d4780c8238
gnu: go-github-com-audriusbutkevicius-cli: Fix tests for go-1.11.
...
* gnu/packages/syncthing.scm (go-github-com-audriusbutkevicius-cli): Fix tests for go-1.11.
2018-11-12 10:29:37 +01:00
46a37b5966
gnu: go-github-com-prometheus-common-expfmt: Fix tests for go-1.11.
...
* gnu/packages/syncthing.scm (go-github-com-prometheus-common-expfmt): Fix tests for go-1.11.
2018-11-12 10:29:31 +01:00
9a65a05201
gnu: go: Update default to 1.11.
...
* gnu/packages/golang.scm (go): Update default to 1.11.
2018-11-12 10:28:46 +01:00
5f9b38ba34
gnu: r-s4vectors: Update to 0.20.1.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.1.
2018-11-11 23:13:48 +01:00
06910a8689
gnu: r-rcmdcheck: Update to 1.3.2.
...
* gnu/packages/cran.scm (r-rcmdcheck): Update to 1.3.2.
2018-11-11 23:13:48 +01:00
2a4c5877a9
gnu: r-ggpubr: Update to 0.1.9.
...
* gnu/packages/cran.scm (r-ggpubr): Update to 0.1.9.
2018-11-11 23:13:48 +01:00
441cf11de1
gnu: r-dplyr: Update to 0.7.8.
...
* gnu/packages/statistics.scm (r-dplyr): Update to 0.7.8.
2018-11-11 23:13:48 +01:00
41d2c26e67
gnu: r-rcpparmadillo: Update to 0.9.200.4.0.
...
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.200.4.0.
2018-11-11 23:13:48 +01:00
23dd886a95
gnu: r-rtsne: Update to 0.15.
...
* gnu/packages/statistics.scm (r-rtsne): Update to 0.15.
2018-11-11 23:13:48 +01:00
7865c8c460
gnu: r-lme4: Update to 1.1-19.
...
* gnu/packages/statistics.scm (r-lme4): Update to 1.1-19.
2018-11-11 23:13:48 +01:00
a509b18087
gnu: webkitgtk@2.22: Adjust to documentation output.
...
This is a follow-up to commit 0ead0b4d2c
2018-11-11 22:47:06 +01:00
aaf0e47f6d
gnu: libtoxcore: Update to 0.0.0-2.bf69b54.
...
* gnu/packages/messaging.scm (libtoxcore): Update to 0.0.0-2.bf69b54.
[native-inputs]: Add check.
2018-11-11 20:51:51 +01:00
e874f34d3f
gnu: mumi: Update to 0.0.0-2.bfd96ce7.
...
* gnu/packages/mail.scm (mumi): Update to 0.0.0-2.bfd96ce7.
2018-11-11 20:51:51 +01:00
ec35067631
gnu: PostgreSQL: Update to 10.6 [fixes CVE-2018-16850].
...
* gnu/packages/databases.scm (postgresql): Update to 10.6.
2018-11-11 14:10:03 -05:00
0ead0b4d2c
gnu: webkitgtk: Include documentation.
...
* gnu/packages/webkit.scm (webkitgtk): Include documentation.
2018-11-11 16:44:46 +01:00
50ee7e93fc
gnu: gtk-doc: Use local docbook-xsl.
...
* gnu/packages/gtk.scm (gtk-doc): Use local docbook-xsl.
2018-11-11 16:41:45 +01:00
89c7894805
gnu: faust-2: Update to 2.5.23.
...
* gnu/packages/audio.scm (faust-2): Update to 2.5.23.
[native-inputs]: Replace llvm-with-rtti with llvm-3.8-with-rtti.
* gnu/packages/llvm.scm (llvm-with-rtti): Rename this variable...
(llvm-3.8-with-rtti): ...to this variable; inherit from llvm-3.8.
2018-11-11 16:19:59 +01:00
37a350ecce
gnu: gajim: Move python-docutils from inputs to native-inputs.
...
* gnu/packages/messaging.scm (gajim): Move python-docutils from inputs to
native-inputs.
2018-11-11 16:00:08 +01:00
60c5b44489
gnu: gajim: Get the second 'wrap-program' phase to return #t.
...
