0c92f3734e
gnu: Add r-rjags.
...
* gnu/packages/cran.scm (r-rjags): New variable.
2018-11-14 15:13:20 +01:00
0bca8643a2
gnu: Add jags.
...
* gnu/packages/statistics.scm (jags): New variable.
2018-11-14 15:13:17 +01:00
51b262f310
gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4.
...
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
Update to 3.4.4.
2018-11-13 23:34:40 +01:00
d34959b8d4
gnu: r-org-mm-eg-db: Update to 3.7.0.
...
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0.
2018-11-13 23:34:40 +01:00
314511b862
gnu: r-org-dm-eg-db: Update to 3.7.0.
...
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
76bd16bcf6
gnu: r-org-ce-eg-db: Update to 3.7.0.
...
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
fc7683fa30
gnu: r-org-hs-eg-db: Update to 3.7.0.
...
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
cb9e6ed702
gnu: r-genomationdata: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0.
2018-11-13 23:34:39 +01:00
13e70f6304
gnu: r-go-db: Update to 3.7.0.
...
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
13a574652b
gnu: r-genomeinfodbdata: Update to 1.2.0.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0.
2018-11-13 23:34:39 +01:00
3f995aaf21
gnu: spice-vdagent: Fix typo in desktop file.
...
Fixes <https://bugs.gnu.org/33346 >.
* gnu/packages/spice.scm (spice-vdagent)[arguments]: Fix typo in
'patch-spice-vdagent.desktop' phase.
2018-11-13 15:26:30 -05:00
c991806a7d
gnu: ImageMagick: Update to 6.9.10-14.
...
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.10-14.
2018-11-14 03:09:37 +08:00
d540137509
gnu: libssh: Fetch source over HTTPS.
...
* gnu/packages/ssh.scm (libssh)[source]: Use HTTPS URL.
2018-11-13 11:43:35 -05:00
978d59737a
gnu: direnv: Build with Go 1.9.
...
* gnu/packages/shellutils.scm (direnv)[native-inputs]: Remove go.
[inputs]: Add go-1.9.
2018-11-13 11:28:23 -05:00
021bf6af18
gnu: Poppler: Fix CVE-2018-19149.
...
* gnu/packages/patches/poppler-CVE-2018-19149.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/pdf.scm (poppler)[replacement]: New field.
(poppler/fixed): New variable.
(poppler-qt4, poppler-qt5): Use package/inherit.
2018-11-13 11:28:23 -05:00
8263b9f71f
gnu: certbot, python-acme: Update to 0.28.0.
...
* gnu/packages/tls.scm (certbot, python-acme): Update to 0.28.0.
2018-11-13 10:10:42 -05:00
3483f82413
gnu: guix: Update to f5a2724.
...
* gnu/packages/package-management.scm (guix): Update to f5a2724
2018-11-13 15:44:25 +01:00
d3f75179e5
services: nscd: Add 'invalidate' and 'statistics' actions.
...
* gnu/services/base.scm (nscd-action-procedure, nscd-actions): New
procedures.
(nscd-shepherd-service): Add 'modules' and 'actions' fields.
* gnu/tests/base.scm (run-basic-test)["nscd invalidate action"]
["nscd invalidate action, wrong table"]: New tests.
* doc/guix.texi (Services): Mention 'herd doc nscd action'.
(Base Services): Document the actions.
2018-11-13 14:59:45 +01:00
190877748e
services: mcron: Fix typo in comment.
...
* gnu/services/mcron.scm (shepherd-schedule-action): Fix typo in comment.
2018-11-13 14:59:45 +01:00
155956449a
gnu: restic: Fix build phase.
...
* gnu/packages/backup.scm (restic)[arguments]: Set "HOME" environment variable
in build phase.
2018-11-13 15:03:15 +03:00
6018683683
gnu: c-toxcore: Fetch sources from git.
...
* gnu/packages/messaging.scm (c-toxcore)[source]: Fetch from git.
2018-11-13 10:51:41 +01:00
7fed5481fe
gnu: wine-staging: Update to 3.20.
...
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.20.
* gnu/packages/wine.scm (wine-staging): Update to 3.20.
2018-11-13 10:24:42 +01:00
0dd60c1c9b
gnu: php: Update to 7.2.12.
...
* gnu/packages/php.scm (php): Update to 7.2.12.
2018-11-12 23:57:42 +01:00
e740a90228
gnu: youtube-dl: Update to 2018.11.07.
...
* gnu/packages/video.scm (youtube-dl): Update to 2018.11.07.
2018-11-12 22:09:12 +05:30
53bcee9ea7
gnu: vifm: Update to 0.10.
...
* gnu/packages/vim.scm (vifm): Update to 0.10.
2018-11-12 12:37:00 +02:00
5c4758415d
gnu: go-github-com-aarzilli-golua: Fix for go-1.11.
...
* gnu/packages/golang.scm (go-github-com-aarzilli-golua)[arguments]: Fix for go-1.11.
[native-inputs]: Remove lua.
[propagated-inputs]: Add lua.
2018-11-12 10:31:23 +01:00
46a4ae2212
gnu: go-github-com-wtolson-go-taglib: Fix tests and build for go-1.11.
...
* gnu/packages/golang.scm (go-github-com-wtolson-go-taglib)[arguments]: Fix tests for go-1.11.
[native-inputs]: Remove pkg-config and taglib.
[propagated-inputs]: Add pkg-config and taglib.
2018-11-12 10:30:10 +01:00
66fa8f0f77
gnu: go-gopkg.in-asn1-ber.v1: Fix tests for go-1.11.
...
* gnu/packages/syncthing.scm (go-gopkg.in-asn1-ber.v1): Fix tests for go-1.11.
2018-11-12 10:29:43 +01:00
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
8c5749f1b5
gnu: python-cffi: Fix test failure on i686.
...
* gnu/packages/patches/python-cffi-x87-stack-clean.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/libffi.scm (python-cffi)[source](patches): Add it.
2018-11-11 17:18:05 +01:00
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.
...
* gnu/packages/telephony.scm (libiax2)[source]: Fetch from git.
2018-11-11 13:06:31 +01:00
5a103bb84e
gnu: libiax2: Remove custom bootstrap phase.
...
* gnu/packages/telephony.scm (libiax2)[arguments]: Remove.
2018-11-11 13:04:08 +01:00
6f3dd09f8d
gnu: libharu: Remove custom bootstrap phase.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* gnu/packages/music.scm (schismtracker)[arguments]: Remove autoconf phase.
2018-11-11 12:19:23 +01:00
8865973848
gnu: lilypond: Use INVOKE.
...
* 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.
...
* 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.
...
* gnu/packages/music.scm (lmms)[source]: Fetch from git.
2018-11-11 12:00:55 +01:00
caa39e56f7
gnu: milkytracker: Fetch sources from git.
...
* 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.
...
* gnu/packages/messaging.scm (libtoxcore)[arguments]: Remove autoconf phase.
2018-11-11 11:33:39 +01:00
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
4cd6ab1b1f
gnu: libjaylink: Remove custom bootstrap phase.
...
* 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
2bdca67351
gnu: python-yapf: Update to 0.24.0.
...
* gnu/packages/python.scm (python-yapf): Update to 0.24.0.
2018-11-11 11:54:32 +02:00
22d04ceda0
gnu: python-rq: Update to 0.12.0.
...
* gnu/packages/databases.scm (python-rq): Update to 0.12.0.
2018-11-11 11:54:28 +02:00
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.
...
* 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.
...
* 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.
...
