Commit graph

10121 commits

Author SHA1 Message Date
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b1186502a4 doc: Fix outdated claim about CRAN importer.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
53088d0045 gnu: commencement: Build Bison deterministically.
Before that entries in liby.a would contain the build time.

* gnu/packages/commencement.scm (bison-boot1): Add #:make-flags.
2015-12-19 00:02:37 +01:00
Ludovic Courtès
3eb34c631a build-system/gnu: Always pass "-D" to strip/objcopy.
* guix/build-system/gnu.scm (gnu-build, gnu-cross-build): Add "-D" to
  #:strip-flags.
* guix/build/gnu-build-system.scm (strip): Likewise.  Also pass "-D" to
  OBJCOPY-COMMAND.
2015-12-18 23:58:51 +01:00
Ludovic Courtès
f1e0c85ad2 gnu: commencement: Build the final Bash with "bison-boot1".
This removes a round of Bison + Flex + M4 + Perl rebuild.

* gnu/packages/commencement.scm (bash-final): Add 'native-inputs'
field pointing to BISON-BOOT1.
2015-12-18 23:57:11 +01:00
Ludovic Courtès
32243bfb57 gnu: commencement: Avoid redundant Perl rebuild.
This removes a redundant (yet different) "perl-boot0" node from the
early derivation graph.

* gnu/packages/commencement.scm (bison-boot1): Move 'native-inputs'
field to the final package.  Previously PERL-BOOT0 got rebuilt with
%BOOT0-INPUTS, leading to a different derivation.
(static-bash-for-glibc): Likewise.
2015-12-18 23:53:00 +01:00
Ludovic Courtès
09964b4fc6 gnu: commencement: Add "-boot0" to early packages.
* gnu/packages/commencement.scm (diffutils-boot0)[name]: New field.
* gnu/packages/commencement.scm (findutils-boot0, file-boot0,
perl-boot0): Change 'name' field to include "-boot0".
2015-12-18 22:19:07 +01:00
Ludovic Courtès
009b53fd1c gnu: gcc: Prefer language-specific variables over 'CPATH'.
Suggested by Andy Wingo <wingo@igalia.com>.
Fixes <http://bugs.gnu.org/22186>.

* gnu/packages/gcc.scm (gcc-4.7)[native-search-paths]: Remove 'CPATH';
add 'C_INCLUDE_PATH' and 'CPLUS_INCLUDE_PATH' instead.
* gnu/packages/gcc.scm (custom-gcc): Add 'search-paths' parameter and
honor it.
(%generic-search-paths): New variable.
(gfortran-4.8, gfortran-4.9, gfortran, gfortran-5, gccgo-4.8): Pass
%GENERIC-SEARCH-PATHS to 'custom-gcc'.
(gcj)[native-search-paths]: New field.
(gcc-objc-4.8, gcc-objc++-4.8): Use 'OBJC_INCLUDE_PATH' and
'OBJCPLUS_INCLUDE_PATH', respectively.
2015-12-18 21:38:49 +01:00
Ludovic Courtès
8309c3899a gnu: commencement: Use GMP 6.0.0a for bootstrapping.
* gnu/packages/multiprecision.scm (gmp-6.0): New variable.
* gnu/packages/commencement.scm (gcc-boot0, gcc-final): Use it.
* gnu/packages/patches/gmp-arm-asm-nothumb.patch: New file, reinstated
from before e414a7d.
* gnu-system.am (dist_patch_DATA): Add it.
2015-12-18 18:38:22 +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