* gnu/packages/messaging.scm (gajim)[arguments]: Get the second 'wrap-program'
phase to return #t.
2018-11-11 16:00:00 +01:00
992a496503
gnu: gajim: Update to 1.1.0.
...
* gnu/packages/messaging.scm (gajim): Update to 1.1.0.
[arguments]: Set #:test-target to "test_nogui". Remove the
'remove-test-resolver' and 'start-xserver' phases.
[inputs]: Remove python-pyasn1. Add python-cssutils, python-keyring and
python-precis-i18n.
2018-11-11 15:59:07 +01:00
a311f42e1b
gnu: python-nbxmpp: Update to 0.6.8.
...
* gnu/packages/messaging.scm (python-nbxmpp): Update to 0.6.8.
2018-11-11 15:59:03 +01:00
4ad3786b7b
gnu: Add python-precis-i18n.
...
* gnu/packages/messaging.scm (python-precis-i18n): New variable.
2018-11-11 15:58:50 +01:00
902068b436
gnu: tiled: Fetch sources from git.
...
* gnu/packages/game-development.scm (tiled)[source]: Fetch from git.
2018-11-11 13:18:27 +01:00
9066424778
gnu: privoxy: Remove custom bootstrap phase.
...
* gnu/packages/tor.scm (privoxy)[arguments]: Remove autoconf phase.
2018-11-11 13:10:56 +01:00
2b61cd37b4
gnu: cifs-utils: Remove autoreconf phase.
...
* gnu/packages/samba.scm (cifs-utils)[arguments]: Remove autoreconf phase.
2018-11-11 13:08:56 +01:00
cd1f661e82
gnu: libiax2: Fetch sources from git.
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* gnu/packages/telephony.scm (libiax2)[source]: Fetch from git.
2018-11-11 13:06:31 +01:00
5a103bb84e
gnu: libiax2: Remove custom bootstrap phase.
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* gnu/packages/telephony.scm (libiax2)[arguments]: Remove.
2018-11-11 13:04:08 +01:00
6f3dd09f8d
gnu: libharu: Remove custom bootstrap phase.
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* gnu/packages/pdf.scm (libharu)[arguments]: Remove autogen phase.
2018-11-11 13:00:53 +01:00
2b2ab39cfc
gnu: libharu: Fetch sources from git.
...
* gnu/packages/pdf.scm (libharu)[source]: Fetch from git.
2018-11-11 13:00:35 +01:00
bc74e9e4cd
gnu: scsh: Remove custom bootstrap phase.
...
* gnu/packages/shells.scm (scsh)[arguments]: Remove autoreconf phase.
2018-11-11 12:56:22 +01:00
e5ff963a6d
gnu: xdelta: Remove custom bootstrap phase.
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* gnu/packages/compression.scm (xdelta)[arguments]: Remove autoconf phase.
2018-11-11 12:52:46 +01:00
0633c77b1b
gnu: xdelta: Fetch sources from git.
...
* gnu/packages/compression.scm (xdelta)[source]: Fetch from git.
2018-11-11 12:52:30 +01:00
112fcafbae
gnu: libtar: Remove custom bootstrap phase.
...
* gnu/packages/compression.scm (libtar)[arguments]: Remove autoconf phase.
2018-11-11 12:47:51 +01:00
3478945948
gnu: minizip: Remove custom bootstrap phase.
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* gnu/packages/compression.scm (minizip)[arguments]: Remove autoreconf phase.
2018-11-11 12:45:52 +01:00
4078beab93
gnu: inotify-tools: Remove custom bootstrap phase.
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* gnu/packages/linux.scm (inotify-tools)[arguments]: Remove.
2018-11-11 12:36:35 +01:00
88f9fea723
gnu: inotify-tools: Fetch sources from git.
...
* gnu/packages/linux.scm (inotify-tools)[source]: Fetch from git.
2018-11-11 12:36:15 +01:00
2286107f60
gnu: par2cmdline: Remove custom bootstrap phase.
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* gnu/packages/backup.scm (par2cmdline)[arguments]: Remove.
2018-11-11 12:31:35 +01:00
5cdbdc2b13
gnu: par2cmdline: Fetch sources from git.
...
* gnu/packages/backup.scm (par2cmdline)[source]: Fetch from git.
