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Author SHA1 Message Date
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Those two packages (from the same author) are no longer maintained and do not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 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
Mathieu Othacehe 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
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
Ludovic Courtès 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
Ludovic Courtès 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 19c924af4f.

* gnu/build/install.scm (register-closure): Move to...
* gnu/build/vm.scm (register-closure): ... here.  New procedure.
* guix/scripts/pack.scm (self-contained-tarball)[build]: Remove
now unneeded 'with-extensions' form and custom (guix config) module.
* tests/guix-pack.sh: Revert the strategy from
commit 19c924af4f.
* tests/pack.scm ("self-contained-tarball"): Likewise.
 2018-11-06 23:21:23 +01:00
Ludovic Courtès 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
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
Oleg Pykhalov 7f860a8be1
gnu: services: dns: Fix 'ddclient-activation'. 
* gnu/services/dns.scm (ddclient-activation): Fix procedure.
 2018-11-06 07:16:44 +03:00
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