* gnu/packages/lxde.scm (lxsession)[arguments]: Remove autoreconf phase and
end rm-stamp phase with #T.
2018-11-11 10:16:43 +01:00
261e421459
gnu: python-pyclipper: Enable tests.
...
* gnu/packages/python.scm (python-pyclipper)[arguments]: Enable tests.
[native-inputs]: Add python-pytest, python-pytest-runner,
python-unittest2.
2018-11-11 11:13:56 +02:00
8189ce6f05
gnu: python-pyclipper: Update to 1.1.0post1.
...
* gnu/packages/python.scm (python-pyclipper): Update to 1.1.0post1.
[source]: Add snippet to remove cythonized source files.
[arguments]: Add custom phase to generate cythonized files.
[native-inputs]: Add python-cython.
[description]: Update clipper library version.
2018-11-11 11:13:56 +02:00
95176544d5
gnu: python-paste: Update to 3.0.4.
...
* gnu/packages/python-web.scm (python-paste): Update to 3.0.4.
[source]: Remove patch, add snippet to remove one test.
[native-inputs]: Add python-pytest, python-pytest-runner.
* gnu/packages/patches/python-paste-remove-website-test.patch: Remove
file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-11-11 11:13:56 +02:00
5ac2b2717f
gnu: python-networkx2: Remove variable.
...
* gnu/packages/python.scm (python-networkx2): Remove variable.
* gnu/packages/patches/python-networkx2-reproducible-build.patch: Remove
file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-11-11 11:13:55 +02:00
c92d056a8b
gnu: python-alembic: Update to 1.0.2.
...
* gnu/packages/databases.scm (python-alembic, python2-alembic): Update
to 1.0.2.
2018-11-11 11:13:53 +02:00
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
28b24e9975
gnu: bitshuffle: Don't use '-march=native'.
...
* gnu/packages/compression.scm (bitshuffle)[arguments]: Add custom phase
to substitute out the '-march=native' compilation flag.
2018-11-11 08:57:16 +02:00
01029e2043
gnu: bitshuffle: Update to 0.3.5.
...
* gnu/packages/compression.scm (bitshuffle): Update to 0.3.5.
[source]: Add snippet to remove cythonized source files.
2018-11-11 08:57:16 +02:00
5528b8e788
gnu: tvtime: Fix building with glibc@2.28.
...
* gnu/packages/tvtime.scm (tvtime)[arguments]: Add custom phase to add
missing import.
2018-11-11 08:57:13 +02:00
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
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
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
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
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
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.
...
* 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.
...
* 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.
...
* 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
1a392ee7ae
gnu: nfs-utils: Fix building with glibc@2.28.
...
* gnu/packages/nfs.scm (nfs-utils)[arguments]: Add custom phase to fix
building with glibc@2.28 .
2018-11-10 22:36:33 +02:00
c1ab159085
gnu: perl-autovivification: Update to 0.18.
...
* gnu/packages/perl.scm (perl-autovivification): Update to 0.18.
2018-11-10 22:36:33 +02:00
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
1de2937283
gnu: idutils: Fix building with glibc@2.28.
...
* gnu/packages/idutils.scm (idutils)[source]: Add snippet to patch
bundled gnulib for glibc@2.28 .
2018-11-10 20:18:37 +02:00
211db9caf7
gnu: sharutils: Remove false comment.
...
This is a follow-up to b50d58b344
2018-11-10 20:18:37 +02:00
9829e0699b
gnu: lbzip2: Remove false comment.
...
This is a follow-up to f268b744b8
2018-11-10 20:18:34 +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
f268b744b8
gnu: lbzip2: Fix building with glibc@2.28.
...
* gnu/packages/compression.scm (lbzip2)[source]: Add snippet to patch
bundled gnulib for glibc@2.28 .
2018-11-10 20:07:56 +02:00
efe0a4a2a7
gnu: dvd+rw-tools: Use invoke.
...
* gnu/packages/cdrom.scm (dvd+rw-tools): Use 'invoke'.
2018-11-10 19:59:30 +02:00
2529c8381f
gnu: dvd+rw-tools: Fix building with glibc@2.28.
...
* gnu/packages/cdrom.scm (dvd+rw-tools)[arguments]: Add custom phase to
add missing import.
2018-11-10 19:59:27 +02:00
8754ea483d
gnu: f2fs-tools: Update to 1.11.0.
...
* gnu/packages/linux.scm (f2fs-tools): Update to 1.11.0.
2018-11-10 19:29:17 +02:00
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
64461ba20a
Merge branch 'master' into core-updates
2018-11-09 17:02:08 +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.
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* gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
2018-11-07 21:41:55 +01:00
9d94ca0ebf
gnu: minced: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
b58d9e4aa2
gnu: metabat: Fetch sources from git.
...
* 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
55174e668f
Merge branch 'master' into core-updates
2018-11-07 21:09:57 +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
1badc85068
gnu: ceph: Update to 13.2.2.
...
* gnu/packages/patches/ceph-skip-unittest_blockdev.patch: Adjust for 13.2.2.
* gnu/packages/patches/ceph-rocksdb-compat.patch: Delete file.
* gnu/packages/patches/ceph-detect-rocksdb.patch,
gnu/packages/patches/ceph-volume-respect-PATH.patch: New files.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/storage.scm (ceph): Update to 13.2.2.
[source]: Don't remove src/dpdk, which has been moved to src/spdk/dpdk and
is purged elsewhere. Drop bundled rapidjson. Adjust patch list.
[arguments]: Add "-DWITH_MGR_DASHBOARD_FRONTEND=OFF" and "-DWITH_SPDK=OFF" to
#:configure-flags. Drop obsolete "-DWITH_EMBEDDED". Add workaround for
<https://bugs.gnu.org/30756 >. Remove obsolete test substitution. Rework
'wrap-python-script' to be less verbose and wrap more scripts.
[native-inputs]: Add GCC-7.
[inputs]: Add OATH-TOOLKIT, RAPIDJSON and PYTHON2-SIX.
2018-11-07 21:01:12 +01:00
2dc28391f3
gnu: kaiju: Update to 1.6.3.
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* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
2018-11-07 20:47:22 +01:00
6fe323bf2e
gnu: kaiju: Fetch sources from git.
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* 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.
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* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
2018-11-07 20:32:29 +01:00
c8f02c1dcb
gnu: grit: Update to 2.0.5.
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* gnu/packages/bioinformatics.scm (grit): Update to 2.0.5.
[arguments]: Simplify.
2018-11-07 20:30:44 +01:00
8d75adbf03
gnu: grit: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
2018-11-07 20:27:10 +01:00
152bebd9e0
gnu: gemma: Update to 0.98.
...
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/gemma-intel-compat.patch: Remove file.
* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.
[source]: Remove patch.
[inputs]: Add eigen, gfortran:lib, and openblas.
[arguments]: Add phase "find-eigen".
2018-11-07 20:26:46 +01:00
b113f39019
gnu: gemma: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
2018-11-07 20:26:45 +01:00
f09e8abc5e
gnu: clementine: Build with sqlite-with-column-metadata.
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* gnu/packages/music.scm (clementine)[inputs]: Use sqlite-with-column-metadata.
Signed-off-by: Leo Famulari <leo@famulari.name>
2018-11-07 14:25:07 -05:00
91b71cfbba
gnu: fxtract: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
2018-11-07 19:55:50 +01:00
7ca49ab57a
gnu: ribodiff: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
2018-11-07 19:48:21 +01:00
239716fb0b
gnu: python-biom-format: Update to 2.1.7.
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* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.7.
[arguments]: Add phases "use-cython", "disable-broken-test", and
"make-files-writable".