2018-11-11 12:31:18 +01:00
2fef54fd64
gnu: hpcguix-web: Do not re-bootstrap.
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* gnu/packages/web.scm (hpcguix-web)[arguments]: Do not run autoreconf after
the bootstrap phase; remove "autoconf" phase to "set-variables"; end phase
with #T.
2018-11-11 12:27:01 +01:00
cbb6a15056
gnu: schismtracker: Remove custom bootstrap phase.
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* gnu/packages/music.scm (schismtracker)[arguments]: Remove autoconf phase.
2018-11-11 12:19:23 +01:00
8865973848
gnu: lilypond: Use INVOKE.
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* gnu/packages/music.scm (lilypond)[arguments]: Use INVOKE and return #T
unconditionally.
2018-11-11 12:15:03 +01:00
3b9e9415fa
gnu: schismtracker: Fetch sources from git.
...
* gnu/packages/music.scm (schismtracker)[source]: Fetch from git.
2018-11-11 12:07:21 +01:00
234a1825b2
gnu: clyrics: Fetch sources from git.
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* gnu/packages/music.scm (clyrics)[source]: Fetch from git.
[native-inputs]: Remove.
[arguments]: Adjust builder.
2018-11-11 12:01:25 +01:00
3a0592ae31
gnu: lmms: Fetch sources from git.
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* gnu/packages/music.scm (lmms)[source]: Fetch from git.
2018-11-11 12:00:55 +01:00
caa39e56f7
gnu: milkytracker: Fetch sources from git.
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* gnu/packages/music.scm (milkytracker)[source]: Fetch from git.
2018-11-11 11:44:24 +01:00
08bc7f2665
gnu: dotconf: Fetch sources from git.
...
* gnu/packages/textutils.scm (dotconf)[source]: Fetch from git.
2018-11-11 11:37:01 +01:00
7a52d0e075
gnu: dotconf: Remove custom bootstrap phase.
...
* gnu/packages/textutils.scm (dotconf)[arguments]: Remove autoreconf phase.
2018-11-11 11:36:39 +01:00
d68a15806b
gnu: libgtextutils: Remove custom bootstrap phase.
...
* gnu/packages/textutils.scm (libgtextutils)[arguments]: Remove.
2018-11-11 11:34:55 +01:00
fab455840e
gnu: libtoxcore: Remove custom bootstrap phase.
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* gnu/packages/messaging.scm (libtoxcore)[arguments]: Remove autoconf phase.
2018-11-11 11:33:39 +01:00
867d9de690
gnu: openocd: Use INVOKE.
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* gnu/packages/embedded.scm (openocd)[arguments]: Use INVOKE and return #T
unconditionally.
2018-11-11 11:32:12 +01:00
4cd6ab1b1f
gnu: libjaylink: Remove custom bootstrap phase.
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* gnu/packages/embedded.scm (libjaylink)[arguments]: Remove.
2018-11-11 11:23:39 +01:00
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
d212ed2f00
gnu: lrdf: Fetch sources from git.
...
* gnu/packages/rdf.scm (lrdf)[source]: Fetch from git.
2018-11-11 11:21:55 +01:00
2cabd29323
gnu: guildhall: Remove custom bootstrap phase.
...
* gnu/packages/guile.scm (guildhall)[arguments]: Remove autogen phase.
2018-11-11 10:38:00 +01:00
34da5c394b
gnu: guile-dsv: Remove custom bootstrap phase.
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* gnu/packages/guile.scm (guile-dsv)[arguments]: Remove autoreconf phase.
2018-11-11 10:22:45 +01:00
5ad728e04c
gnu: opendht: Remove custom bootstrap phase.
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* gnu/packages/crypto.scm (opendht)[arguments]: Remove autoconf phase.
2018-11-11 10:21:02 +01:00
974056c05e
gnu: opendht: Fetch sources from git.
...
* gnu/packages/crypto.scm (opendht)[source]: Fetch from git.
2018-11-11 10:20:36 +01:00
a49b5322c5
gnu: lxsession: Remove custom bootstrap phase.
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* gnu/packages/lxde.scm (lxsession)[arguments]: Remove autoreconf phase and
end rm-stamp phase with #T.
2018-11-11 10:16:43 +01:00
f1f1cebdd3
gnu: mdbtools: Fetch sources from git.
