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31401 Commits

Author SHA1 Message Date
Ricardo Wurmus fab455840e
gnu: libtoxcore: Remove custom bootstrap phase. 
* gnu/packages/messaging.scm (libtoxcore)[arguments]: Remove autoconf phase.
 2018-11-11 11:33:39 +01:00
Ricardo Wurmus 867d9de690
gnu: openocd: Use INVOKE. 
* gnu/packages/embedded.scm (openocd)[arguments]: Use INVOKE and return #T
unconditionally.
 2018-11-11 11:32:12 +01:00
Ricardo Wurmus 4cd6ab1b1f
gnu: libjaylink: Remove custom bootstrap phase. 
* gnu/packages/embedded.scm (libjaylink)[arguments]: Remove.
 2018-11-11 11:23:39 +01:00
Ricardo Wurmus a69cc70dea
gnu: lrdf: Replace bootstrap phase. 
* gnu/packages/rdf.scm (lrdf)[arguments]: Remove autoreconf phase; replace
bootstrap phase instead.
 2018-11-11 11:22:22 +01:00
Ricardo Wurmus d212ed2f00
gnu: lrdf: Fetch sources from git. 
* gnu/packages/rdf.scm (lrdf)[source]: Fetch from git.
 2018-11-11 11:21:55 +01:00
Ricardo Wurmus 2cabd29323
gnu: guildhall: Remove custom bootstrap phase. 
* gnu/packages/guile.scm (guildhall)[arguments]: Remove autogen phase.
 2018-11-11 10:38:00 +01:00
Ricardo Wurmus 34da5c394b
gnu: guile-dsv: Remove custom bootstrap phase. 
* gnu/packages/guile.scm (guile-dsv)[arguments]: Remove autoreconf phase.
 2018-11-11 10:22:45 +01:00
Ricardo Wurmus 5ad728e04c
gnu: opendht: Remove custom bootstrap phase. 
* gnu/packages/crypto.scm (opendht)[arguments]: Remove autoconf phase.
 2018-11-11 10:21:02 +01:00
Ricardo Wurmus 974056c05e
gnu: opendht: Fetch sources from git. 
* gnu/packages/crypto.scm (opendht)[source]: Fetch from git.
 2018-11-11 10:20:36 +01:00
Ricardo Wurmus a49b5322c5
gnu: lxsession: Remove custom bootstrap phase. 
* gnu/packages/lxde.scm (lxsession)[arguments]: Remove autoreconf phase and
end rm-stamp phase with #T.
 2018-11-11 10:16:43 +01:00
Ricardo Wurmus f1f1cebdd3
gnu: mdbtools: Fetch sources from git. 
* gnu/packages/databases.scm (mdbtools)[source]: Fetch from git.
 2018-11-11 10:09:54 +01:00
Ricardo Wurmus f626b71923
gnu: mdbtools: Remove custom bootstrap phase. 
* gnu/packages/databases.scm (mdbtools)[arguments]: Remove.
 2018-11-11 10:05:56 +01:00
Ricardo Wurmus 1410e178bb
gnu: pianobar: Fetch sources from git. 
* gnu/packages/music.scm (pianobar)[source]: Fetch from git.
 2018-11-11 10:03:06 +01:00
Ricardo Wurmus 487e3f5a80
gnu: ibus-rime: Fetch sources from git. 
* gnu/packages/ibus.scm (ibus-rime)[source]: Fetch from git.
 2018-11-11 10:03:06 +01:00
Ricardo Wurmus 863742856c
gnu: librime: Fetch sources from git. 
* gnu/packages/ibus.scm (librime)[source]: Fetch from git.
 2018-11-11 10:03:06 +01:00
Efraim Flashner cab70d4c2a
gnu: perl-autovivification: Update to 0.18. 
* gnu/packages/perl.scm (perl-autovivification): Update to 0.18.
 2018-11-11 08:21:59 +02:00
Mark H Weaver 717d29e25b
gnu: icecat: Add more fixes from mozilla-esr60. 
* gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes
from the upstream mozilla-esr60 source repository.
 2018-11-10 20:29:19 -05:00
Mark H Weaver 3b14494616
gnu: icecat: Update to 60.3.0-gnu1. 
* gnu/packages/gnuzilla.scm (icecat): Update to 60.3.0-gnu1.
[source]: Switch back to the normal source URI.  Remove patches that
are no longer applicable.