[propagated-inputs]: Add python-flake8.
[native-inputs]: Add python-cython, python-pytest, and python-pytest-cov.
2018-11-07 19:47:07 +01:00
007a81d5cf
gnu: python-biom-format: Fetch source from git.
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* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Fetch from
git.
2018-11-07 19:10:36 +01:00
383cb7b8e6
gnu: bioawk: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
2018-11-07 19:06:30 +01:00
20ee3e8b76
gnu: bedtools-2.18: Fetch sources from stable URL.
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* gnu/packages/bioinformatics.scm (bedtools-2.18)[source]: Use stable release
tarball instead of generated tag tarball.
2018-11-07 18:52:46 +01:00
8e58319c45
gnu: bamtools: Fetch sources from git.
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* 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.
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* gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools.
[inputs]: Add prodigal, bwa, samtools, and minimap2.
2018-11-07 17:19:53 +01:00
fff67cc8a7
gnu: prodigal: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
2018-11-07 17:19:53 +01:00
e2568df74e
gnu: rocksdb: Update to 5.15.10.
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* gnu/packages/databases.scm (rocksdb): Update to 5.15.10.
2018-11-07 16:06:56 +01:00
8dd3665883
gnu: rocksdb: Don't use unstable tarball.
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* gnu/packages/databases.scm (rocksdb)[source]: Use GIT-FETCH.
2018-11-07 16:06:56 +01:00
dcb45127e0
services: cuirass: Add 'ttl' configuration field.
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.0.
[inputs]: Remove netcdf.
[propagated-inputs]: Add r-ncdf4.
2018-11-07 12:27:16 +01:00
37200dbcc3
gnu: r-rhdf5lib: Update to 1.4.0.
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* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.0.
[source]: Add snippet to remove bundled binaries.
[arguments]: Replace references to hdf5 with references to hdf5-1.10.
[native-inputs]: Likewise.
[propagated-inputs]: Replace hdf5 with hdf5-1.10.
2018-11-07 12:27:16 +01:00
8e48d36f26
gnu: r-hdf5array: Update to 1.10.0.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.16.0.
2018-11-07 12:26:33 +01:00
286157dc49
gnu: Add r-biocneighbors.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* gnu/packages/bioconductor.scm (r-hpar): Update to 1.24.0.
2018-11-07 12:26:31 +01:00
1e605c030f
gnu: Add r-biocmanager.
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* gnu/packages/cran.scm (r-biocmanager): New variable.
2018-11-07 12:26:31 +01:00
b58940cb03
gnu: Add r-ncdf4.
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* gnu/packages/cran.scm (r-ncdf4): New variable.
2018-11-07 12:26:31 +01:00
bfa5662e38
gnu: Add r-rcppannoy.
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* 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].
...
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.
...
* 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.
...
* 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.
...
* 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."
...
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.
...
* 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'.
...
* gnu/services/dns.scm (ddclient-activation): Fix procedure.
2018-11-06 07:16:44 +03:00
3bd83e6db2
gnu: qtbase: Remove obsolete patch.
...
This patch is no longer needed since 7930cfc989
2018-11-06 00:04:31 +01:00
f4a5faa9dc
Merge branch 'master' into core-updates
2018-11-05 23:56:22 +01:00
adde15186d
gnu: xf86-video-intel: Update to commit 0932a6b37ba6d5c9e916a1cb6ab89c3205b81a0c.
...
* 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.
...
* gnu/packages/ssh.scm (libssh): Update to 0.7.7.
2018-11-05 23:46:38 +01:00
b5a887637c
gnu: strace: Update to 4.25.
...
* gnu/packages/linux.scm (strace): Update to 4.25.
2018-11-05 23:46:38 +01:00
876428dd98
gnu: libmtp: Update to 1.1.16.
...
* gnu/packages/libusb.scm (libmtp): Update to 1.1.16.
2018-11-05 23:46:38 +01:00
039241bc96
gnu: libgit2: Update to 0.26.8.
...
* gnu/packages/version-control.scm (libgit2): Update to 0.26.8.
2018-11-05 23:46:38 +01:00
c98a7e6b91
gnu: i3-wm: Update to 4.16.
...
* gnu/packages/wm.scm (i3-wm): Update to 4.16.
2018-11-05 23:46:38 +01:00
9c415f96ec
gnu: libgphoto2: Update to 2.5.20.
...
* gnu/packages/photo.scm (libgphoto2): Update to 2.5.20.
2018-11-05 23:46:38 +01:00
66044a3698
gnu: glm: Update to 0.9.9.3.
...
* gnu/packages/maths.scm (glm): Update to 0.9.9.3.
2018-11-05 23:46:38 +01:00
64b60f38e7
gnu: ffmpeg: Update to 4.0.3.
...
* gnu/packages/video.scm (ffmpeg): Update to 4.0.3.
2018-11-05 23:46:38 +01:00
c5e5711002
gnu: ffmpeg@3.4: Update to 3.4.5.
...
* gnu/packages/video.scm (ffmpeg-3.4): Update to 3.4.5.
2018-11-05 23:46:37 +01:00
196653145a
gnu: feh: Update to 2.28.1.
...
* gnu/packages/image-viewers.scm (feh): Update to 2.28.1.
2018-11-05 23:46:37 +01:00
00815eea38
gnu: libsoup: Update to 2.64.2.
...
* gnu/packages/gnome.scm (libsoup): Update to 2.64.2.
2018-11-05 23:46:37 +01:00
0a56ffdf1f
gnu: mono: Update home page.
...
* gnu/packages/mono.scm (mono)[home-page]: Use HTTPS.
2018-11-05 23:46:37 +01:00
288d24800d
gnu: ruby-rack: Update to 2.0.6 [fixes CVE-2018-{16470,16471}].
...
* gnu/packages/ruby.scm (ruby-rack): Update to 2.0.6.
2018-11-05 16:22:11 -05:00
426ffb830a
gnu: emacs-mu4e-conversation: Update to 20181105.
...
* gnu/packages/emacs.scm (emacs-mu4e-conversation): Update to 20181105.
2018-11-05 20:22:06 +01:00
695db2f98a
gnu: Add emacs-helm-slime.
...
* gnu/packages/emacs.scm (emacs-helm-slime): New variable.
2018-11-05 13:58:33 +01:00
c9f3d38be4
gnu: linux-libre: Update to 4.19.1.
...
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.19.1.
(%linux-libre-hash): Update hash.
2018-11-05 04:00:45 -05:00
28c717213d
gnu: linux-libre@4.14: Update to 4.14.79.
...
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.79.
(%linux-libre-4.14-hash): Update hash.
2018-11-05 04:00:43 -05:00
cddc044ce7
libreoffice: honor '--cores=...' during build.
...
* gnu/packages/libreoffice.scm (libreoffice)[configure-flags]: Add
'--with-parallelism' flag.
2018-11-04 21:56:39 -06:00
64eb038eef
gnu: Add fswatch.
...
* gnu/packages/monitoring.scm (fswatch): New variable.
2018-11-05 03:01:21 +01:00
1417f50317
gnu: python-ilinkedlist: Update to 0.2.0.
...
* gnu/packages/python.scm (python-ilinkedlist): Update to 0.2.0.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-05 00:08:47 +01:00
b6e9514864
gnu: pelican: Update to 3.7.1.
...
* gnu/packages/python.scm (pelican): Update to 3.7.1.
[home-page]: Use HTTPS URL.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-05 00:08:47 +01:00
c834bd3bb2
gnu: xonotic: Add icon and category to desktop files.
