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Ludovic Courtès
856ae5e6c7 build-system/gnu: Strip with '--strip-all' instead of '--strip-debug'. 
This saves 19% on the 'bin' directory of Coreutils, and certainly
helpful for things like Git's 'libexec' directory.

* guix/build-system/gnu.scm (gnu-build): Change default value for
  #:strip-flags to '("--strip-all").
* guix/build/gnu-build-system.scm (strip): Ditto.
* gnu/packages/linux.scm (linux-libre)[arguments]: Add #:strip-flags.
 2014-12-27 19:20:18 +01:00
Mark H Weaver
9a224ac2e3 gnu: Use patch --force instead of --batch. 
* gnu/packages/linux.scm (linux-libre, net-tools): Pass "--force" to patch,
  instead of "--batch".
* gnu/packages/mit-krb5.scm (mit-krb5): Ditto.
 2014-12-27 08:45:17 -05:00
Ludovic Courtès
6aa47e3883 build-system/gnu: Add support for non-directory search paths. 
Partly fixes <http://bugs.gnu.org/18033>.

* guix/build/utils.scm (search-path-as-list): Rename 'sub-directories'
  parameter to 'files'.  Add #:type parameter and honor it.
  (set-path-environment-variable): Likewise.  Pass #:type to
  'search-path-as-list'.
* guix/packages.scm (search-path-specification->sexp): Add 'directory as
  the last item of the tuple.
* guix/build/gnu-build-system.scm (set-paths): Add 'type' to search-path
  pattern.  Pass #:type to 'set-path-environment-variable'.
 2014-12-27 12:25:31 +01:00
Ludovic Courtès
8c89f514bf gnu: gettext: Update to 0.19.4. 
* gnu/packages/gettext.scm (gnu-gettext): Update to 0.19.4.
 2014-12-27 12:25:31 +01:00
Ludovic Courtès
84c84ce7bf gnu: binutils: Update to 2.25. 
* gnu/packages/base.scm (binutils): Update to 2.25.
 2014-12-27 12:25:31 +01:00
Mark H Weaver
6ac8aa3d75 gnu: m4: Remove already-applied patch. 
* gnu/packages/patches/m4-readlink-EINVAL.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.
* gnu/packages/m4.scm (m4): Remove patch.
 2014-12-26 20:26:10 -05:00
Ludovic Courtès
0d12bc744e gnu: gcc-4.8: Update to 4.8.4. 
* gnu/packages/gcc.scm (gcc-4.8): Update to 4.8.4.  Remove patch.
* gnu/packages/patches/gcc-fix-pr61801.patch: Remove.
* gnu-system.am (dist_patch_DATA): Adjust accordingly.
 2014-12-27 00:17:43 +01:00
Ludovic Courtès
763a401ed1 Merge branch 'master' into core-updates 2014-12-26 23:31:04 +01:00
Ludovic Courtès
9426440781 packages: Apply patches with "patch --force". 
Fixes <http://bugs.gnu.org/19402>.
Reported by Mark H Weaver <mhw@netris.org>.

* guix/packages.scm (patch-and-repack): Change "--batch" to "--force".
 2014-12-26 23:30:29 +01:00
Ludovic Courtès
bf7688fe4d nls: Add French translation for packages. 2014-12-26 23:28:13 +01:00
Ricardo Wurmus
be7134bf75 gnu: Add pysam. 
* gnu/packages/python.scm (python-pysam, python2-pysam): New variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-26 23:28:13 +01:00
Ricardo Wurmus
ee97be9fb4 gnu: Add fastjar. 
* gnu/packages/compression.scm (fastjar): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-26 23:28:13 +01:00
Mark H Weaver
fb916f4dd6 gnu: qemu: Update to 2.2.0. 
* gnu/packages/qemu.scm (qemu): Update to 2.2.0.
 2014-12-26 09:01:15 -05:00
Mark H Weaver
53a427cf20 gnu: ntp: Update to 4.2.8. 
* gnu/packages/ntp.scm (ntp): Update to 4.2.8.  Add openssl to inputs.
  Add pkg-config to native-inputs.  Change source URI to archive.ntp.org.
 2014-12-25 00:19:36 -05:00
Ludovic Courtès
764c077b30 Revert "gnu: matplotlib: Comment out python2-matplotlib." 
This reverts commit afc720d34c.
 2014-12-23 19:17:17 +01:00
Ludovic Courtès
78a2745370 build-system/python: Fix 'package-with-explicit-python'. 
Reported by Federico Beffa <beffa@ieee.org>
and Eric Bavier <ericbavier@gmail.com>.

