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10384 Commits

Author SHA1 Message Date
Leo Famulari f0150f8724 gnu: grub: Add fix for CVE-2015-8730. 
* gnu/packages/patches/grub-CVE-2015-8370.patch: New file.
* gnu-system.am (dist_patch_DATA): Register patch.
* gnu/packages/grub.scm: Apply patch.
 2015-12-21 12:33:55 -05:00
Ricardo Wurmus e2cd1d0fb9 gnu: Add GenomicRanges. 
* gnu/packages/bioinformatics.scm (r-genomicranges): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus 0e7d5560de gnu: Add XVector. 
* gnu/packages/bioinformatics.scm (r-xvector): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus bf7764b74f gnu: Add GenomeInfoDb. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus 78addcb0eb gnu: Add IRanges. 
* gnu/packages/bioinformatics.scm (r-iranges): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus 7485129e4f gnu: Add S4Vectors. 
* gnu/packages/bioinformatics.scm (r-s4vectors): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus d29b25c490 gnu: Add BiocGenerics. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus 9fba89e829 gnu: Add r-acsnminer. 
* gnu/packages/bioinformatics.scm (r-acsnminer): New variable.
 2015-12-21 17:21:26 +01:00
Ricardo Wurmus 9e47f30b08 gnu: Add r-gridextra. 
* gnu/packages/statistics.scm (r-gridextra): New variable.
 2015-12-21 17:21:26 +01:00
Ricardo Wurmus b73751c8ff gnu: Add r-gtable. 
* gnu/packages/statistics.scm (r-gtable): New variable.
 2015-12-21 17:21:26 +01:00
Ricardo Wurmus 77bdb276e9 gnu: Add r-rmarkdown. 
* gnu/packages/statistics.scm (r-rmarkdown): New variable.
* gnu/packages/haskell.scm: Do not select libxml2 from the xml module to
  prevent circular package module imports.
 2015-12-21 17:13:44 +01:00
Ricardo Wurmus 4c1f2705b5 gnu: Add r-catools. 
* gnu/packages/statistics.scm (r-catools): New variable.
 2015-12-21 17:13:44 +01:00
Ricardo Wurmus bb6d2dadf7 gnu: Add r-bitops. 
* gnu/packages/statistics.scm (r-bitops): New variable.
 2015-12-21 17:13:44 +01:00
Ricardo Wurmus 8406138b72 gnu: Add AdaptiveSparsity. 
* gnu/packages/machine-learning.scm (r-adaptivesparsity): New variable.
 2015-12-21 16:05:38 +01:00
Ricardo Wurmus e22d4ca4c4 gnu: Add r-rcpparmadillo. 
* gnu/packages/maths.scm (armadillo-for-rcpparmadillo): New variable.
* gnu/packages/statistics.scm (r-rcpparmadillo): New variable.
 2015-12-21 16:05:37 +01:00
Ricardo Wurmus b15e47f9e6 gnu: Add armadillo. 
* gnu/packages/maths.scm (armadillo): New variable.
 2015-12-21 15:47:40 +01:00
Ricardo Wurmus b1186502a4 doc: Fix outdated claim about CRAN importer. 
* doc/guix.texi: The CRAN importer no longer extracts information from
  the HTML package description but from the package's DESCRIPTION file.
 2015-12-21 15:25:10 +01:00
Ricardo Wurmus be036757bd import: Drop empty list items. 
* guix/import/cran.scm (listify): Remove empty strings from result list.
 2015-12-21 15:24:54 +01:00
Ricardo Wurmus 0cb5bc2cff http-client: Support basic authentication. 
* guix/http-client.scm (http-fetch): Add Authorization header to request
  when the URI contains userinfo.
 2015-12-21 15:24:44 +01:00
Ricardo Wurmus 086e498bcf gnu: Add libgit2. 
* gnu/packages/version-control.scm (libgit2): New variable.
 2015-12-21 15:22:14 +01:00
Ben Woodcroft 02f35bb5a7 gnu: mafft: Update to 7.267. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.267.
[arguments]: Don't include mafft-homologs manpage.
[inputs]: Add gawk and grep.
[propagated-inputs]: Add coreutils.
 2015-12-21 15:16:01 +01:00
Mathieu Lirzin 1ef3f91a70 gnu: rxvt-unicode: Install the terminal capability data. 
This provides the necessary terminal capability data, which are required
by ncurses-based applications.