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* gnu/packages/games.scm (xonotic): Add icon ("xonotic") and category
("Game") to the .desktop files for Xonotic.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-05 00:08:47 +01:00
688d1a01e4
artwork: Clone over HTTPS.
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Suggested by Leo Famulari <leo@famulari.name>
at <https://lists.gnu.org/archive/html/help-guix/2018-11/msg00039.html >.
* gnu/artwork.scm (%artwork-repository): Switch to HTTPS URL.
2018-11-05 00:08:47 +01:00
ab3c60ace3
install: Parameterize the profile name for 'populate-single-profile-directory'.
...
* gnu/build/install.scm (populate-single-profile-directory): Add
#:profile-name. Replace hard-coded occurrences of "guix-profile" with
PROFILE-NAME. Make the symlink part under /root a function of
PROFILE-NAME.
2018-11-05 00:08:46 +01:00
97b7b96efc
gnu: go-github-com-urfave-cli: Remove duplicate declaration.
...
* gnu/packages/golang.scm (go-github-com-urfave-cli): Remove duplicate declaration.
2018-11-04 23:33:24 +01:00
30012b7408
gnu: myrepos: Wrap the webcheckout binary.
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* gnu/packages/version-control.scm (myrepos)[arguments]: Add a custom
'wrap-webcheckout phase to wrap webcheckout with its perl libraries.
[inputs]: Add perl-encode-locale, perl-html-parser, perl-http-date,
perl-http-message, perl-libwww, perl-try-tiny, perl-uri.
2018-11-04 12:45:27 +02:00
f909e21797
gnu: debian-archive-keyring: Update to 2018.1.
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* gnu/packages/debian.scm (debian-archive-keyring): Update to 2018.1.
[source]: Download from git repository.
2018-11-04 12:00:13 +02:00
2e77bbed71
gnu: ruby@2.3: Update to 2.3.8.
...
* gnu/packages/ruby.scm (ruby@2.3): Update to 2.3.8.
2018-11-04 12:00:13 +02:00
d4b5e4bb73
gnu: debootstrap: Update to 1.0.109.
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* gnu/packages/debian.scm (debootstrap): Update to 1.0.109.
2018-11-04 12:00:10 +02:00
3e84ce51fb
gnu: mpop: Update to 1.4.0.
...
* gnu/packages/mail.scm (mpop): Update to 1.4.0.
2018-11-04 10:36:17 +05:30
e9f305a1c8
gnu: sbcl-lift: Don't keep the bundled website.
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* gnu/packages/lisp.scm (sbcl-lift)[source]: Remove bundled website.
[arguments]: Remove custom 'make-gzips-writable phase.
2018-11-03 20:43:35 +02:00
0e091b3e93
gnu: totem: Update to 3.26.2.
...
* gnu/packages/gnome.scm (totem): Update to 3.26.2.
2018-11-03 15:44:40 +01:00
504f0cf198
gnu: emacs-debbugs: Update to 0.16.
...
* gnu/packages/emacs.scm (emacs-debbugs): Update to 0.16.
2018-11-03 15:44:24 +01:00
a7c8574f39
gnu: perl-image-exiftool: Update to 11.11.
...
* gnu/packages/photo.scm (perl-image-exiftool): Update to 11.11.
2018-11-03 15:16:42 +01:00
46c8f53ba8
gnu: emacs-dired-du: Update to 0.5.1.
...
* gnu/packages/emacs.scm (emacs-dired-du): Update to 0.5.1.
2018-11-03 15:16:20 +01:00
8e5c59868c
gnu: diffoscope: Update to 104.
...
* gnu/packages/package-management.scm (diffoscope): Update to 104.
2018-11-03 15:16:02 +01:00
b1c7f5fff9
gnu: emacs-emms: Update to 5.1.
...
* gnu/packages/emacs.scm (emacs-emms): Update to 5.1.
2018-11-03 19:14:05 +05:30
3995e85462
gnu: tor: Update to 0.3.4.9.
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* gnu/packages/tor.scm (tor): Update to 0.3.4.9.
2018-11-02 19:51:12 +01:00
ff349415b2
gnu: python-apache-libcloud: Update to 2.3.0.
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* gnu/packages/python.scm (python-apache-libcloud)
(python2-apache-libcloud): Update to 2.3.0.
2018-11-02 14:32:24 +01:00
722aac1ea1
Merge remote-tracking branch 'origin/wip-rust' into master.
2018-11-02 11:01:45 +01:00
b3325eb306
gnu: Go 1.11: Avoid unnecessary store references.
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This shrinks the closure of Go 1.11 from 1379 MiB to 581 MiB.
Fixes <https://bugs.gnu.org/32949 >.
* gnu/packages/golang.scm (go-1.11)[arguments]: Add a 'delete-extraneous-files'
phase.
2018-11-01 23:23:09 -04:00
16b89ecc1f
gnu: Add openjdk10.
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* gnu/packages/java.scm (openjdk10): New variable.
2018-11-01 21:16:59 +01:00
dd74105925
gnu: Add openjdk9.
...
* gnu/packages/java.scm (openjdk9): New variable.
2018-11-01 20:34:08 +01:00
7571ec3576
gnu: MPD: Update to 0.20.23.
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* gnu/packages/mpd.scm (mpd): Update to 0.20.23.
2018-11-01 15:30:05 -04:00
33279c2a19
gnu: mpd-mpc: Update to 0.31.
...
* gnu/packages/mpd.scm (mpd-mpc): Update to 0.31.
[native-inputs]: Add python-sphinx.
2018-11-01 15:30:05 -04:00
361dd8a556
gnu: icecast: Update to 2.4.4 [fixes CVE-2018-18820].
...
* gnu/packages/xiph.scm (icecast): Update to 2.4.4.
2018-11-01 12:33:14 -04:00
d7ca1899aa
gnu: mame: Update to 0.203.
...
* gnu/packages/emulators.scm (mame): Update to 0.203.
2018-11-01 09:24:52 +01:00
a769a4d432
gnu: xpra: Update to 2.4.1.
...
* gnu/packages/xorg.scm (xpra): Update to 2.4.1.
2018-11-01 08:32:45 +01:00
e7039f10ec
gnu: dolphin-emu: Use ffmpeg instead of ffmpeg@3.4.
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* gnu/packages/emulators.scm (dolphin-emu): Use ffmpeg instead of ffmpeg@3.4.
2018-11-01 08:20:13 +01:00
ee3dd7a83a
gnu: sdl2: Update to 2.0.9.
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* gnu/packages/sdl.scm (sdl2): Update to 2.0.9.
2018-11-01 08:20:13 +01:00
66a2a47117
gnu: whois: Update to 5.4.0.
...
* gnu/packages/networking.scm (whois): Update to 5.4.0.
2018-11-01 04:34:25 +01:00
38fda1cc36
gnu: highlight: Update to 3.47.
...
* gnu/packages/pretty-print.scm (highlight): Update to 3.47.
2018-11-01 04:34:25 +01:00
a72d337fbc
gnu: python-jsonrpclib-pelix: Update to 0.3.2.
...
* gnu/packages/python.scm (python-jsonrpclib-pelix): Update to 0.3.2.
[arguments]: Disable #:tests?.
2018-11-01 04:34:25 +01:00
60ed87871d
gnu: python-pynacl: Update to 1.3.0.
...
* gnu/packages/python-crypto.scm (python-pynacl): Update to 1.3.0.
2018-11-01 04:34:24 +01:00
351a12b0a7
gnu: oniguruma: Update to 6.9.0.
...
* gnu/packages/textutils.scm (oniguruma): Update to 6.9.0.