...
* gnu/packages/databases.scm (mdbtools)[source]: Fetch from git.
2018-11-11 10:09:54 +01:00
f626b71923
gnu: mdbtools: Remove custom bootstrap phase.
...
* gnu/packages/databases.scm (mdbtools)[arguments]: Remove.
2018-11-11 10:05:56 +01:00
1410e178bb
gnu: pianobar: Fetch sources from git.
...
* gnu/packages/music.scm (pianobar)[source]: Fetch from git.
2018-11-11 10:03:06 +01:00
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
863742856c
gnu: librime: Fetch sources from git.
...
* gnu/packages/ibus.scm (librime)[source]: Fetch from git.
2018-11-11 10:03:06 +01:00
cab70d4c2a
gnu: perl-autovivification: Update to 0.18.
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* gnu/packages/perl.scm (perl-autovivification): Update to 0.18.
2018-11-11 08:21:59 +02:00
717d29e25b
gnu: icecat: Add more fixes from mozilla-esr60.
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* gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes
from the upstream mozilla-esr60 source repository.
2018-11-10 20:29:19 -05:00
3b14494616
gnu: icecat: Update to 60.3.0-gnu1.
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* 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
e22842f5ca
gnu: linux-libre@4.14: Update to 4.14.80.
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* 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
62168a5558
gnu: linux-libre@4.9: Update to 4.9.136.
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* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.136.
2018-11-10 20:23:15 -05:00
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
4cbbb16045
gnu: nxbelld: Remove custom bootstrap phase.
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* gnu/packages/xdisorg.scm (nxbelld)[arguments]: Remove autoreconf phase.
2018-11-10 23:42:54 +01:00
f116e1fcae
gnu: wmclock: Remove custom bootstrap phase.
...
* gnu/packages/gnustep.scm (wmclock)[arguments]: Remove.
2018-11-10 23:42:54 +01:00
e17f867c62
gnu: wmbattery: Remove custom bootstrap phase.
...
* gnu/packages/gnustep.scm (wmbattery)[arguments]: Remove autoconf phase.
2018-11-10 23:42:54 +01:00
7db147ec45
gnu: rtmidi: Remove custom bootstrap phase.
...
* gnu/packages/audio.scm (rtmidi)[arguments]: Remove autoconf phase.
2018-11-10 23:42:54 +01:00
cdb4048d72
gnu: portaudio: Remove custom bootstrap phase.
...
* gnu/packages/audio.scm (portaudio)[arguments]: Remove autoreconf phase.
2018-11-10 23:42:54 +01:00
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
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
1329f095bb
gnu: Add rime-data.
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* gnu/packages/ibus.scm (rime-data): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-10 23:33:47 +01:00
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
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
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
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
30288ae57e
gnu: mdadm: Update to 4.1.
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* gnu/packages/linux.scm (mdadm): Update to 4.1.
2018-11-10 23:33:46 +01:00
37ebc19cfb
gnu: msgpack: Remove custom bootstrap phase.
...
* gnu/packages/serialization.scm (msgpack)[arguments]: Remove.
2018-11-10 23:30:52 +01:00
bed4eb373e
gnu: gxtuner: Fetch sources from git.
...
* gnu/packages/music.scm (gxtuner)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
a7fde1a86d
gnu: cava: Fetch sources from git.
...
* gnu/packages/audio.scm (cava)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
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
b249ff5d37
gnu: dcadec: Fetch sources from git.
...
* gnu/packages/audio.scm (dcadec)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
4289a306b7
gnu: cuetools: Fetch sources from git.
...
* gnu/packages/audio.scm (cuetools)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
8e5995e397
gnu: xjackfreak: Fetch sources from git.
...
* gnu/packages/audio.scm (xjackfreak)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
458baefb40
gnu: rsound: Fetch sources from git.
...
* gnu/packages/audio.scm (rsound)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
eca7729301
gnu: rtmidi: Fetch sources from git.
...
* gnu/packages/audio.scm (rtmidi)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
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
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
917dc89672
gnu: csound: Fetch sources from git.
...
* gnu/packages/audio.scm (csound)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
b255365cd1
gnu: lvtk: Fetch sources from git.
...