* gnu/packages/xdisorg.scm (rxvt-unicode)[native-inputs]: Add ncurses.
[arguments]: Set the destination of the terminfo files.
[native-search-path]: New field.  Make them automatically available to
the user.
 2015-12-21 13:35:34 +01:00
Efraim Flashner 72d8b5baf4 gnu: msmtp: Update to 1.6.3. 
* gnu/packages/mail.scm (msmtp): Update to 1.6.3.
[inputs]: Add libsecret.
 2015-12-21 09:36:15 +02:00
Efraim Flashner ec92806ae5 gnu: claws-mail: Update to 3.13.1. 
* gnu/packages/mail.scm (claws-mail): Update to 3.13.1.
 2015-12-21 09:17:47 +02:00
Efraim Flashner 56918e26cf gnu: python-cython: Update to 0.23.4. 
* gnu/packages/python.scm (python-cython): Update to 0.23.4.
 2015-12-21 06:55:13 +02:00
David Thompson e99711af22 gnu: ruby: Update to 2.2.4. 
This version fixes CVE-2015-7551.

* gnu/packages/ruby.scm (ruby): Update to 2.2.4.
 2015-12-20 22:40:53 -05:00
Ludovic Courtès c5b303c57f lint: The CPE name of GRUB is "grub2". 
Reported by Leo Famulari.

* guix/scripts/lint.scm (package-name->cpe-name): Add "grub".
 2015-12-20 22:34:22 +01:00
Ludovic Courtès 724a7d9c74 packages: Remove now redundant graph procedures. 
These procedures are now redundant with those in (guix graph) and are no
longer used since commit a51cbecb.

* gnu/packages.scm (vhash-refq, package-dependencies)
(package-direct-dependents, package-transitive-dependents)
(package-covering-dependents): Remove.
 2015-12-20 22:34:22 +01:00
Ludovic Courtès ccda8f7d7f profiles: Honor search paths of propagated inputs. 
Fixes <http://bugs.gnu.org/22073>.
Reported by Federico Beffa <beffa@ieee.org>.

* guix/profiles.scm (package->manifest-entry): Use
'package-transitive-native-search-paths' when computing
'search-paths' field.
* tests/profiles.scm ("package->manifest-entry, search paths"): New test.
 2015-12-20 22:34:22 +01:00
Ludovic Courtès aa8e051532 packages: Add 'package-transitive-native-search-paths'. 
* guix/packages.scm (package-transitive-native-search-paths): New
procedure.
* tests/packages.scm ("package-transitive-native-search-paths"): New
test.
 2015-12-20 22:34:22 +01:00
Efraim Flashner 54b7f63a72 gnu: offlineimap: Update to 6.6.0. 
* gnu/packages/mail.scm (offlineimap): Update to 6.6.0.
 2015-12-20 21:39:18 +02:00
Efraim Flashner b5d47a5a53 gnu: gnupg: Update to 1.4.20. 
* gnu/packages/gnupg.scm (gnupg-1): Update to 1.4.20.
 2015-12-20 20:07:31 +02:00
宋文武 a4df575631 gnu: Add gnome-shell. 
* gnu/packages/gnome.scm (gnome-shell): New variable.
 2015-12-20 18:59:22 +08:00
宋文武 b645146f00 gnu: Add gnome-control-center. 
* gnu/packages/gnome.scm (gnome-control-center): New variable.
 2015-12-20 18:59:22 +08:00
宋文武 b96c42605b gnu: Add gnome-bluetooth. 
* gnu/packages/gnome.scm (gnome-bluetooth): New variable.
 2015-12-20 18:59:22 +08:00
宋文武 8e1dd04f45 gnu: Add libgtop. 
* gnu/packages/gnome.scm (libgtop): New variable.
 2015-12-20 18:59:21 +08:00
宋文武 e682327976 gnu: Add colord-gtk. 
* gnu/packages/freedesktop.scm (colord-gtk): New variable.
 2015-12-20 18:59:21 +08:00
宋文武 6976e7d2ff gnu: Add telepathy-logger. 
* gnu/packages/freedesktop.scm (telepathy-logger): New variable.
 2015-12-20 18:59:21 +08:00
Efraim Flashner ff80b96378 gnu: tilda: Update to 1.3.1. 
* gnu/packages/terminals.scm (tilda): Update to 1.3.1.
 2015-12-20 09:40:56 +02:00
Ludovic Courtès 604d20a251 gnu: Add tlsdate. 
* gnu/packages/ntp.scm (tlsdate): New variable.
 2015-12-19 23:16:18 +01:00
宋文武 04dc6c9992 gnu: mpv: Update to 0.14.0. 
* gnu/packages/video.scm (mpv): Update to 0.14.0.
 2015-12-19 12:21:59 +08:00
宋文武 599fd84227 gnu: mpv: Fix build by using pkg-config for smbclient. 
This is a followup to commit 710964d.