2018-11-01 04:34:24 +01:00
33bddd309c
gnu: motion: Install translations.
...
* gnu/packages/video.scm (motion)[native-inputs]: Add gettext-minimal.
2018-11-01 04:34:24 +01:00
2ea678fabf
gnu: motion: Don't use unstable tarball.
...
* gnu/packages/video.scm (motion)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
2018-11-01 04:34:24 +01:00
4fbcfc1482
Keep (gnu packages video) module imports in order.
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* gnu/packages/video.scm (define-module): Re-order module imports
alphabetically.
2018-11-01 04:33:54 +01:00
c3069cd183
gnu: motion: Update to 4.2.
...
* gnu/packages/video.scm (motion): Update to 4.2.
2018-11-01 04:32:35 +01:00
2930a39b16
gnu: julia: Update objconv input to 2018-10-07.
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* gnu/packages/julia.scm (julia)[input]: Update objconf to 2018-10-07.
2018-11-01 04:32:35 +01:00
c16913d34d
gnu: myrepos: Update to 1.20180726.
...
* gnu/packages/version-control.scm (myrepos): Update to 1.20180726.
[source]: Remove patch.
* gnu/packages/patches/myrepos-CVE-2018-7032.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-10-31 21:57:02 +02:00
c438e0cc74
gnu: curl: Update grafted replacement to 7.62.0 [security fixes].
...
Fixes CVE-2018-{16839,16840,16842}.
* gnu/packages/curl.scm (curl)[replacement]: Update to 7.62.0.
(curl-7.61.1): Replace with ...
(curl-7.62.0): ... new variable.
2018-10-31 13:54:20 -04:00
124e9d6e0a
gnu: dolphin-emu: Update to commit 22ddd11.
...
* gnu/packages/emulators.scm (dolphin-emu): Update to commit 22ddd11.
[arguments]: Return #t with phase 'fixgcc7.
2018-10-31 10:40:04 +01:00
3126bee69a
gnu: wine-staging: Update to 3.19.
...
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.19.
* gnu/packages/wine.scm (wine-staging): Update to 3.19.
2018-10-31 09:39:55 +01:00
a45a92ccd8
gnu: webkitgtk@2.22: Update to 2.22.3.
...
* gnu/packages/webkit.scm (webkitgtk-2.22): Update to 2.22.3.
2018-10-31 01:47:52 -04:00
c7ac8e36e2
gnu: quaternion: Update to 0.0.9.3.
...
* gnu/packages/messaging.scm (quaternion): Update to 0.0.9.3.
[inputs]: Add qtquickcontrols, qtsvg and qttools.
[arguments]: Remove fix-libqmatrixclient-dynamic-linking phase. Add
wrap-program phase.
2018-10-31 09:31:59 +05:30
c6588749a6
gnu: libqmatrixclient: Update to 0.4.0.
...
* gnu/packages/messaging.scm (libqmatrixclient): Update to 0.4.0.
2018-10-31 09:31:59 +05:30
b590951ff2
gnu: meandmyshadow: Update home page.
...
* gnu/packages/games.scm (meandmyshadow)[home-page]: Follow permanent
redirect.
2018-10-31 02:31:18 +01:00
1d9a9d27ae
gnu: meandmyshadow: Update to 0.5.
...
* gnu/packages/games.scm (meandmyshadow): Update to 0.5.
[source]: Add unreleased bugfix patch.
[arguments]: Remove obsolete ‘set-sdl'paths’ phase.
[inputs]: Switch to SDL 2. Add lua. Remove libx11, mesa, and glu.
* gnu/packages/patches/meandmyshadow-define-paths-earlier.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2018-10-31 02:31:18 +01:00
4cae7e67f3
gnu: hyperrogue: Update to 10.4x.
...
* gnu/packages/games.scm (hyperrogue): Update to 10.4x.
2018-10-30 23:40:43 +01:00
21fc352bad
gnu: yosys: Don't use unstable tarball.
...
* gnu/packages/fpga.scm (yosys)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2018-10-30 23:40:43 +01:00
becee7029f
gnu: disorderfs: Update to 0.5.5.
...
* gnu/packages/file-systems.scm (disorderfs): Update to 0.5.5.
2018-10-30 23:40:42 +01:00
58cd3123ac
gnu: pulseview: Update to 0.4.1.
...
* gnu/packages/electronics.scm (pulseview): Update to 0.4.1.
[arguments]: Remove CMAKE_CXX_FLAGS from #:configure-flags. (Keep)
build(ing) the unit tests. Add a ‘remove-empty-doc-directory’ phase.
2018-10-30 23:40:42 +01:00
61c58b7827
gnu: sigrok-cli: Update to 0.7.1.
...
* gnu/packages/electronics.scm (sigrok-cli): Update to 0.7.1.
2018-10-30 23:40:42 +01:00
295fc4152a
gnu: cloc: Update to 1.80.
...
* gnu/packages/code.scm (cloc): Update to 1.80.
2018-10-30 23:40:42 +01:00
1204402a90
gnu: python-partd: Update to 0.3.9.
...
* gnu/packages/python.scm (python-partd): Update to 0.3.9.
2018-10-30 23:40:42 +01:00
fd649d1e68
gnu: Add r-r2glmm.
...
* gnu/packages/cran.scm (r-r2glmm): New variable.
2018-10-30 22:47:35 +01:00
7c02dd6268
gnu: Add r-lmertest.
...
* gnu/packages/cran.scm (r-lmertest): New variable.
2018-10-30 22:47:26 +01:00
49863fd695
gnu: Add r-afex.
...
* gnu/packages/cran.scm (r-afex): New variable.
2018-10-30 22:47:18 +01:00
20ff6e3a34
gnu: Add r-mvabund.
...
* gnu/packages/cran.scm (r-mvabund): New variable.
2018-10-30 22:47:10 +01:00
4fb35ebd8d
gnu: Add r-rcppgsl.
...
* gnu/packages/cran.scm (r-rcppgsl): New variable.
2018-10-30 22:47:00 +01:00
373cef0a0c
gnu: Add r-tweedie.
...
* gnu/packages/cran.scm (r-tweedie): New variable.
2018-10-30 22:46:47 +01:00
32499b26e6
gnu: Add r-clusteval.
...
* gnu/packages/cran.scm (r-clusteval): New variable.
2018-10-30 22:13:01 +01:00
7a06cdfa8c
gnu: r-analytics: Update to 3.0.
...
* gnu/packages/cran.scm (r-analytics): Update to 3.0.
[propagated-inputs]: Add r-vim.
2018-10-30 21:48:10 +01:00
e5f9e9fa79
gnu: r-radiant-data: Update to 0.9.7.
...
* gnu/packages/cran.scm (r-radiant-data): Update to 0.9.7.
[propagated-inputs]: Add r-shinyfiles and r-summarytools.
2018-10-30 21:48:10 +01:00
39528a5ee9
gnu: r-pracma: Update to 2.1.8.
...
* gnu/packages/maths.scm (r-pracma): Update to 2.1.8.
[propagated-inputs]: Remove r-quadprog.
2018-10-30 21:48:10 +01:00
4633c8e6fc
gnu: r-shinydashboard: Update to 0.7.1.
...
* gnu/packages/web.scm (r-shinydashboard): Update to 0.7.1.
[propagated-inputs]: Add r-promises.
2018-10-30 21:48:10 +01:00
65279cc8f3
gnu: Add r-shinyfiles.
...
* gnu/packages/web.scm (r-shinyfiles): New variable.
2018-10-30 21:48:10 +01:00
a056e2251e
gnu: r-htmlwidgets: Update to 1.3.