* gnu/packages/patches/icecat-CVE-2018-12383.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-11-10 20:28:32 -05:00
Mark H Weaver e22842f5ca
gnu: linux-libre@4.14: Update to 4.14.80. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.80.
(%linux-libre-4.14-hash): Update hash.
 2018-11-10 20:23:57 -05:00
Mark H Weaver 62168a5558
gnu: linux-libre@4.9: Update to 4.9.136. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.136.
 2018-11-10 20:23:15 -05:00
Mark H Weaver fc43d6d4d9
gnu: linux-libre@4.4: Update to 4.4.163. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.163.
 2018-11-10 20:22:30 -05:00
Ricardo Wurmus 4cbbb16045
gnu: nxbelld: Remove custom bootstrap phase. 
* gnu/packages/xdisorg.scm (nxbelld)[arguments]: Remove autoreconf phase.
 2018-11-10 23:42:54 +01:00
Ricardo Wurmus f116e1fcae
gnu: wmclock: Remove custom bootstrap phase. 
* gnu/packages/gnustep.scm (wmclock)[arguments]: Remove.
 2018-11-10 23:42:54 +01:00
Ricardo Wurmus e17f867c62
gnu: wmbattery: Remove custom bootstrap phase. 
* gnu/packages/gnustep.scm (wmbattery)[arguments]: Remove autoconf phase.
 2018-11-10 23:42:54 +01:00
Ricardo Wurmus 7db147ec45
gnu: rtmidi: Remove custom bootstrap phase. 
* gnu/packages/audio.scm (rtmidi)[arguments]: Remove autoconf phase.
 2018-11-10 23:42:54 +01:00
Ricardo Wurmus cdb4048d72
gnu: portaudio: Remove custom bootstrap phase. 
* gnu/packages/audio.scm (portaudio)[arguments]: Remove autoreconf phase.
 2018-11-10 23:42:54 +01:00
Pierre Langlois 78e3d554d1
gnu: Add emacs-ivy-rich. 
* gnu/packages/emacs.scm (emacs-ivy-rich): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-10 23:33:47 +01:00
Meiyo Peng d5b23d2b7d
gnu: Add ibus-rime. 
* gnu/packages/ibus.scm (ibus-rime): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-10 23:33:47 +01:00
Meiyo Peng 1329f095bb
gnu: Add rime-data. 
* gnu/packages/ibus.scm (rime-data): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-10 23:33:47 +01:00
Meiyo Peng 78209a165b
gnu: Add librime. 
* gnu/packages/ibus.scm (librime): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-10 23:33:47 +01:00
Meiyo Peng 2f968763c3
gnu: ibus: Indent code properly. 
* gnu/packages/ibus.scm (ibus, ibus-libpinyin): Indent code properly.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-10 23:33:47 +01:00
Meiyo Peng 1a0363cf07
gnu: Add opencc. 
* gnu/packages/textutils.scm (opencc): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-10 23:33:46 +01:00
Meiyo Peng 9d466489cd
gnu: Add marisa. 
* gnu/packages/datastructures.scm (marisa): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-10 23:33:46 +01:00
Ludovic Courtès 30288ae57e
gnu: mdadm: Update to 4.1. 
* gnu/packages/linux.scm (mdadm): Update to 4.1.
 2018-11-10 23:33:46 +01:00
Ricardo Wurmus 37ebc19cfb
gnu: msgpack: Remove custom bootstrap phase. 
* gnu/packages/serialization.scm (msgpack)[arguments]: Remove.
 2018-11-10 23:30:52 +01:00
Ricardo Wurmus bed4eb373e
gnu: gxtuner: Fetch sources from git. 
* gnu/packages/music.scm (gxtuner)[source]: Fetch from git.
 2018-11-10 23:29:26 +01:00
Ricardo Wurmus a7fde1a86d
gnu: cava: Fetch sources from git. 
* gnu/packages/audio.scm (cava)[source]: Fetch from git.
 2018-11-10 23:29:26 +01:00
Ricardo Wurmus c2a2d364df
gnu: cli-visualizer: Fetch sources from git. 
* gnu/packages/audio.scm (cli-visualizer)[source]: Fetch from git.
 2018-11-10 23:29:26 +01:00
Ricardo Wurmus b249ff5d37
gnu: dcadec: Fetch sources from git. 
* gnu/packages/audio.scm (dcadec)[source]: Fetch from git.