* gnu/packages/audio.scm (lvtk)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
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
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
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
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
74c903edab
Add missing license import.
...
* gnu/packages/mail.scm: Import agpl3+.
2018-11-10 22:37:07 +01:00
e3a4703174
gnu: Add mumi.
...
* gnu/packages/mail.scm (mumi): New variable.
2018-11-10 22:36:13 +01:00
2d900b0464
gnu: Add guile-debbugs-next.
...
* gnu/packages/guile.scm (guile-debbugs-next): New variable.
2018-11-10 22:36:13 +01:00
7453785624
gnu: Add guile-email.
...
* gnu/packages/guile.scm (guile-email): New variable.
2018-11-10 22:36:13 +01:00
95906eee18
gnu: guile-ics: Remove custom bootstrap phase.
...
* gnu/packages/guile.scm (guile-ics)[arguments]: Remove.
2018-11-10 22:36:13 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
06bc7b82f7
gnu: Add r-arm.
...
* gnu/packages/cran.scm (r-arm): New variable.
2018-11-09 18:04:37 +01:00
cf383cf08f
gnu: Add r-feature.
...
* gnu/packages/cran.scm (r-feature): New variable.
2018-11-09 18:04:37 +01:00
da256afb9e
gnu: Add r-ks.
...
* gnu/packages/cran.scm (r-ks): New variable.
2018-11-09 18:04:37 +01:00
4106e6ad87
gnu: Add r-misc3d.
...
* gnu/packages/cran.scm (r-misc3d): New variable.
2018-11-09 18:04:36 +01:00
213e72a18d
gnu: Add r-multicool.
...
* gnu/packages/cran.scm (r-multicool): New variable.
2018-11-09 18:04:36 +01:00
f338e4807f
gnu: Add r-rgl.
...
* gnu/packages/cran.scm (r-rgl): New variable.
2018-11-09 18:04:36 +01:00
a961ae469c
gnu: Add r-destiny.
...
* gnu/packages/bioconductor.scm (r-destiny): New variable.
2018-11-09 17:15:31 +01:00
ff939ef4d5
gnu: Add r-h5.
...
* gnu/packages/cran.scm (r-h5): New variable.
2018-11-09 16:57:13 +01:00
3a4c6288c8
gnu: Add r-aggregation.
...
* gnu/packages/cran.scm (r-aggregation): New variable.
2018-11-09 16:57:13 +01:00
8a587c89af
gnu: Add r-savr.
...
* gnu/packages/bioconductor.scm (r-savr): New variable.
2018-11-09 16:45:21 +01:00
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
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
ddd925f608
gnu: Add emacs-gtk-look.
...
* gnu/packages/emacs.scm (emacs-gtk-look): New variable.
2018-11-09 11:55:08 +01:00
2cce23bfb8
gnu: Add xmlrpc-c.
...
* gnu/packages/xml.scm (xmlrpc-c): New variable.
2018-11-09 11:55:08 +01:00
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
1b12b572a5
gnu: powertabeditor: Fetch sources from git.
...
* gnu/packages/music.scm (powertabeditor)[source]: Fetch from git.
2018-11-09 08:37:53 +01:00
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
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
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
2705780f3f
gnu: Add emacs-clang-format.
...
* gnu/packages/emacs.scm (emacs-clang-format): New variable.
2018-11-08 13:08:26 +01:00
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
988b78ba28
gnu: Add fstrcmp.
...
* gnu/packages/kodi.scm (fstrcmp): New variable.
2018-11-08 12:01:20 +02:00
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
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
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
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
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
4e82946888
gnu: cmus: Fetch sources from git.
...
* gnu/packages/music.scm (cmus)[source]: Fetch from git.
2018-11-08 10:10:06 +01:00
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
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
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
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
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
9f527c9199
gnu: sailfish: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use INVOKE instead of
SYSTEM*.
2018-11-08 09:52:46 +01:00
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
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
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
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
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
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
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
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
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
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
0881d62f25
gnu: newick-utils: Remove custom autoconf phase.
...
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove.
2018-11-08 09:10:58 +01:00
e35dce0170
gnu: mash: Remove custom autoconf phase.
...
* gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase.
2018-11-08 09:10:20 +01:00
31c41a8cfe
gnu: vsearch: Remove custom autogen phase.
...
* gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove.
2018-11-08 09:04:34 +01:00
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
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
c098c49b3e
gnu: sailfish: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
2018-11-08 08:53:54 +01:00
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
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
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
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
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
e2f36385d3
gnu: Add spread-sheet-widget.
...
* gnu/packages/gtk.scm (spread-sheet-widget): New public variable.
2018-11-07 17:46:25 -05:00
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
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
7145f4e519
gnu: ritornello: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
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
6236524409
gnu: sortmerna: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
273df99d7d
gnu: vsearch: Fetch source from git.
...
* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
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
37e285be43
gnu: preseq: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
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
019fcdf20a
gnu: seqtk: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
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
d9ba126d17
gnu: python2-biom-format: Fix build.
...
This is a follow-up to commit 239716fb0b
2018-11-07 23:17:34 +01:00
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.
...
* 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.
...
* 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.
...
* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
2018-11-07 21:41:56 +01:00
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
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
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
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
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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
2018-11-07 19:55:50 +01:00
7ca49ab57a
gnu: ribodiff: Fetch sources from git.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
2018-11-07 17:19:53 +01:00
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
08759829cf
gnu: cuirass: Update to 0b40dca.
...
* gnu/packages/ci.scm (cuirass): Update to 0b40dca.
2018-11-07 16:06:42 +01:00
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
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.
...
* 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
bb47aca5e7
gnu: Add hdf5-1.10.
...
* gnu/packages/maths.scm (hdf5-1.10): New variable.
2018-11-07 12:26:33 +01:00
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
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
286157dc49
gnu: Add r-biocneighbors.
...
* gnu/packages/bioconductor.scm (r-biocneighbors): New variable.
2018-11-07 12:26:33 +01:00
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
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
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
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
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
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
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
bbc4787cf2
gnu: r-interactionset: Update to 1.10.0.
...
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.10.0.
2018-11-07 12:26:32 +01:00
c4fed658a9
gnu: r-riboseqr: Update to 1.16.0.
...
* gnu/packages/bioconductor.scm (r-riboseqr): Update to 1.16.0.
2018-11-07 12:26:32 +01:00
e22e462b33
gnu: r-riboprofiling: Update to 1.12.0.
...
* gnu/packages/bioconductor.scm (r-riboprofiling): Update to 1.12.0.
2018-11-07 12:26:32 +01:00
e9427b2c78
gnu: r-ripseeker: Update to 1.22.0.
...
* gnu/packages/bioconductor.scm (r-ripseeker): Update to 1.22.0.
2018-11-07 12:26:32 +01:00
aa802eafb6
gnu: r-chipcomp: Update to 1.12.0.
...
* gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.12.0.
2018-11-07 12:26:32 +01:00
4728e27511
gnu: r-bayseq: Update to 2.16.0.
...
* gnu/packages/bioconductor.scm (r-bayseq): Update to 2.16.0.
2018-11-07 12:26:32 +01:00
57d2fcd9ee
gnu: r-chippeakanno: Update to 3.16.0.
...
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.16.0.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
2018-11-07 12:26:32 +01:00
14520b640e
gnu: r-graph: Update to 1.60.0.
...
* gnu/packages/bioconductor.scm (r-graph): Update to 1.60.0.
2018-11-07 12:26:32 +01:00
95ee4a466b
gnu: r-multtest: Update to 2.38.0.
...
* gnu/packages/bioconductor.scm (r-multtest): Update to 2.38.0.
2018-11-07 12:26:32 +01:00
a92f523026
gnu: r-qdnaseq: Update to 1.18.0.
...
* gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.18.0.
2018-11-07 12:26:32 +01:00
9add0933d0
gnu: r-cghcall: Update to 2.44.0.
...
* gnu/packages/bioconductor.scm (r-cghcall): Update to 2.44.0.
2018-11-07 12:26:32 +01:00
46cdceef4c
gnu: r-cghbase: Update to 1.42.0.
...
* gnu/packages/bioconductor.scm (r-cghbase): Update to 1.42.0.
2018-11-07 12:26:32 +01:00
f1c606ce8c
gnu: r-marray: Update to 1.60.0.
...
* gnu/packages/bioconductor.scm (r-marray): Update to 1.60.0.
