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* gnu: grub: Add fix for CVE-2015-8730.Leo Famulari2015-12-21
| | | | | | * gnu/packages/patches/grub-CVE-2015-8370.patch: New file. * gnu-system.am (dist_patch_DATA): Register patch. * gnu/packages/grub.scm: Apply patch.
* gnu: Add GenomicRanges.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): New variable.
* gnu: Add XVector.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-xvector): New variable.
* gnu: Add GenomeInfoDb.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): New variable.
* gnu: Add IRanges.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-iranges): New variable.
* gnu: Add S4Vectors.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): New variable.
* gnu: Add BiocGenerics.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-biocgenerics): New variable.
* gnu: Add r-acsnminer.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-acsnminer): New variable.
* gnu: Add r-gridextra.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/statistics.scm (r-gridextra): New variable.
* gnu: Add r-gtable.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/statistics.scm (r-gtable): New variable.
* gnu: Add r-rmarkdown.Ricardo Wurmus2015-12-21
| | | | | | * 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.
* gnu: Add r-catools.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/statistics.scm (r-catools): New variable.
* gnu: Add r-bitops.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/statistics.scm (r-bitops): New variable.
* gnu: Add AdaptiveSparsity.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/machine-learning.scm (r-adaptivesparsity): New variable.
* gnu: Add r-rcpparmadillo.Ricardo Wurmus2015-12-21
| | | | | * gnu/packages/maths.scm (armadillo-for-rcpparmadillo): New variable. * gnu/packages/statistics.scm (r-rcpparmadillo): New variable.
* gnu: Add armadillo.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/maths.scm (armadillo): New variable.
* doc: Fix outdated claim about CRAN importer.Ricardo Wurmus2015-12-21
| | | | | * doc/guix.texi: The CRAN importer no longer extracts information from the HTML package description but from the package's DESCRIPTION file.
* import: Drop empty list items.Ricardo Wurmus2015-12-21
| | | | * guix/import/cran.scm (listify): Remove empty strings from result list.
* http-client: Support basic authentication.Ricardo Wurmus2015-12-21
| | | | | * guix/http-client.scm (http-fetch): Add Authorization header to request when the URI contains userinfo.
* gnu: Add libgit2.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/version-control.scm (libgit2): New variable.
* gnu: mafft: Update to 7.267.Ben Woodcroft2015-12-21
| | | | | | | * 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.
* gnu: rxvt-unicode: Install the terminal capability data.Mathieu Lirzin2015-12-21
| | | | | | | | | | 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.
* gnu: msmtp: Update to 1.6.3.Efraim Flashner2015-12-21
| | | | | * gnu/packages/mail.scm (msmtp): Update to 1.6.3. [inputs]: Add libsecret.
* gnu: claws-mail: Update to 3.13.1.Efraim Flashner2015-12-21
| | | | * gnu/packages/mail.scm (claws-mail): Update to 3.13.1.
* gnu: python-cython: Update to 0.23.4.Efraim Flashner2015-12-21
| | | | * gnu/packages/python.scm (python-cython): Update to 0.23.4.
* gnu: ruby: Update to 2.2.4.David Thompson2015-12-20
| | | | | | This version fixes CVE-2015-7551. * gnu/packages/ruby.scm (ruby): Update to 2.2.4.
* lint: The CPE name of GRUB is "grub2".Ludovic Courtès2015-12-20
| | | | | | Reported by Leo Famulari. * guix/scripts/lint.scm (package-name->cpe-name): Add "grub".
* packages: Remove now redundant graph procedures.Ludovic Courtès2015-12-20
| | | | | | | | | 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.
* profiles: Honor search paths of propagated inputs.Ludovic Courtès2015-12-20
| | | | | | | | | | 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.
* packages: Add 'package-transitive-native-search-paths'.Ludovic Courtès2015-12-20
| | | | | | | * guix/packages.scm (package-transitive-native-search-paths): New procedure. * tests/packages.scm ("package-transitive-native-search-paths"): New test.
* gnu: offlineimap: Update to 6.6.0.Efraim Flashner2015-12-20
| | | | * gnu/packages/mail.scm (offlineimap): Update to 6.6.0.
* gnu: gnupg: Update to 1.4.20.Efraim Flashner2015-12-20
| | | | * gnu/packages/gnupg.scm (gnupg-1): Update to 1.4.20.
* gnu: Add gnome-shell.宋文武2015-12-20
| | | | * gnu/packages/gnome.scm (gnome-shell): New variable.
* gnu: Add gnome-control-center.宋文武2015-12-20
| | | | * gnu/packages/gnome.scm (gnome-control-center): New variable.
* gnu: Add gnome-bluetooth.宋文武2015-12-20
| | | | * gnu/packages/gnome.scm (gnome-bluetooth): New variable.
* gnu: Add libgtop.宋文武2015-12-20
| | | | * gnu/packages/gnome.scm (libgtop): New variable.
* gnu: Add colord-gtk.宋文武2015-12-20
| | | | * gnu/packages/freedesktop.scm (colord-gtk): New variable.
* gnu: Add telepathy-logger.宋文武2015-12-20
| | | | * gnu/packages/freedesktop.scm (telepathy-logger): New variable.
* gnu: tilda: Update to 1.3.1.Efraim Flashner2015-12-20
| | | | * gnu/packages/terminals.scm (tilda): Update to 1.3.1.
* gnu: Add tlsdate.Ludovic Courtès2015-12-19
| | | | * gnu/packages/ntp.scm (tlsdate): New variable.
* gnu: mpv: Update to 0.14.0.宋文武2015-12-19
| | | | * gnu/packages/video.scm (mpv): Update to 0.14.0.
* gnu: mpv: Fix build by using pkg-config for smbclient.宋文武2015-12-19
| | | | | | This is a followup to commit 710964d. * gnu/packages/video.scm (mpv)[arguments]: Remove 'patch-wscript' phase.
* gnu: agg: Update URLs.Ludovic Courtès2015-12-19
| | | | | * gnu/packages/graphics.scm (agg)[source, home-page]: Add up-to-date URLs.
* gnu: Use #:prefix when importing (guix licenses).Ludovic Courtès2015-12-19
| | | | | | | | | 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.
* gnu: Do not #:select from (gnu packages …) modules.Ludovic Courtès2015-12-19
| | | | | | | | | | | 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.
* gnu: key-mon: Remove unnecessary propagated inputs.Ludovic Courtès2015-12-18
| | | | | | * gnu/packages/key-mon.scm (key-mon)[propagated-inputs]: Rename to... [inputs]: ... this. Propagated was unnecessary since the 'key-mon' program is wrapped.
* gnu: python2-pygtk: Add "doc" output.Ludovic Courtès2015-12-18
| | | | | * gnu/packages/gtk.scm (python2-pygtk)[outputs]: New field. [arguments]: Add 'set-gtk-doc-directory' phase.
* gnu: python2-pygtk: Use 'modify-phases'.Ludovic Courtès2015-12-18
| | | | * gnu/packages/gtk.scm (python2-pygtk)[arguments]: Use 'modify-phases'.
* gnu: gimp: Add "doc" output.Ludovic Courtès2015-12-18
| | | | * gnu/packages/gimp.scm (gimp)[outputs, arguments]: New fields.
* gnu: goffice: Add "doc" output.Ludovic Courtès2015-12-18
| | | | | * gnu/packages/gnome.scm (goffice)[outputs, arguments]: New fields. (goffice-0.8)[arguments]: Append arguments from GOFFICE.
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