 2018-11-10 23:29:26 +01:00
Ricardo Wurmus 4289a306b7
gnu: cuetools: Fetch sources from git. 
* gnu/packages/audio.scm (cuetools)[source]: Fetch from git.
 2018-11-10 23:29:26 +01:00
Ricardo Wurmus 8e5995e397
gnu: xjackfreak: Fetch sources from git. 
* gnu/packages/audio.scm (xjackfreak)[source]: Fetch from git.
 2018-11-10 23:29:26 +01:00
Ricardo Wurmus 458baefb40
gnu: rsound: Fetch sources from git. 
* gnu/packages/audio.scm (rsound)[source]: Fetch from git.
 2018-11-10 23:29:26 +01:00
Ricardo Wurmus eca7729301
gnu: rtmidi: Fetch sources from git. 
* gnu/packages/audio.scm (rtmidi)[source]: Fetch from git.
 2018-11-10 23:29:26 +01:00
Ricardo Wurmus 0b8db03504
gnu: infamous-plugins: Fetch sources from git. 
* gnu/packages/audio.scm (infamous-plugins)[source]: Fetch from git.
 2018-11-10 23:29:26 +01:00
Ricardo Wurmus 2ae2395422
gnu: swh-plugins-lv2: Fetch sources from git. 
* gnu/packages/audio.scm (swh-plugins-lv2)[source]: Fetch from git.
 2018-11-10 23:29:26 +01:00
Ricardo Wurmus 917dc89672
gnu: csound: Fetch sources from git. 
* gnu/packages/audio.scm (csound)[source]: Fetch from git.
 2018-11-10 23:29:26 +01:00
Ricardo Wurmus b255365cd1
gnu: lvtk: Fetch sources from git. 
* gnu/packages/audio.scm (lvtk)[source]: Fetch from git.
 2018-11-10 23:29:26 +01:00
Ricardo Wurmus 78eff85770
gnu: ams-lv2: Fetch sources from git. 
* gnu/packages/music.scm (ams-lv2)[source]: Fetch from git.
 2018-11-10 23:29:25 +01:00
Ricardo Wurmus 57906fad59
gnu: portmidi-for-extempore: Fetch sources from git. 
* gnu/packages/music.scm (portmidi-for-extempore)[source]: Fetch from git.
 2018-11-10 23:29:25 +01:00
Ricardo Wurmus ca364e7a3c
gnu: jalv-select: Fetch sources from git. 
* gnu/packages/music.scm (jalv-select)[source]: Fetch from git.
[arguments]: Add phase make-manpages-writable.
 2018-11-10 23:29:25 +01:00
Nicolas Goaziou 79b8341292
gnu: emacs-circe: Update to 2.10. 
* gnu/packages/emacs.scm (emacs-circe): Update to 2.10.
 2018-11-10 23:27:05 +01:00
Ricardo Wurmus 74c903edab
Add missing license import. 
* gnu/packages/mail.scm: Import agpl3+.
 2018-11-10 22:37:07 +01:00
Ricardo Wurmus e3a4703174
gnu: Add mumi. 
* gnu/packages/mail.scm (mumi): New variable.
 2018-11-10 22:36:13 +01:00
Ricardo Wurmus 2d900b0464
gnu: Add guile-debbugs-next. 
* gnu/packages/guile.scm (guile-debbugs-next): New variable.
 2018-11-10 22:36:13 +01:00
Ricardo Wurmus 7453785624
gnu: Add guile-email. 
* gnu/packages/guile.scm (guile-email): New variable.
 2018-11-10 22:36:13 +01:00
Ricardo Wurmus 95906eee18
gnu: guile-ics: Remove custom bootstrap phase. 
* gnu/packages/guile.scm (guile-ics)[arguments]: Remove.
 2018-11-10 22:36:13 +01:00
Efraim Flashner e8b9aaf0b1
mtd-utils: Update to 2.0.2. 
* gnu/packages/linux.scm (mtd-utils): Update to 2.0.2.
[arguments]: Remove 'test-target, 'make-flags. Re-enable 'configure
phase. Add 'configure-flag for the unit-tests.
[native-inputs]: Add cmocka, pkg-config.
 2018-11-10 20:54:34 +02:00
Clément Lassieur a7553a7360
services: dovecot: Set correct default value for the "auth" service. 
* gnu/services/mail.scm (dovecot-configuration): Set 'service-count' to 0 for
the "auth" service.