2018-11-07 12:26:32 +01:00
98652568a4
gnu: r-diffbind: Update to 2.10.0.
...
* gnu/packages/bioconductor.scm (r-diffbind): Update to 2.10.0.
2018-11-07 12:26:31 +01:00
6168692159
gnu: r-hpar: Update to 1.24.0.
...
* gnu/packages/bioconductor.scm (r-hpar): Update to 1.24.0.
2018-11-07 12:26:31 +01:00
1e605c030f
gnu: Add r-biocmanager.
...
* gnu/packages/cran.scm (r-biocmanager): New variable.
2018-11-07 12:26:31 +01:00
b58940cb03
gnu: Add r-ncdf4.
...
* gnu/packages/cran.scm (r-ncdf4): New variable.
2018-11-07 12:26:31 +01:00
bfa5662e38
gnu: Add r-rcppannoy.
...
* gnu/packages/cran.scm (r-rcppannoy): New variable.
2018-11-07 12:26:31 +01:00
8243f4e55a
gnu: slang: Use a correct location for terminfo dirs.
...
As termcap is disabled and no terminfo directory is given, slang is not able
to query terminal capabilities. Specifying a correct path for terminfo will
automatically disable termcap support in the configuration.
* gnu/packages/slang.scm (slang)[source]: Remove the snippet disabling
termcap.
[arguments]: Set MISC_TERMINFO_DIRS to a correct location.
2018-11-07 18:39:19 +09:00
a7903ca150
gnu: terminals: Change libtsm and kmscon repositories.
...
Those two packages (from the same author) are no longer maintained and do not
even compile. Switch to a fork that is maintained even if it does not have any
release yet.
* gnu/packages/terminals.scm (libtsm)[origin]: Use
"https://github.com/Aetf/libtsm " as new origin and switch to git-fetch method.
(kmscon)[origin]: Use "https://github.com/Aetf/kmscon " as new origin and
switch to git-fetch method.
2018-11-07 18:27:01 +09:00
2d9dace8c2
services: kmscon: Add an auto-login option.
...
Add an auto-login option that behaves as the one of mingetty-service.
* gnu/services/base.scm (kmscon-configuration)[auto-login]: New field.
(kmscon-service-type): Pass it to kmscon command.
* doc/guix.texi (Base Services): Document it.
2018-11-07 18:21:42 +09:00
f4e8bc5f25
services: kmscon: Do not switch to vt at start.
...
* gnu/services/base.scm (kmscon-service-type): Add "--no-switchvt" to kmscon
command.
2018-11-07 18:15:00 +09:00
581720bc74
gnu: Add guile-newt.
...
* gnu/packages/guile.scm (guile-newt): New variable.
2018-11-07 18:09:30 +09:00
cbb5d2e145
gnu: kodi: Fix typo.
...
This is a follow-up to 2c17bd7b29
2018-11-07 10:38:13 +02:00
02e2133bd2
gnu: LibreOffice: Update to 6.1.3.2.
...
* gnu/packages/libreoffice.scm (libreoffice): Update to 6.1.3.2.
2018-11-06 23:13:50 -05:00
b20aef98a0
gnu: GnuPG: Update to 2.2.11.
...
* gnu/packages/gnupg.scm (gnupg): Update to 2.2.11.
2018-11-06 17:26:45 -05:00
c5ce2db569
install: Add 'install-database-and-gc-roots'.
...
* gnu/build/install.scm (%root-profile): New variable.
(install-database-and-gc-roots): New procedure.
(populate-single-profile-directory): Replace inline code with a call to
'install-database-and-gc-roots'.
2018-11-06 23:21:24 +01:00
b27ef1d46c
pack: Import (guix store database) only when '--localstatedir' is passed.
...
This is another way to address <https://bugs.gnu.org/32184 >, which was
previously addressed in commit 19c924af4f19c924af4f
2018-11-06 23:21:23 +01:00
ec4c81fe32
pack: Move store database creation to a separate derivation.
...
* guix/scripts/pack.scm (store-database): New procedure.
(self-contained-tarball): Use it when LOCALSTATEDIR? is true.
Remove 'schema' and add 'database'.
[build]: Pass DATABASE to 'populate-single-profile-directory'.
(squashfs-image): Remove #:deduplicate? parameter.