...
* gnu/packages/web.scm (r-htmlwidgets): Update to 1.3.
2018-10-30 21:48:10 +01:00
f697ef4a0d
gnu: r-servr: Update to 0.11.
...
* gnu/packages/web.scm (r-servr): Update to 0.11.
2018-10-30 21:48:10 +01:00
8871a51350
gnu: r-webshot: Update to 0.5.1.
...
* gnu/packages/cran.scm (r-webshot): Update to 0.5.1.
[propagated-inputs]: Add r-callr; remove r-processx and r-withr.
2018-10-30 21:48:09 +01:00
d42f741035
gnu: r-dendextend: Update to 1.9.0.
...
* gnu/packages/cran.scm (r-dendextend): Update to 1.9.0.
2018-10-30 21:48:09 +01:00
31c8d9fe00
gnu: r-emmeans: Update to 1.3.0.
...
* gnu/packages/cran.scm (r-emmeans): Update to 1.3.0.
2018-10-30 21:48:09 +01:00
bec74196ea
gnu: r-abps: Update to 0.3.
...
* gnu/packages/cran.scm (r-abps): Update to 0.3.
2018-10-30 21:48:09 +01:00
464676a970
gnu: r-proc: Update to 1.13.0.
...
* gnu/packages/cran.scm (r-proc): Update to 1.13.0.
2018-10-30 21:48:03 +01:00
71d995392b
gnu: r-rdpack: Update to 0.10-1.
...
* gnu/packages/cran.scm (r-rdpack): Update to 0.10-1.
2018-10-30 21:47:54 +01:00
081af9fae7
gnu: r-hdf5r: Update to 1.0.1.
...
* gnu/packages/cran.scm (r-hdf5r): Update to 1.0.1.
2018-10-30 21:47:46 +01:00
08645fcff5
gnu: r-fansi: Update to 0.4.0.
...
* gnu/packages/cran.scm (r-fansi): Update to 0.4.0.
2018-10-30 21:47:37 +01:00
7608984fe9
gnu: r-later: Update to 0.7.5.
...
* gnu/packages/cran.scm (r-later): Update to 0.7.5.
2018-10-30 21:47:28 +01:00
80234d3294
gnu: r-maptools: Update to 0.9-4.
...
* gnu/packages/cran.scm (r-maptools): Update to 0.9-4.
2018-10-30 21:47:20 +01:00
fda8dd58c2
gnu: r-shinyace: Update to 0.3.2.
...
* gnu/packages/cran.scm (r-shinyace): Update to 0.3.2.
2018-10-30 21:47:06 +01:00
02c57c018a
gnu: r-np: Update to 0.60-9.
...
* gnu/packages/cran.scm (r-np): Update to 0.60-9.
2018-10-30 21:46:57 +01:00
44de41b572
gnu: r-expm: Update to 0.999-3.
...
* gnu/packages/cran.scm (r-expm): Update to 0.999-3.
2018-10-30 21:46:48 +01:00
484e81f73a
gnu: r-cubature: Update to 1.4-1.
...
* gnu/packages/cran.scm (r-cubature): Update to 1.4-1.
2018-10-30 21:46:36 +01:00
905734fd7c
gnu: r-extradistr: Update to 1.8.10.
...
* gnu/packages/cran.scm (r-extradistr): Update to 1.8.10.
2018-10-30 21:46:26 +01:00
534bf85b9d
gnu: r-ttr: Update to 0.23-4.
...
* gnu/packages/cran.scm (r-ttr): Update to 0.23-4.
2018-10-30 21:46:17 +01:00
dda4ce560f
gnu: r-tinytex: Update to 0.9.
...
* gnu/packages/cran.scm (r-tinytex): Update to 0.9.
2018-10-30 21:46:10 +01:00
a8de3090d8
gnu: r-xfun: Update to 0.4.
...
* gnu/packages/cran.scm (r-xfun): Update to 0.4.
2018-10-30 21:46:00 +01:00
8c456dff26
gnu: r-fitdistrplus: Update to 1.0-11.
...
* gnu/packages/cran.scm (r-fitdistrplus): Update to 1.0-11.
[propagated-inputs]: Add r-npsurv.
2018-10-30 21:45:51 +01:00
bba80fadbe
gnu: r-magic: Update to 1.5-9.
...
* gnu/packages/cran.scm (r-magic): Update to 1.5-9.
2018-10-30 21:45:42 +01:00
5621b8403b
gnu: r-sm: Update to 2.2-5.6.
...
* gnu/packages/cran.scm (r-sm): Update to 2.2-5.6.
2018-10-30 21:45:32 +01:00
870faab4b7
gnu: r-xts: Update to 0.11-1.
...
* gnu/packages/cran.scm (r-xts): Update to 0.11-1.
2018-10-30 21:45:16 +01:00
16a39c2d56
gnu: r-ggridges: Update to 0.5.1.
...
* gnu/packages/cran.scm (r-ggridges): Update to 0.5.1.
2018-10-30 21:45:07 +01:00
9e82d6080e
gnu: r-cli: Update to 1.0.1.
...
* gnu/packages/cran.scm (r-cli): Update to 1.0.1.
2018-10-30 21:44:59 +01:00
2b8126a4ec
gnu: r-reshape: Update to 0.8.8.
...
* gnu/packages/cran.scm (r-reshape): Update to 0.8.8.
2018-10-30 21:44:48 +01:00
ecdfca05c8
gnu: r-ffbase: Update to 0.12.5.
...
* gnu/packages/cran.scm (r-ffbase): Update to 0.12.5.
2018-10-30 21:44:38 +01:00
674c818560
gnu: r-rcpp: Update to 0.12.19.
...
* gnu/packages/cran.scm (r-rcpp): Update to 0.12.19.
2018-10-30 21:44:28 +01:00
0ab28e5450
gnu: r-pkgload: Update to 1.0.1.
...
* gnu/packages/cran.scm (r-pkgload): Update to 1.0.1.
2018-10-30 21:43:38 +01:00
2657e666cb
gnu: r-pkgbuild: Update to 1.0.2.
...
* gnu/packages/cran.scm (r-pkgbuild): Update to 1.0.2.
[propagated-inputs]: Add r-cli and r-prettyunits.
2018-10-30 21:43:28 +01:00
7e127ab128
gnu: r-ps: Update to 1.2.0.
...
* gnu/packages/cran.scm (r-ps): Update to 1.2.0.
2018-10-30 21:43:19 +01:00
b62e104b84
gnu: r-ape: Update to 5.2.
...
* gnu/packages/cran.scm (r-ape): Update to 5.2.
2018-10-30 21:43:10 +01:00
1c9906c2dd
gnu: r-reprex: Update to 0.2.1.
...
* gnu/packages/cran.scm (r-reprex): Update to 0.2.1.
[propagated-inputs]: Add r-fs, remove r-knitr.
2018-10-30 21:42:59 +01:00
6b451c0801
gnu: r-gprofiler: Update to 0.6.7.
...
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.7.
2018-10-30 21:42:48 +01:00
4fc6609a0c
gnu: r-keggrest: Update to 1.20.2.
...
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.2.
2018-10-30 21:42:39 +01:00
67cfb83ff1
gnu: r-msnbase: Update to 2.6.4.
...
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.4.
2018-10-30 21:42:31 +01:00
807d961cc9
gnu: r-methylkit: Update to 1.6.3.
...
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.3.
2018-10-30 21:42:20 +01:00
ac0166450d
gnu: r-wgcna: Update to 1.66.
...
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.66.