 2018-11-10 19:12:21 +01:00
Clément Lassieur be8dd4a5fe
services: dovecot: Allow to set 'process-limit'. 
* doc/guix.texi (Mail Services): Update accordingly.
* gnu/services/mail.scm (service-configuration)[process-limit]: New field.
(dovecot-configuration)[services]: Set 'process-limit' to its correct default
value.
 2018-11-10 19:12:18 +01:00
Clément Lassieur 8d9bb4b4d0
services: dovecot: Allow to set 'client-limit'. 
* doc/guix.texi (Mail Services): Update accordingly.
* gnu/services/mail.scm (service-configuration)[client-limit]: New field.
(dovecot-configuration)[services]: Set 'client-limit' to its correct default
value.
 2018-11-10 19:12:14 +01:00
Efraim Flashner 005ec8d09c
gnu: f2fs-tools: Update to 1.11.0. 
* gnu/packages/linux.scm (f2fs-tools): Update to 1.11.0.
 2018-11-10 19:29:05 +02:00
Ricardo Wurmus 03a415365a
gnu: r-ensembldb: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.1.
 2018-11-09 19:41:54 +01:00
Ricardo Wurmus 88514b9124
gnu: r-biostrings: Update to 2.50.1. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.1.
 2018-11-09 19:41:53 +01:00
Ricardo Wurmus 77bea84ba1
gnu: r-biocviews: Update to 1.50.5. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.5.
 2018-11-09 19:41:53 +01:00
Ricardo Wurmus 317f5a5a91
gnu: r-sn: Update to 1.5-3. 
* gnu/packages/statistics.scm (r-sn): Update to 1.5-3.
 2018-11-09 19:41:53 +01:00
Ricardo Wurmus 5174f06b0c
gnu: r-rgooglemaps: Update to 1.4.3. 
* gnu/packages/geo.scm (r-rgooglemaps): Update to 1.4.3.
 2018-11-09 19:41:53 +01:00
Ricardo Wurmus 492ec49890
gnu: r-tmb: Update to 1.7.15. 
* gnu/packages/cran.scm (r-tmb): Update to 1.7.15.
 2018-11-09 19:41:53 +01:00
Ricardo Wurmus fccb24501a
gnu: r-jomo: Update to 2.6-5. 
* gnu/packages/cran.scm (r-jomo): Update to 2.6-5.
[propagated-inputs]: Add r-mass.
 2018-11-09 19:41:50 +01:00
Ricardo Wurmus f87a18e660
gnu: r-rcpp: Update to 1.0.0. 
* gnu/packages/cran.scm (r-rcpp): Update to 1.0.0.
[native-inputs]: Add r-knitr.
 2018-11-09 19:01:42 +01:00
Ricardo Wurmus 06bc7b82f7
gnu: Add r-arm. 
* gnu/packages/cran.scm (r-arm): New variable.
 2018-11-09 18:04:37 +01:00
Ricardo Wurmus cf383cf08f
gnu: Add r-feature. 
* gnu/packages/cran.scm (r-feature): New variable.
 2018-11-09 18:04:37 +01:00
Ricardo Wurmus da256afb9e
gnu: Add r-ks. 
* gnu/packages/cran.scm (r-ks): New variable.
 2018-11-09 18:04:37 +01:00
Ricardo Wurmus 4106e6ad87
gnu: Add r-misc3d. 
* gnu/packages/cran.scm (r-misc3d): New variable.
 2018-11-09 18:04:36 +01:00
Ricardo Wurmus 213e72a18d
gnu: Add r-multicool. 
* gnu/packages/cran.scm (r-multicool): New variable.
 2018-11-09 18:04:36 +01:00
Ricardo Wurmus f338e4807f
gnu: Add r-rgl. 
* gnu/packages/cran.scm (r-rgl): New variable.
 2018-11-09 18:04:36 +01:00
Ricardo Wurmus a961ae469c
gnu: Add r-destiny. 
* gnu/packages/bioconductor.scm (r-destiny): New variable.
 2018-11-09 17:15:31 +01:00
Ricardo Wurmus ff939ef4d5
gnu: Add r-h5. 
* gnu/packages/cran.scm (r-h5): New variable.
 2018-11-09 16:57:13 +01:00
Ricardo Wurmus 3a4c6288c8
gnu: Add r-aggregation. 
* gnu/packages/cran.scm (r-aggregation): New variable.
 2018-11-09 16:57:13 +01:00
Ricardo Wurmus 8a587c89af
gnu: Add r-savr. 
