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29708 Commits

Author SHA1 Message Date
Leo Famulari 7f6485e70c
gnu: icedtea@2: Update to 2.6.13 [security fixes]. 
Fixes CVE-2018-{2579,2588,2599,2602,2603,2618,2629,2633,2634,2637,2641,2663,
2677,2678}.

* gnu/packages/java.scm (icedtea-7): Update to 2.6.13.
 2018-03-16 10:53:10 -04:00
Ricardo Wurmus c1c9cc664b
gnu: Add pigx. 
* gnu/packages/bioinformatics.scm (pigx): New variable.
 2018-03-16 15:40:31 +01:00
Ricardo Wurmus fe52a215e5
gnu: pigx-rnaseq: Disable memory hungry test. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase to
disable a memory hungry test.
 2018-03-16 15:40:31 +01:00
Leo Famulari 77166eb758
gnu: util-linux: Fix CVE-2018-7738. 
* gnu/packages/patches/util-linux-CVE-2018-7738.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/linux.scm (util-linux)[replacement]: New field.
(util-linux/fixed): New variable.
 2018-03-16 10:31:52 -04:00
Konrad Hinsen 5d818b3557
gnu: Add emacs-deft. 
* gnu/packages/emacs.scm (emacs-deft): New variable.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2018-03-16 17:04:14 +03:00
Konrad Hinsen 22d628148c
gnu: Add emacs-exec-path-from-shell. 
* gnu/packages/emacs.scm (emacs-exec-path-from-shell): New variable.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2018-03-16 16:44:23 +03:00
Ricardo Wurmus 46264c73a6
gnu: Add pigx-scrnaseq. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): New variable.
 2018-03-16 11:15:04 +01:00
Ricardo Wurmus b44437c549
gnu: kentutils: Build with mariadb. 
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
 2018-03-16 10:01:07 +01:00
Mark H Weaver 3e5783e292
linux-initrd: Autoload known-module-aliases, again. 
Fixes a regression introduced in 8ab10c19d7.

* gnu/system/mapped-devices.scm: Autoload 'known-module-aliases'.
 2018-03-15 23:08:02 -04:00
Mark H Weaver 8e4ce40269
gnu: linux-libre: Update to 4.15.10. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.15.10.
(%linux-libre-hash): Update hash.
 2018-03-15 19:17:22 -04:00
Mark H Weaver 570d79c8df
gnu: linux-libre@4.14: Update to 4.14.27. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.27.
(%linux-libre-4.14-hash): Update hash.
 2018-03-15 19:16:25 -04:00
Ludovic Courtès 8ab10c19d7
linux-initrd: Move 'check-device-initrd-modules' elsewhere. 
This mostly reverts ca23693d28, which
introduced a circular dependency between (gnu system linux-initrd)
and (gnu system mapped-devices).

Reported by Eric Bavier.

* gnu/system/linux-initrd.scm (check-device-initrd-modules): Move to...
* gnu/system/mapped-devices.scm (check-device-initrd-modules): ... here.
* po/guix/POTFILES.in: Adjust accordingly.
 2018-03-15 23:46:16 +01:00
Alex ter Weele d661ed521e
gnu: idris: Provide the right versions of dependencies. 
Previously it would fail to build.  See <https://bugs.gnu.org/30741>.

* gnu/packages/idris.scm (idris)[inputs]: alphebetize
  ghc-vector-binary-instances and ghc-async. Use ghc-aeson-1.1.2.0,
  ghc-cheapskate-0.1.0.5, and ghc-trifecta-1.6.2.1. Remove ghc-aeson,
  ghc-cheapskate, ghc-parsers, ghc-tasty, ghc-tasty-golden, ghc-tasty-rerun,
  ghc-trifecta, and ghc-zlib.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-03-15 23:46:16 +01:00
Alex ter Weele 866b19086e
gnu: Add ghc-cheapskate-0.1.0.5. 
* gnu/packages/idris.scm (ghc-cheapskate-0.1.0.5): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-03-15 23:46:16 +01:00
Alex ter Weele 78dc985bee
gnu: Add ghc-trifecta-1.6.2.1. 
* gnu/packages/idris.scm (ghc-trifecta-1.6.2.1): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-03-15 23:46:15 +01:00
Alex ter Weele 9c7e17fd61
gnu: Add ghc-aeson-1.1.2.0. 
* gnu/packages/idris.scm (ghc-aeson-1.1.2.0): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-03-15 23:46:15 +01:00
Diego Nicola Barbato dab03baa0a
gnu: qtox: Wrap executable and fix misplaced comma (unquote). 
* gnu/packages/messaging.scm (qtox)[arguments]: Add phase
"wrap-executable".
[inputs]: Fix misplaced comma (unquote).

