnbase: Update to 2.8.3.

* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.3.

5 years agognu: r-mzid: Update to 1.20.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:03:04 +0000 (23:03 +0100)]
gnu: r-mzid: Update to 1.20.1.

* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.20.1.

5 years agognu: r-mzr: Update to 2.16.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:02:54 +0000 (23:02 +0100)]
gnu: r-mzr: Update to 2.16.1.

* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.1.

5 years agognu: r-sva: Update to 3.30.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:02:45 +0000 (23:02 +0100)]
gnu: r-sva: Update to 3.30.1.

* gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.1.

5 years agognu: r-methylkit: Update to 1.8.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:02:34 +0000 (23:02 +0100)]
gnu: r-methylkit: Update to 1.8.1.

* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.1.

5 years agognu: r-copywriter: Update to 2.14.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:02:23 +0000 (23:02 +0100)]
gnu: r-copywriter: Update to 2.14.1.

* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.1.

5 years agognu: r-rhdf5: Update to 2.26.2.
Ricardo Wurmus [Sat, 12 Jan 2019 22:02:13 +0000 (23:02 +0100)]
gnu: r-rhdf5: Update to 2.26.2.

* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.2.

5 years agognu: r-tximport: Update to 1.10.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:02:03 +0000 (23:02 +0100)]
gnu: r-tximport: Update to 1.10.1.

* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.1.

5 years agognu: r-genomicalignments: Update to 1.18.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:01:49 +0000 (23:01 +0100)]
gnu: r-genomicalignments: Update to 1.18.1.

* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.1.

5 years agognu: r-biostrings: Update to 2.50.2.
Ricardo Wurmus [Sat, 12 Jan 2019 22:01:39 +0000 (23:01 +0100)]
gnu: r-biostrings: Update to 2.50.2.

* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.2.

5 years agognu: r-biocparallel: Update to 1.16.5.
Ricardo Wurmus [Sat, 12 Jan 2019 22:01:29 +0000 (23:01 +0100)]
gnu: r-biocparallel: Update to 1.16.5.

* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.5.

5 years agognu: r-limma: Update to 3.38.3.
Ricardo Wurmus [Sat, 12 Jan 2019 22:01:19 +0000 (23:01 +0100)]
gnu: r-limma: Update to 3.38.3.

* gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.3.

5 years agognu: r-variantannotation: Update to 1.28.8.
Ricardo Wurmus [Sat, 12 Jan 2019 22:01:07 +0000 (23:01 +0100)]
gnu: r-variantannotation: Update to 1.28.8.

* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.8.

5 years agognu: r-edger: Update to 3.24.3.
Ricardo Wurmus [Sat, 12 Jan 2019 22:00:58 +0000 (23:00 +0100)]
gnu: r-edger: Update to 3.24.3.

* gnu/packages/bioinformatics.scm (r-edger): Update to 3.24.3.

5 years agognu: r-biocviews: Update to 1.50.10.
Ricardo Wurmus [Sat, 12 Jan 2019 22:00:47 +0000 (23:00 +0100)]
gnu: r-biocviews: Update to 1.50.10.

* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.10.

5 years agognu: r-systempiper: Update to 1.16.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:00:37 +0000 (23:00 +0100)]
gnu: r-systempiper: Update to 1.16.1.

* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.16.1.

5 years agognu: r-rbgl: Update to 1.58.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:00:20 +0000 (23:00 +0100)]
gnu: r-rbgl: Update to 1.58.1.

* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.1.

5 years agognu: r-dexseq: Update to 1.28.1.
Ricardo Wurmus [Sat, 12 Jan 2019 22:00:10 +0000 (23:00 +0100)]
gnu: r-dexseq: Update to 1.28.1.

* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.1.

5 years agognu: r-deseq2: Update to 1.22.2.
Ricardo Wurmus [Sat, 12 Jan 2019 22:00:01 +0000 (23:00 +0100)]
gnu: r-deseq2: Update to 1.22.2.

* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.2.

5 years agognu: r-scran: Update to 1.10.2.
Ricardo Wurmus [Sat, 12 Jan 2019 21:59:36 +0000 (22:59 +0100)]
gnu: r-scran: Update to 1.10.2.

* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.2.