* gnu/packages/bioconductor.scm (r-savr): New variable.
 2018-11-09 16:45:21 +01:00
Ricardo Wurmus cee9ab244f
gnu: r-with-tests: Update to 3.5.1. 
* gnu/packages/statistics.scm (r-with-tests): Update to 3.5.1.
 2018-11-09 14:07:26 +01:00
Ricardo Wurmus 2eaaadb4d6
gnu: r-with-tests: Use INVOKE. 
* gnu/packages/statistics.scm (r-with-tests)[arguments]: Use INVOKE and
return #T unconditionally.
 2018-11-09 14:07:22 +01:00
Pierre Neidhardt ddd925f608
gnu: Add emacs-gtk-look. 
* gnu/packages/emacs.scm (emacs-gtk-look): New variable.
 2018-11-09 11:55:08 +01:00
Pierre Neidhardt 2cce23bfb8
gnu: Add xmlrpc-c. 
* gnu/packages/xml.scm (xmlrpc-c): New variable.
 2018-11-09 11:55:08 +01:00
Mathieu Othacehe 97f33b05ec
gnu: guile-newt: Update to revision 1. 
* gnu/packages/guile.scm (guile-newt): Update to revision 1.
 2018-11-09 19:39:14 +09:00
Ricardo Wurmus 1b12b572a5
gnu: powertabeditor: Fetch sources from git. 
* gnu/packages/music.scm (powertabeditor)[source]: Fetch from git.
 2018-11-09 08:37:53 +01:00
Ricardo Wurmus b1b82aed5d
gnu: powertabeditor: Use INVOKE. 
* gnu/packages/music.scm (powertabeditor)[arguments]: Use INVOKE and return #T
unconditionally.
 2018-11-09 08:37:53 +01:00
Kei Kebreau e4b62e229e
gnu: wxmaxima: Update to 18.10.1. 
* gnu/packages/maths.scm (wxmaxima): Update to 18.10.1.
[source]: Update URL and remove patch.
* gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch: Remove
file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
 2018-11-09 01:09:06 -05:00
Leo Famulari 41d2b7f50b
gnu: PostgreSQL 9: Update to 9.6.11 [fixes CVE-2018-16850]. 
* gnu/packages/databases.scm (postgresql-9.6): Update to 9.6.11.
 2018-11-08 13:42:56 -05:00
Pierre Neidhardt 2705780f3f
gnu: Add emacs-clang-format. 
* gnu/packages/emacs.scm (emacs-clang-format): New variable.
 2018-11-08 13:08:26 +01:00
Efraim Flashner e3407254d5
gnu: kodi: Update to 18.0b5. 
* gnu/packages/kodi.scm (kodi): Update to 18.0b5.
[source]: Update snippet.
[inputs]: Add flatbuffers, fstrcmp.
(crossguid): Update to commit fef89a4174a7bf8cd99fa9154864ce9e8e3bf989.
(libdvdnav/kodi, libdvdread/kodi): Update to 6.0.0-Leia-Alpha-3.
(libdvdcss/kodi): Update to 1.4.2-Leia-Beta-5.
 2018-11-08 12:01:24 +02:00
Efraim Flashner 988b78ba28
gnu: Add fstrcmp. 
* gnu/packages/kodi.scm (fstrcmp): New variable.
 2018-11-08 12:01:20 +02:00
Stefan Stefanović ec86863113
services: elogind: Fix spelling errors of left value fields in elogind config file. 
* gnu/services/desktop.scm (elogind-configuration-file)[ini-file]:
    Fix spelling of left value fields:
    InhibitDelayMaxSecs, HoldoffTimeoutSecs, IdleActionSeconds, RemoveIpc.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-08 10:24:35 +01:00
Luther Thompson 9870b9f7f8
gnu: python-ilinkedlist: Update to 0.3.1. 
* gnu/packages/python.scm (python-ilinkedlist): Update to 0.3.1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-08 10:24:26 +01:00
Vagrant Cascadian 195e081b43
gnu: Add python-pyelftools. 
* gnu/packages/python.scm (python-pyelftools):
  New public variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-08 10:24:22 +01:00
Ricardo Wurmus 69cb939ee7
gnu: libmusicbrainz: Use INVOKE. 
* gnu/packages/music.scm (libmusicbrainz)[arguments]: Use INVOKE and return #T
unconditionally.
