Commit Graph

29276 Commits (2f28ffd81d72307fb3ddf775662c74bac92101a5)

Author SHA1 Message Date
Ricardo Wurmus e22e462b33
gnu: r-riboprofiling: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-riboprofiling): Update to 1.12.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus e9427b2c78
gnu: r-ripseeker: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-ripseeker): Update to 1.22.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus aa802eafb6
gnu: r-chipcomp: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.12.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 4728e27511
gnu: r-bayseq: Update to 2.16.0.
* gnu/packages/bioconductor.scm (r-bayseq): Update to 2.16.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 57d2fcd9ee
gnu: r-chippeakanno: Update to 3.16.0.
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.16.0.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 14520b640e
gnu: r-graph: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-graph): Update to 1.60.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 95ee4a466b
gnu: r-multtest: Update to 2.38.0.
* gnu/packages/bioconductor.scm (r-multtest): Update to 2.38.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus a92f523026
gnu: r-qdnaseq: Update to 1.18.0.
* gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.18.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 9add0933d0
gnu: r-cghcall: Update to 2.44.0.
* gnu/packages/bioconductor.scm (r-cghcall): Update to 2.44.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 46cdceef4c
gnu: r-cghbase: Update to 1.42.0.
* gnu/packages/bioconductor.scm (r-cghbase): Update to 1.42.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus f1c606ce8c
gnu: r-marray: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-marray): Update to 1.60.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 98652568a4
gnu: r-diffbind: Update to 2.10.0.
* gnu/packages/bioconductor.scm (r-diffbind): Update to 2.10.0.
2018-11-07 12:26:31 +01:00
Ricardo Wurmus 6168692159
gnu: r-hpar: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-hpar): Update to 1.24.0.
2018-11-07 12:26:31 +01:00
Ricardo Wurmus 1e605c030f
gnu: Add r-biocmanager.
* gnu/packages/cran.scm (r-biocmanager): New variable.
2018-11-07 12:26:31 +01:00
Ricardo Wurmus b58940cb03
gnu: Add r-ncdf4.
* gnu/packages/cran.scm (r-ncdf4): New variable.
2018-11-07 12:26:31 +01:00
Ricardo Wurmus bfa5662e38
gnu: Add r-rcppannoy.
* gnu/packages/cran.scm (r-rcppannoy): New variable.
2018-11-07 12:26:31 +01:00
Mathieu Othacehe 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
Mathieu Othacehe 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
Mathieu Othacehe 581720bc74
gnu: Add guile-newt.
* gnu/packages/guile.scm (guile-newt): New variable.
2018-11-07 18:09:30 +09:00
Efraim Flashner cbb5d2e145
gnu: kodi: Fix typo.
This is a follow-up to 2c17bd7b29.