2018-10-30 21:42:09 +01:00
1182460750
gnu: r-go-db: Update to 3.6.0.
...
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.6.0.
2018-10-30 21:42:00 +01:00
466bf3af89
gnu: r-genomicfeatures: Update to 1.32.3.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.3.
2018-10-30 21:41:12 +01:00
dd0216e0e7
gnu: r-delayedarray: Update to 0.6.6.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.6.
2018-10-30 21:40:57 +01:00
72408357fa
gnu: r-genomicranges: Update to 1.32.7.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.7.
2018-10-30 21:40:48 +01:00
9dad1957ab
gnu: r-limma: Update to 3.36.5.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.5.
2018-10-30 21:40:40 +01:00
57cf6a14f0
gnu: r-edger: Update to 3.22.5.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.5.
2018-10-30 21:40:32 +01:00
eb890466fa
gnu: r-genomeinfodbdata: Update to 1.1.0.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.1.0.
2018-10-30 21:40:22 +01:00
e563acb96b
gnu: r-iranges: Update to 2.14.12.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.12.
2018-10-30 21:40:12 +01:00
192c19f484
gnu: r-vegan: Update to 2.5-3.
...
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-3.
2018-10-30 21:40:00 +01:00
696e1ce263
gnu: r-graph: Update to 1.58.2.
...
* gnu/packages/bioconductor.scm (r-graph): Update to 1.58.2.
2018-10-30 21:39:50 +01:00
6ab5670aba
gnu: r-nloptr: Update to 1.2.1.
...
* gnu/packages/statistics.scm (r-nloptr): Update to 1.2.1.
[native-inputs]: Add r-knitr and gfortran.
2018-10-30 21:39:39 +01:00
c5bd8a7c23
gnu: r-devtools: Update to 2.0.1.
...
* gnu/packages/statistics.scm (r-devtools): Update to 2.0.1.
[propagated-inputs]: Remove r-whisker; add r-callr, r-cli, r-pkgbuild,
r-pkgload, r-rcmdcheck, r-remotes, r-sessioninfo, and r-usethis.
2018-10-30 21:39:29 +01:00
aa99568639
gnu: r-evaluate: Update to 0.12.
...
* gnu/packages/statistics.scm (r-evaluate): Update to 0.12.
[propagated-inputs]: Remove r-stringr.
2018-10-30 21:39:16 +01:00
60aac7ec16
gnu: r-robustbase: Update to 0.93-3.
...
* gnu/packages/statistics.scm (r-robustbase): Update to 0.93-3.
2018-10-30 21:39:06 +01:00
16508df1d3
gnu: r-cardata: Update to 3.0-2.
...
* gnu/packages/statistics.scm (r-cardata): Update to 3.0-2.
2018-10-30 21:38:55 +01:00
98a4b9d040
gnu: r-zoo: Update to 1.8-4.
...
* gnu/packages/statistics.scm (r-zoo): Update to 1.8-4.
2018-10-30 21:38:35 +01:00
834f203c07
gnu: r-tidyselect: Update to 0.2.5.
...
* gnu/packages/statistics.scm (r-tidyselect): Update to 0.2.5.
2018-10-30 21:38:25 +01:00
33fb92aacd
gnu: r-doparallel: Update to 1.0.14.
...
* gnu/packages/statistics.scm (r-doparallel): Update to 1.0.14.
2018-10-30 21:38:16 +01:00
3ea7aefd59
gnu: r-snow: Update to 0.4-3.
...
* gnu/packages/statistics.scm (r-snow): Update to 0.4-3.
2018-10-30 21:38:03 +01:00
62a7492c90
gnu: r-plotrix: Update to 3.7-4.
...
* gnu/packages/statistics.scm (r-plotrix): Update to 3.7-4.
2018-10-30 21:37:53 +01:00
943cab4f72
gnu: r-rstudioapi: Update to 0.8.
...
* gnu/packages/statistics.scm (r-rstudioapi): Update to 0.8.
2018-10-30 21:37:35 +01:00
960425c9e3
gnu: r-commonmark: Update to 1.6.
...
* gnu/packages/statistics.scm (r-commonmark): Update to 1.6.
2018-10-30 21:37:25 +01:00
e028eaa992
gnu: r-coda: Update to 0.19-2.
...
* gnu/packages/statistics.scm (r-coda): Update to 0.19-2.
2018-10-30 21:37:14 +01:00
672ba7494b
gnu: r-data-table: Update to 1.11.8.
...
* gnu/packages/statistics.scm (r-data-table): Update to 1.11.8.
2018-10-30 21:37:03 +01:00
f75ee8c691
gnu: r-dplyr: Update to 0.7.7.
...
* gnu/packages/statistics.scm (r-dplyr): Update to 0.7.7.
2018-10-30 21:36:54 +01:00
17f6198f06
gnu: r-rlang: Update to 0.3.0.1.
...
* gnu/packages/statistics.scm (r-rlang): Update to 0.3.0.1.
2018-10-30 21:36:44 +01:00
822863f8f9
gnu: r-r6: Update to 2.3.0.
...
* gnu/packages/statistics.scm (r-r6): Update to 2.3.0.
2018-10-30 21:36:35 +01:00
3a83251c4f
gnu: r-testthat: Update to 2.0.1.
...
* gnu/packages/statistics.scm (r-testthat): Update to 2.0.1.
2018-10-30 21:36:24 +01:00
cb448dd251
gnu: r-microbenchmark: Update to 1.4-6.
...
* gnu/packages/statistics.scm (r-microbenchmark): Update to 1.4-6.
2018-10-30 21:36:13 +01:00
9f7438355d
gnu: r-mine: Update to 0.6.
...
* gnu/packages/statistics.scm (r-mine): Update to 0.6.
2018-10-30 21:36:04 +01:00
9413424d2d
gnu: r-ggplot2: Update to 3.1.0.
...
* gnu/packages/statistics.scm (r-ggplot2): Update to 3.1.0.
2018-10-30 21:35:52 +01:00
058394967c
gnu: r-digest: Update to 0.6.18.
...
* gnu/packages/statistics.scm (r-digest): Update to 0.6.18.
2018-10-30 21:35:40 +01:00
b85f805090
gnu: r-mgcv: Update to 1.8-25.
...
* gnu/packages/statistics.scm (r-mgcv): Update to 1.8-25.
2018-10-30 21:35:26 +01:00
2f5e8f6094
gnu: r-mass: Update to 7.3-51.
...
* gnu/packages/statistics.scm (r-mass): Update to 7.3-51.
2018-10-30 21:35:12 +01:00
2ea75a8369
gnu: Add r-npsurv.
...
* gnu/packages/cran.scm (r-npsurv): New variable.
2018-10-30 21:35:03 +01:00
7c7ee6cf4c
gnu: Add r-lsei.
...
* gnu/packages/cran.scm (r-lsei): New variable.
2018-10-30 21:34:55 +01:00
74cc74e434
gnu: Add r-summarytools.
...
* gnu/packages/cran.scm (r-summarytools): New variable.
2018-10-30 21:34:45 +01:00
319a80ce96
gnu: Add r-pander.
...
* gnu/packages/cran.scm (r-pander): New variable.
2018-10-30 21:34:35 +01:00
9b02d1a11e
gnu: Add r-rapportools.
...
* gnu/packages/cran.scm (r-rapportools): New variable.
2018-10-30 21:34:25 +01:00
5df4e27fec
gnu: Add r-rcmdcheck.
...
* gnu/packages/cran.scm (r-rcmdcheck): New variable.
2018-10-30 21:34:15 +01:00
7d8f34707a
gnu: Add r-xopen.