[build]: Remove (gnu build install) and (guix config) from the imported
modules. Remove 'with-extensions'.
* gnu/build/install.scm (populate-single-profile-directory): Remove
#:deduplicate?, #:register?, and #:schema; add #:database. Remove call
to 'register-closure' and simply copy DATABASE instead.
2018-11-06 23:21:23 +01:00
c6b05bacc0
gnu: nginx: Update to 1.14.1 [security fixes].
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This fixes CVE-2018-16843, CVE-2018-16844, and CVE-2018-16845.
* gnu/packages/web.scm (nginx): Update to 1.14.1.
2018-11-06 21:34:30 +01:00
f25614229b
gnu: Syncthing: Update to 0.14.52.
...
* gnu/packages/syncthing.scm (syncthing): Update to 0.14.52.
2018-11-06 11:16:22 -05:00
4cceb1432a
gnu: libgit2: Work around test failures on 32-bit platforms.
...
* gnu/packages/patches/libgit2-oom-test.patch: New file.
* gnu/packages/version-control.scm (libgit2)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
2018-11-06 17:08:46 +01:00
158c02dffa
gnu: Add xcb-util-errors.
...
* gnu/packages/xorg.scm (xcb-util-errors): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-06 17:00:02 +01:00
3527f600b5
gnu: guile-sqlite3: Update home page.
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* gnu/packages/guile.scm (guile-sqlite3)[home-page]: Update.
2018-11-06 17:00:01 +01:00
cddc0300b7
gnu: Add r-weights.
...
* gnu/packages/cran.scm (r-weights): New variable.
Signed-off-by: Gábor Boskovits <boskovits@gmail.com>
2018-11-06 16:06:42 +01:00
fe4fb278b8
gnu: youtube-dl: Update to 2018.11.03.
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* gnu/packages/video.scm (youtube-dl): Update to 2018.11.03.
2018-11-06 15:34:37 +01:00
b1eeeb8dd4
gnu: terraform-docs: Update to 0.5.0.
...
* gnu/packages/terraform.scm (terraform-docs): Update to 0.5.0.
[native-inputs]: Remove them all.
2018-11-06 15:34:36 +01:00
c3b8300af3
gnu: jq: Don't use NAME in source URI.
...
* gnu/packages/web.scm (jq)[source]: Code more hard.
2018-11-06 15:34:36 +01:00
418dd6adb5
gnu: jq: Update to 1.6.
...
* gnu/packages/web.scm (jq): Update to 1.6.
[source]: Remove upstreamed patch.
* gnu/packages/patches/jq-CVE-2015-8863.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-11-06 15:34:36 +01:00
c58f3ebaf8
gnu: ffmpeg: Update to 4.1.
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* gnu/packages/video.scm (ffmpeg): Update to 4.1.
2018-11-06 12:02:59 +01:00
730e5fbc66
Revert "gnu: c-ares: Update to 1.15.0."
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c-ares has more than 3000 dependant packages.
This reverts commit b588adc96f
2018-11-06 12:22:02 +02:00
b588adc96f
gnu: c-ares: Update to 1.15.0.
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* gnu/packages/adns.scm (c-ares): Update to 1.15.0.
2018-11-06 08:32:56 +02:00
7f860a8be1
gnu: services: dns: Fix 'ddclient-activation'.
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* gnu/services/dns.scm (ddclient-activation): Fix procedure.
2018-11-06 07:16:44 +03:00
adde15186d
gnu: xf86-video-intel: Update to commit 0932a6b37ba6d5c9e916a1cb6ab89c3205b81a0c.
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* gnu/packages/xorg.scm (xf86-video-intel): Update to 2.99.917-11.0932a6b.
2018-11-05 23:53:30 +01:00
208e82297c
gnu: xapian: Update to 1.4.9.
...
* gnu/packages/patches/xapian-revert-5489fb2f8.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/search.scm (xapian): Update to 1.4.9.
[source](patches): Remove.
(python-xapian-bindings): Update to 1.4.9.
2018-11-05 23:46:38 +01:00
d79c8148cc
gnu: libssh: Update to 0.7.7.
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* gnu/packages/ssh.scm (libssh): Update to 0.7.7.
2018-11-05 23:46:38 +01:00
Pierre Neidhardt