 2018-11-08 10:17:15 +01:00
Ricardo Wurmus 9ab90ead36
gnu: pd: Remove custom autoconf phase. 
* gnu/packages/music.scm (pd)[arguments]: Remove custom autoconf phase.
 2018-11-08 10:14:08 +01:00
Ricardo Wurmus 4e82946888
gnu: cmus: Fetch sources from git. 
* gnu/packages/music.scm (cmus)[source]: Fetch from git.
 2018-11-08 10:10:06 +01:00
Ricardo Wurmus ec618c2005
gnu: cmus: Use INVOKE. 
* gnu/packages/music.scm (cmus)[arguments]: Use INVOKE and return #T
unconditionally.
 2018-11-08 10:09:32 +01:00
Ricardo Wurmus 9c30cba431
gnu: pcc: Use INVOKE. 
* gnu/packages/c.scm (pcc)[arguments]: Use INVOKE and return #T
unconditionally.
 2018-11-08 10:08:09 +01:00
Ricardo Wurmus a1e83a9856
gnu: pplacer-scripts: Use INVOKE. 
* gnu/packages/bioinformatics.scm (pplacer-scripts)[arguments]: Use INVOKE and
return #T unconditionally.
 2018-11-08 10:06:35 +01:00
Ricardo Wurmus ce49fdcce9
gnu: roary: Use INVOKE. 
* gnu/packages/bioinformatics.scm (roary)[arguments]: Use INVOKE and return #T
unconditionally.
 2018-11-08 09:58:05 +01:00
Ricardo Wurmus a9542937c8
gnu: seek: Use INVOKE. 
* gnu/packages/bioinformatics.scm (seek)[arguments]: Use INVOKE and return #T
unconditionally; patch "gen_tools_am" shebang in "bootstrap" phase.
 2018-11-08 09:54:22 +01:00
Ricardo Wurmus 9f527c9199
gnu: sailfish: Use INVOKE. 
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use INVOKE instead of
SYSTEM*.
 2018-11-08 09:52:46 +01:00
Ricardo Wurmus 86c6928ea3
gnu: vsearch: Update to 2.9.1. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.9.1.
* gnu/packages/patches/vsearch-unbundle-cityhash.patch: Update.
 2018-11-08 09:46:42 +01:00
Ricardo Wurmus 15c9609482
gnu: sra-tools: Update to 2.9.3. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.3.
[arguments]: Remove build phase patch-away-glibc-conflict.
 2018-11-08 09:46:05 +01:00
Ricardo Wurmus b17333414f
gnu: plink-ng: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (plink-ng)[source]: Fetch from git.
 2018-11-08 09:30:59 +01:00
Ricardo Wurmus 87408854ec
gnu: ncbi-vdb: Update to 2.9.3. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.3.
 2018-11-08 09:30:16 +01:00
Ricardo Wurmus 8d3eaa9262
gnu: ngs-sdk: Update to 2.9.3. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.3.
 2018-11-08 09:29:58 +01:00
Ricardo Wurmus 3da3cedf76
gnu: ngs-sdk: Use INVOKE. 
* gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Use INVOKE and
return #T unconditionally.
 2018-11-08 09:15:05 +01:00
Ricardo Wurmus e78e54d029
gnu: emboss: Use INVOKE. 
* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use INVOKE and
return #T unconditionally.
 2018-11-08 09:14:09 +01:00
Ricardo Wurmus 8b685c4720
gnu: taxtastic: Use INVOKE. 
* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Use INVOKE and
return #T unconditionally.
 2018-11-08 09:13:35 +01:00
Ricardo Wurmus 2e2d88539c
gnu: sra-tools: Use INVOKE. 
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use INVOKE and
return #T unconditionally.
 2018-11-08 09:12:43 +01:00
Ricardo Wurmus 179416467f
gnu: muscle: Use INVOKE. 
* gnu/packages/bioinformatics.scm (muscle)[arguments]: Use INVOKE and
return #T unconditionally.
 2018-11-08 09:11:38 +01:00
Ricardo Wurmus 0881d62f25
gnu: newick-utils: Remove custom autoconf phase. 
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove.
 2018-11-08 09:10:58 +01:00
Ricardo Wurmus e35dce0170
gnu: mash: Remove custom autoconf phase. 
* gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase.
 2018-11-08 09:10:20 +01:00
Ricardo Wurmus 31c41a8cfe
gnu: vsearch: Remove custom autogen phase. 
* gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove.
 2018-11-08 09:04:34 +01:00
Ricardo Wurmus c527d36f02
gnu: java-picard-1.113: Use INVOKE. 
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE
and return #T unconditionally.
 2018-11-08 09:02:34 +01:00
Ricardo Wurmus e438c96558
gnu: fraggenescan: Use INVOKE. 
* gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in
build phases and return #T unconditionally.
 2018-11-08 08:58:46 +01:00
Ricardo Wurmus c098c49b3e
gnu: sailfish: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
 2018-11-08 08:53:54 +01:00
Ricardo Wurmus 4031e7f1ec
gnu: ngs-sdk: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (ngs-sdk)[source]: Fetch from git.
 2018-11-08 08:53:53 +01:00
Ricardo Wurmus 6a7d9ee39f
gnu: ncbi-vdb: Use INVOKE and end phases on #T. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use INVOKE and
unconditionally end phases with #T.
 2018-11-08 08:53:53 +01:00
Ricardo Wurmus 3398dfb764
gnu: ncbi-vdb: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[source]: Fetch from git.
[arguments]: Add phase to make checkout writable.
 2018-11-08 08:53:53 +01:00
Ricardo Wurmus e0f1aa2d2b
gnu: tadbit: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (tadbit)[source]: Fetch from git.
[version]: Use "2.0.0" instead of "2.0".
 2018-11-08 08:53:50 +01:00
Kei Kebreau ed33049cdc
gnu: pspp: Update to 1.2.0. 
* gnu/packages/statistics.scm (pspp): Update to 1.2.0.
[inputs]: Add spread-sheet-widget.
[native-inputs]: Add autoconf, python-2, and texinfo.
 2018-11-07 17:46:25 -05:00
Kei Kebreau e2f36385d3
gnu: Add spread-sheet-widget. 
* gnu/packages/gtk.scm (spread-sheet-widget): New public variable.
 2018-11-07 17:46:25 -05:00
Ricardo Wurmus f3f34b132c
gnu: filevercmp: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (filevercmp)[source]: Fetch from git.
[arguments]: Add #T to the end of the install phase.
 2018-11-07 23:17:36 +01:00
Ricardo Wurmus 3b888065da
gnu: ritornello: Update to 2.0.1. 
* gnu/packages/bioinformatics.scm (ritornello): Update to 2.0.1.
[arguments]: Adjust file patching.
 2018-11-07 23:17:36 +01:00
Ricardo Wurmus 7145f4e519
gnu: ritornello: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus e0a8fc85dd
gnu: snap-aligner: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (snap-aligner)[source]: Fetch from git.
[arguments]: Use INVOKE.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 6236524409
gnu: sortmerna: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 273df99d7d
gnu: vsearch: Fetch source from git. 
* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 67caa4b773
gnu: preseq: Update to 2.0.3. 
* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.3.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 37e285be43
gnu: preseq: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 63f3255e13
gnu: seqtk: Update to 1.3. 
* gnu/packages/bioinformatics.scm (seqtk): Update to 1.3.
[source]: Remove outdated snippet.
[arguments]: Use INVOKE and return #T unconditionally.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 019fcdf20a
gnu: seqtk: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus b9d0c3564b
gnu: raxml: Update to 8.2.12. 
* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.12.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus d9ba126d17
gnu: python2-biom-format: Fix build. 
This is a follow-up to commit 239716fb0b.

* gnu/packages/bioinformatics.scm (python2-biom-format)[arguments]: Modify
phases of base package.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus 4715d4af17
gnu: raxml: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus 5e242b02c3
gnu: pyicoteo: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
 2018-11-07 23:17:34 +01:00
Efraim Flashner 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
Ricardo Wurmus 2b773a9273
gnu: sra-tools: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git.
 2018-11-07 21:41:56 +01:00
Ricardo Wurmus 55698df260
gnu: libgff: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
 2018-11-07 21:41:56 +01:00
Ricardo Wurmus 4257c10ad2
gnu: kentutils: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git.
[arguments]: Add phase "fix-permissions".
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 1a20bcadf3
gnu: r-seqgl: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus a2b9d6a8d0
gnu: pplacer: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git.
[arguments]: Make files writable; use INVOKE.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 6052264b56
gnu: minced: Update to 0.3.2. 
* gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 9d94ca0ebf
gnu: minced: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
 2018-11-07 21:41:55 +01:00
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