...
* gnu/packages/cran.scm (r-xopen): New variable.
2018-10-30 21:34:05 +01:00
cbc8e6dd4a
gnu: Add r-remotes.
...
* gnu/packages/cran.scm (r-remotes): New variable.
2018-10-30 21:33:56 +01:00
993426244e
gnu: Add r-sessioninfo.
...
* gnu/packages/cran.scm (r-sessioninfo): New variable.
2018-10-30 21:33:47 +01:00
efefd3ec42
gnu: Add r-usethis.
...
* gnu/packages/cran.scm (r-usethis): New variable.
2018-10-30 21:33:37 +01:00
153e5b2ddc
gnu: Add r-clisymbols.
...
* gnu/packages/cran.scm (r-clisymbols): New variable.
2018-10-30 21:33:25 +01:00
d6871153c8
gnu: Add r-fs.
...
* gnu/packages/cran.scm (r-fs): New variable.
2018-10-30 21:33:13 +01:00
21405e81e7
gnu: Add r-gh.
...
* gnu/packages/cran.scm (r-gh): New variable.
2018-10-30 21:33:00 +01:00
03f8011220
gnu: Add r-ini.
...
* gnu/packages/cran.scm (r-ini): New variable.
2018-10-30 21:32:45 +01:00
4df3e06210
gnu: rust: Document upstream's assessment.
...
* gnu/packages/patches/rust-1.25-accept-more-detailed-gdb-lines.patch: Add URL.
2018-10-30 20:42:04 +01:00
52bc7df1a1
gnu: rust: Remove binary bootstrapper.
...
* gnu/packages/rust.scm (rust-bootstrap): Delete variable.
2018-10-30 20:42:00 +01:00
44d530ef09
gnu: rust@1.23.0: Bootstrap from rust@1.22.0.
...
* gnu/packages/rust.scm (rust-1.23): Bootstrap from rust@1.22.0.
2018-10-30 20:41:55 +01:00
a75b8c08c0
gnu: rust@1.23.0: Inherit from rust@1.22.0.
...
* gnu/packages/rust.scm (rust-1.23)[inherit]: Inherit from rust-1.22.
[arguments]: Inherit from rust-1.22. Delete "remove-ar" phase.
2018-10-30 20:41:50 +01:00
7bf169f75c
gnu: rust: Hide "ar" entry from rust@1.21.0.
...
* gnu/packages/rust.scm (rust-1.21)[arguments]<#:phases>[remove-ar]: New
phase.
2018-10-30 20:41:45 +01:00
46cb1c97cb
gnu: rust: Accept more detailed gdb lines for simple enums.
...
* gnu/packages/patches/rust-1.25-accept-more-detailed-gdb-lines.patch: Modify.
* gnu/packages/rust.scm (rust-1.25)[arguments]<#:phases>[disable-nil-enum-test]:
Delete phase.
2018-10-30 20:20:55 +01:00
a6f2afeee1
gnu: zathura-pdf-mupdf: Simplify arguments.
...
* gnu/packages/pdf.scm (zathura-pdf-mupdf)[arguments]: Remove custom
'patch-plugin-directory phase, replacd with configure-flag.
2018-10-30 11:15:40 +02:00
24fc8f055d
gnu: zathura-pdf-mupdf: Update to 0.3.4.
...
* gnu/packages/pdf.scm (zathura-pdf-mupdf): Update to 0.3.4.
[source]: Remove patch.
* gnu/packages/patches/zathura-pdf-mupdf-link-to-jpeg-libraries.patch:
Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-10-30 11:15:39 +02:00
e726f0939e
gnu: mupdf: Update license list.
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* gnu/packages/pdf.scm (mupdf)[license]: Update the license list.
2018-10-30 11:15:36 +02:00
b1435fe735
gnu: mupdf: Update to 1.14.
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* gnu/packages/pdf.scm (mupdf): Update to 1.14.
[source]: Don't remove all the bundled libraries.
[arguments]: Add 'configure-flags to use system libraries.
2018-10-30 11:15:09 +02:00
f8ddf719f3
gnu: mujs: Install shared library.
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* gnu/packages/javascript.scm (mujs)[arguments]: Add custom phase to
install libmujs.so.
2018-10-30 11:03:48 +02:00
1371e2250a
gnu: mujs: Update to 1.0.5.
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* gnu/packages/javascript.scm (mujs): Update to 1.0.5.
2018-10-30 11:03:06 +02:00
a2717e6986
gnu: calcurse: Use HTTPS URLs.
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Reported by Marco van Hulten <marco@hulten.org>.
* gnu/packages/calcurse.scm (calcurse)[source, home-page]: Use HTTPS URLs.
2018-10-29 20:45:57 -04:00
b4c93a78c8
gnu: xorg-server: Update to 1.20.3 [fixes CVE-2018-14665].
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* gnu/packages/xorg.scm (xorg-server): Update to 1.20.3.
2018-10-28 18:22:46 -04:00
81f12f33b7
gnu: linux-libre: Enable BOCHS DRM support.
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* gnu/packages/aux-files/linux-libre/4.19-x86_64.conf: Build DRM BOCHS support
as a module. It adds DRM support for BOCHS dispi vga interface used by
qemu (-vga std option). It will also be useful for QEMU 3.0 to enable the new
"bochs-display" display device.
* gnu/packages/aux-files/linux-libre/4.19-i686.conf: Ditto.
2018-10-28 20:42:50 +09:00
852a5692bb
gnu: qt@4: Use invoke.
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* gnu/packages/qt.scm (qt@4)[arguments]: Use invoke.
2018-10-28 09:52:46 +02:00
1f71daf499
gnu: qt@4: Update build config.
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* gnu/packages/qt.scm (qt@4)[arguments]: Substitute hardcoded '/bin/ls'
invocation. Add configure-flags to not build the examples or demos.
Don't use the precompiled headers.
2018-10-28 09:52:38 +02:00
3ea61f9642
gnu: qt: Use invoke.
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* gnu/packages/qt.scm (qt)[arguments]: Use invoke.
2018-10-28 09:52:16 +02:00
124351efad
gnu: qt: Add vulkan support.
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* gnu/packages/qt.scm (qt, qtbase)[native-inputs]: Add vulkan-headers.
(qt@4)[native-inputs]: Don't add vulkan-headers.
(qttools)[native-inputs]: Add vulkan-headers.
2018-10-28 09:51:56 +02:00
d28af1991a
gnu: qt: Use system sqlite.
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* gnu/packages/databases.scm (sqlite-with-column-metadata): New
variable.
* gnu/packages/qt.scm (qt, qtbase)[source]: Remove bundled sqlite.
[inputs]: Add sqlite-with-column-metadata.
[arguments]: Add configure-flag to use system sqlite.
2018-10-28 09:51:25 +02:00
7930cfc989
gnu: qt: Update to 5.11.2.
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* gnu/packages/qt.scm (qt, qtbase, qtsvg, qtimageformats, qtx11extras,
qtxmlpatterns, qtdeclarative, qtconnectivity, qtwebsockets, qtsensors,
qtmultimedia, qtwayland, qtserialport, qtserialbus, qtwebchannel,
qtwebglplugin, qtwebview, qtlocation, qttools, qtscript,
qtquickcontrols, qtquickcontrols2, qtgraphicaleffects, qtgamepad,
qtscxml, qtpurchasing, qtcanvas3d, qtcharts, qtdatavis3d, qtnetworkauth,
qtremoteobjects, qtspeech): Update to 5.11.2.
2018-10-28 09:51:05 +02:00
Ricardo Wurmus