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-03-15 23:46:15 +01:00
Ludovic Courtès e1d0f2aa87
vm: Use 'invoke' instead of 'system*'. 
* gnu/build/vm.scm (load-in-linux-vm, initialize-partition-table)
(create-ext-file-system, create-fat-file-system)
(install-efi, make-iso9660-image): Use 'invoke' instead
of (unless (zero? (system* ...)) (error ...)).
 2018-03-15 23:46:15 +01:00
Tobias Geerinckx-Rice 0ab5aa056d
gnu: dmenu: Update to 4.8. 
* gnu/packages/suckless.scm (dmenu): Update to 4.8.
 2018-03-15 20:13:29 +01:00
Tobias Geerinckx-Rice 35edaa22aa
gnu: you-get: Update to 0.4.1040. 
* gnu/packages/video.scm (you-get): Update to 0.4.1040.
 2018-03-15 20:12:57 +01:00
Tobias Geerinckx-Rice fdae9718a1
gnu: intel-gpu-tools: Update to 1.22. 
* gnu/packages/admin.scm (intel-gpu-tools): Update to 1.22.
[inputs]: Add eudev.
 2018-03-15 19:52:29 +01:00
Tobias Geerinckx-Rice 896bbb0356
gnu: libburn: Update to 1.4.8. 
* gnu/packages/cdrom.scm (libburn): Update to 1.4.8.
 2018-03-15 19:11:16 +01:00
Tobias Geerinckx-Rice 2773c244b1
gnu: libisofs: Fix description typos. 
* gnu/packages/cdrom.scm (libisofs)[description]: Spell ‘file system’ as
‘file system’.
 2018-03-15 19:11:16 +01:00
Tobias Geerinckx-Rice d87d3f963e
gnu: libisofs: Update to 1.4.8. 
* gnu/packages/cdrom.scm (libisofs): Update to 1.4.8.
 2018-03-15 19:11:16 +01:00
Tobias Geerinckx-Rice 7b8d3a5e1e
gnu: gtksourceview: Update to 3.24.7. 
* gnu/packages/gtk.scm (gtksourceview): Update to 3.24.7.
 2018-03-15 19:11:15 +01:00
Tobias Geerinckx-Rice 7c9b7c5c6d
gnu: xdg-user-dirs: Update to 0.17. 
* gnu/packages/freedesktop.scm (xdg-user-dirs): Update to 0.17.
 2018-03-15 19:11:15 +01:00
Tobias Geerinckx-Rice 5ade82bbb8
gnu: r-scatterplot3d: Update to 0.3-41. 
* gnu/packages/cran.scm (r-scatterplot3d): Update to 0.3-41.
 2018-03-15 19:11:15 +01:00
Tobias Geerinckx-Rice 8027f84d8f
gnu: acpica: Update to 20180313. 
* gnu/packages/admin.scm (acpica): Update to 20180313.
 2018-03-15 19:11:15 +01:00
Tobias Geerinckx-Rice 47653b3933
gnu: octave: Update to 4.2.2. 
* gnu/packages/maths.scm (octave): Update to 4.2.2.
 2018-03-15 19:11:15 +01:00
Tobias Geerinckx-Rice 1a7cc9efcd
gnu: cifs-utils: Update to 6.8. 
* gnu/packages/samba.scm (cifs-utils): Update to 6.8.
 2018-03-15 19:11:14 +01:00
Tobias Geerinckx-Rice 96b4f5adc2
gnu: autoconf-archive: Update to 2018.03.13. 
* gnu/packages/autotools.scm (autoconf-archive): Update to 2018.03.13.
 2018-03-15 19:11:14 +01:00
Tobias Geerinckx-Rice 97c794942a
gnu: perl-string-toidentifier-en: Update to 0.12. 
* gnu/packages/language.scm (perl-string-toidentifier-en): Update to 0.12.
 2018-03-15 19:11:14 +01:00