* gnu/packages/video.scm (mpv)[arguments]: Remove 'patch-wscript' phase.
 2015-12-19 12:15:59 +08:00
Ludovic Courtès 7db0799dc9 gnu: agg: Update URLs. 
* gnu/packages/graphics.scm (agg)[source, home-page]: Add up-to-date
URLs.
 2015-12-19 00:42:10 +01:00
Ludovic Courtès 3ac732715d gnu: Use #:prefix when importing (guix licenses). 
This works around a problem with #:hide, whereby Guile would report
'zlib', 'openssl', and/or 'expat as colliding bindings at run time
despite the #:hide.

* gnu/packages/linux.scm: Use #:prefix license for (guix licenses).
* gnu/packages/haskell.scm: Likewise.
 2015-12-19 00:34:00 +01:00
Ludovic Courtès 793bcc1933 gnu: Do not #:select from (gnu packages …) modules. 
This is to avoid <http://bugs.gnu.org/15540>.

* gnu/packages/bittorrent.scm: Do not #:select from (gnu packages
compression).
* gnu/packages/dictionaries.scm: Likewise.
* gnu/packages/disk.scm: Likewise.
* gnu/packages/gimp.scm: Likewise.
* gnu/packages/haskell.scm: Likewise.
 2015-12-19 00:22:42 +01:00
Ludovic Courtès bf46f74160 gnu: key-mon: Remove unnecessary propagated inputs. 
* gnu/packages/key-mon.scm (key-mon)[propagated-inputs]: Rename to...
[inputs]: ... this.  Propagated was unnecessary since the 'key-mon'
program is wrapped.
 2015-12-18 11:04:22 +01:00
Ludovic Courtès 594e7b479a gnu: python2-pygtk: Add "doc" output. 
* gnu/packages/gtk.scm (python2-pygtk)[outputs]: New field.
[arguments]: Add 'set-gtk-doc-directory' phase.
 2015-12-18 11:04:22 +01:00
Ludovic Courtès ae115bc75a gnu: python2-pygtk: Use 'modify-phases'. 
* gnu/packages/gtk.scm (python2-pygtk)[arguments]: Use 'modify-phases'.
 2015-12-18 11:04:22 +01:00
Ludovic Courtès be4fbbe01b gnu: gimp: Add "doc" output. 
* gnu/packages/gimp.scm (gimp)[outputs, arguments]: New fields.
 2015-12-18 11:04:22 +01:00
Ludovic Courtès 72a06d3e32 gnu: goffice: Add "doc" output. 
* gnu/packages/gnome.scm (goffice)[outputs, arguments]: New fields.
(goffice-0.8)[arguments]: Append arguments from GOFFICE.
 2015-12-18 11:04:22 +01:00