* gnu/packages/kodi.scm (kodi)[arguments]: Remove unwanted symbols.
2018-11-07 10:38:13 +02:00
Leo Famulari 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
Leo Famulari 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
Marius Bakke 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
Leo Famulari 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
Ludovic Courtès 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
Stefan Stefanović 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
Ludovic Courtès 3527f600b5
gnu: guile-sqlite3: Update home page.
* gnu/packages/guile.scm (guile-sqlite3)[home-page]: Update.
2018-11-06 17:00:01 +01:00
lakshmi 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
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 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
Rutger Helling c58f3ebaf8
gnu: ffmpeg: Update to 4.1.
* gnu/packages/video.scm (ffmpeg): Update to 4.1.
2018-11-06 12:02:59 +01:00
Efraim Flashner 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
Efraim Flashner 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
Marius Bakke 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
Marius Bakke 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
Marius Bakke 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
Marius Bakke b5a887637c
gnu: strace: Update to 4.25.
* gnu/packages/linux.scm (strace): Update to 4.25.
2018-11-05 23:46:38 +01:00
Marius Bakke 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
Marius Bakke 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
Marius Bakke 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
Marius Bakke 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
Marius Bakke 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
Marius Bakke 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
Marius Bakke 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
Marius Bakke 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
Marius Bakke 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
Marius Bakke 0a56ffdf1f
gnu: mono: Update home page.
* gnu/packages/mono.scm (mono)[home-page]: Use HTTPS.
2018-11-05 23:46:37 +01:00
Leo Famulari 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
Pierre Neidhardt 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
Pierre Neidhardt 695db2f98a
gnu: Add emacs-helm-slime.
* gnu/packages/emacs.scm (emacs-helm-slime): New variable.
2018-11-05 13:58:33 +01:00
Mark H Weaver 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
Mark H Weaver 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
Eric Bavier 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
Danny Milosavljevic 64eb038eef
gnu: Add fswatch.
* gnu/packages/monitoring.scm (fswatch): New variable.
2018-11-05 03:01:21 +01:00
Luther Thompson 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
Vagrant Cascadian 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
Pkill -9 c834bd3bb2
gnu: xonotic: Add icon and category to desktop files.
* 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
Pierre Neidhardt 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
Efraim Flashner 30012b7408
gnu: myrepos: Wrap the webcheckout binary.
* 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
Efraim Flashner f909e21797
gnu: debian-archive-keyring: Update to 2018.1.
* gnu/packages/debian.scm (debian-archive-keyring): Update to 2018.1.
[source]: Download from git repository.
2018-11-04 12:00:13 +02:00
Efraim Flashner 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
Efraim Flashner d4b5e4bb73
gnu: debootstrap: Update to 1.0.109.
* gnu/packages/debian.scm (debootstrap): Update to 1.0.109.
2018-11-04 12:00:10 +02:00
Arun Isaac 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
Efraim Flashner e9f305a1c8
gnu: sbcl-lift: Don't keep the bundled website.
* 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
Ludovic Courtès 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
Ludovic Courtès 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
Ludovic Courtès 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
Ludovic Courtès 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
Ludovic Courtès 8e5c59868c
gnu: diffoscope: Update to 104.
* gnu/packages/package-management.scm (diffoscope): Update to 104.
2018-11-03 15:16:02 +01:00
Arun Isaac 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
Tobias Geerinckx-Rice 3995e85462
gnu: tor: Update to 0.3.4.9.
* gnu/packages/tor.scm (tor): Update to 0.3.4.9.
2018-11-02 19:51:12 +01:00
Julien Lepiller ff349415b2
gnu: python-apache-libcloud: Update to 2.3.0.
* gnu/packages/python.scm (python-apache-libcloud)
(python2-apache-libcloud): Update to 2.3.0.
2018-11-02 14:32:24 +01:00
Danny Milosavljevic 722aac1ea1
Merge remote-tracking branch 'origin/wip-rust' into master. 2018-11-02 11:01:45 +01:00
Leo Famulari b3325eb306
gnu: Go 1.11: Avoid unnecessary store references.
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
Leo Famulari 7571ec3576
gnu: MPD: Update to 0.20.23.
* gnu/packages/mpd.scm (mpd): Update to 0.20.23.
2018-11-01 15:30:05 -04:00
Leo Famulari 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
Leo Famulari 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
Rutger Helling d7ca1899aa
gnu: mame: Update to 0.203.
* gnu/packages/emulators.scm (mame): Update to 0.203.
2018-11-01 09:24:52 +01:00
Rutger Helling 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
Rutger Helling e7039f10ec
gnu: dolphin-emu: Use ffmpeg instead of ffmpeg@3.4.
* gnu/packages/emulators.scm (dolphin-emu): Use ffmpeg instead of ffmpeg@3.4.
2018-11-01 08:20:13 +01:00
Rutger Helling ee3dd7a83a
gnu: sdl2: Update to 2.0.9.
* gnu/packages/sdl.scm (sdl2): Update to 2.0.9.
2018-11-01 08:20:13 +01:00
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 33bddd309c
gnu: motion: Install translations.
* gnu/packages/video.scm (motion)[native-inputs]: Add gettext-minimal.
2018-11-01 04:34:24 +01:00
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 4fbcfc1482
Keep (gnu packages video) module imports in order.
* gnu/packages/video.scm (define-module): Re-order module imports
alphabetically.
2018-11-01 04:33:54 +01:00
Tobias Geerinckx-Rice c3069cd183
gnu: motion: Update to 4.2.
* gnu/packages/video.scm (motion): Update to 4.2.
2018-11-01 04:32:35 +01:00
Tobias Geerinckx-Rice 2930a39b16
gnu: julia: Update objconv input to 2018-10-07.
* gnu/packages/julia.scm (julia)[input]: Update objconf to 2018-10-07.
2018-11-01 04:32:35 +01:00
Efraim Flashner 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
Leo Famulari 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
Rutger Helling 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
Rutger Helling 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
Mark H Weaver 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
Arun Isaac 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
Arun Isaac 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