Tobias Geerinckx-Rice cd75b642d9
gnu: perl-lingua-en-inflect-phrase: Update to 0.20. 
* gnu/packages/language.scm (perl-lingua-en-inflect-phrase): Update to 0.20.
 2018-03-15 19:11:14 +01:00
Tobias Geerinckx-Rice b9d020056d
gnu: bind: Use INVOKE. 
* gnu/packages/dns.scm (isc-bind)[arguments]: Substitute INVOKE for
SYSTEM* and end phase with an explicit #t.
 2018-03-15 19:11:13 +01:00
Leo Famulari 20ecede969
gnu: shadow: Fix CVE-2018-7169. 
* gnu/packages/patches/shadow-CVE-2018-7169.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/admin.scm (shadow)[source]: Use it.
 2018-03-15 13:13:35 -04:00
Leo Famulari 71f9ca53e5
gnu: certbot: Update to 0.22.0. 
* gnu/packages/tls.scm (certbot, python-acme): Update to 0.22.0.
 2018-03-15 12:19:11 -04:00
Leo Famulari 8d4f34d6c9
gnu: Add python-feather-format. 
* gnu/packages/serialization.scm (python-feather-format,
python2-feather-format): New variables.
 2018-03-15 10:57:53 -04:00
Leo Famulari 5e5ac7102c
gnu: Add python-pyarrow. 
* gnu/packages/databases.scm (python-pyarrow, python2-pyarrow): New variables.
 2018-03-15 10:57:52 -04:00
Leo Famulari dae7661a0d
gnu: Add apache-arrow. 
* gnu/packages/databases.scm (apache-arrow): New variable.
 2018-03-15 10:57:52 -04:00
Leo Famulari 2ed0ef2fb7
gnu: Add google-brotli. 
* gnu/packages/compression.scm (google-brotli): New variable.
 2018-03-15 10:57:52 -04:00
Leo Famulari 9f1c0e03ec
gnu: Add r-feather. 
* gnu/packages/serialization.scm (r-feather): New variable.
 2018-03-15 10:57:52 -04:00
Leo Famulari 5b19776e05
gnu: Add r-ggmap. 
* gnu/packages/geo.scm (r-ggmap): New variable.
 2018-03-15 10:57:52 -04:00
Leo Famulari da4dde6109
gnu: Add r-jpeg. 
* gnu/packages/image.scm (r-jpeg): New variable.
 2018-03-15 10:57:51 -04:00
Leo Famulari 32cbbac11a
gnu: Add Diversitree. 
* gnu/packages/bioinformatics.scm (r-diversitree): New variable.
 2018-03-15 10:57:51 -04:00
Leo Famulari 799ad71bfc
gnu: Add r-desolve. 
* gnu/packages/maths.scm (r-desolve): New variable.
 2018-03-15 10:57:51 -04:00
Leo Famulari 41835f947e
gnu: Add r-subplex. 
gnu/packages/maths.scm (r-subplex): New variable.
 2018-03-15 10:57:51 -04:00
Leo Famulari 24fb9a5591
gnu: Add r-geosphere. 
*  gnu/packages/geo.scm (r-geosphere): New variable.
 2018-03-15 10:57:51 -04:00
Leo Famulari 9ddf42099b
gnu: Add Rgooglemaps. 
* gnu/packages/geo.scm (r-rgooglemaps): New variable.
 2018-03-15 10:57:50 -04:00
Leo Famulari ebc4bd5b54
gnu: Add r-mapproj. 
* gnu/packages/geo.scm (r-mapproj): New variable.
 2018-03-15 10:57:50 -04:00
Leo Famulari 3d60f4265e
gnu: Add r-maps. 
* gnu/packages/geo.scm (r-maps): New variable.
 2018-03-15 10:57:50 -04:00