* guix/build-system/python.scm (package-with-explicit-python): Do
  nothing when P's build system is not PYTHON-BUILD-SYSTEM.
 2014-12-23 19:14:52 +01:00
Federico Beffa
afc720d34c gnu: matplotlib: Comment out python2-matplotlib. 
* gnu/packages/python.scm (python2-matplotlib, python2-scipy, python2-numpy):
  Comment out python2-matplotlib and the packages making use of it as the
  generation of the derivation of these packages takes very long.
 2014-12-23 17:56:48 +01:00
Mark H Weaver
a193b8248b Optimize package-transitive-supported-systems. 
* guix/packages.scm (first-value): Remove.
  (define-memoized/v): New macro.
  (package-transitive-supported-systems): Rewrite.
 2014-12-21 20:12:18 -05:00
Ludovic Courtès
d95523fb8b packages: Sort Scheme file lists used by 'fold-packages'. 
* gnu/packages.scm (scheme-files): Call 'sort' on result.
 2014-12-21 12:29:14 +01:00
Mark H Weaver
ce44657aab Really remove the 'nix-upstream' submodule. 
* nix-upstream: Remove subproject.
 2014-12-20 15:02:26 -05:00
宋文武
eea3e54c59 gnu: Add xfce4-terminal. 
* gnu/packages/xfce.scm (xfce4-terminal): New variable.
 2014-12-20 13:06:01 +08:00
宋文武
ea57378f24 gnu: Add vte. 
* gnu/packages/gnome.scm (vte, vte/gtk+-2): New variables.
 2014-12-20 13:01:47 +08:00
宋文武
24d56899a1 services: xorg: Make SLiM sessions configurable. 
* gnu/services/xorg.scm (%default-xsessions): New variable.
  (xsessions-directory): New procedure.
  (slim-service): Add #:sessions and #:auto-login-session parameters.
  [slim.cfg]: Honor #:sessions.
  (xinitrc): Adjust accordingly.
 2014-12-20 11:12:00 +08:00
Ludovic Courtès
9ac97e83e9 Remove 'nix-upstream' submodule. 
* nix/sync-with-upstream: Remove.
* bootstrap: Remove uses of 'git submodule' and 'sync-with-usptream'.
* .gitmodules: Remove.
 2014-12-19 23:18:49 +01:00
Ludovic Courtès
36457566f9 Merge branch 'nix' into 'master'. 2014-12-19 22:47:37 +01:00
Ricardo Wurmus
2c7ee16720 gnu: Add bowtie 
* gnu/packages/bioinformatics.scm (bowtie): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-19 18:50:28 +01:00
Ludovic Courtès
7f5c2a9cc1 services: static-networking-service: Switch to (guix build syscalls). 
* gnu/services/networking.scm (static-networking-service): Remove
  #:inetutils parameter.  Rewrite using 'configure-network-interface'
  and 'set-network-interface-flags'.
 2014-12-19 17:15:53 +01:00
Ludovic Courtès
c9bf64d6d7 syscalls: Add more procedures for network interfaces. 
* guix/build/syscalls.scm (sizeof*, type-size, write-type, write-types,
  read-type, read-types, define-c-struct): New macros.
  (SIOCSIFFLAGS, SIOCGIFADDR, SIOCSIFADDR): New variables.
  (sockaddr-in, sockaddr-in6): New C structs.
  (write-socket-address!, read-socket-address,
  set-network-interface-flags, set-network-interface-address,
  network-interface-address, configure-network-interface): New
  procedures.
 2014-12-19 17:15:53 +01:00
Ricardo Wurmus
cdae969ae5 gnu: Add Clone. 
* gnu/packages/perl.scm (perl-clone): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-19 17:15:53 +01:00
Federico Beffa
9e0997230c gnu: cairocffi: Move to python module. 
* gnu/packages/gtk.scm, gnu/packages/python.scm (python-cairocffi,
  python2-cairocffi): Move variables from gtk to python module to avoid
  circular dependency.

Reported by Mark H Weaver <mhw@netris.org>
 2014-12-18 22:00:19 +01:00
Federico Beffa
25f9a068f2 gnu: matplotlib: Add gtk3 backends and optional dependency. Adjust inputs. 
* gnu/packages/python.scm (python-matplotlib, python2-matplotlib): Add gtk3
  backends with the necessary inputs and a 'configure-environment' phase.  Add
  the optional 'python-pillow' dependency.  Move 'python-pyparsing' from
  'inputs' to 'propagated-inputs' as it is required at run time.
 2014-12-18 17:58:10 +01:00
Federico Beffa
63cd6e5a95 gnu: Add cairocffi. 
* gnu/packages/gtk.scm (python-cairocffi, python2-cairocffi): New variables.
 2014-12-18 17:58:10 +01:00
Federico Beffa
6fa144692c gnu: Add xcffib 
* gnu/packages/python.scm (python-xcffib, python2-xcffib): New variables.
 2014-12-18 17:58:10 +01:00
Federico Beffa
6f8fe4b29e build/python-build-system: Fix easy-install.pth collisions. 
* guix/build/python-build-system.scm (rename-pth-file): New rename-pth-file
  phase and corresponding function.
 2014-12-18 17:58:10 +01:00
Ludovic Courtès
46a3e00b5b gnu: icecat: Build with PulseAudio support. 
* gnu/packages/gnuzilla.scm (icecat)[arguments]: Add
  --enable-pulseaudio.
 2014-12-17 14:06:59 +01:00
Jason Self
80db9915a0 gnu: linux-libre: Update to 3.18.1 
* gnu/packages/linux.scm (linux-libre): Update to version 3.18.1.
 2014-12-17 04:30:52 -08:00
Ricardo Wurmus
7576cbd6da gnu: Add Test::Simple. 
* gnu/packages/perl.scm (perl-test-simple): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-17 00:11:28 +01:00
Ricardo Wurmus
0ad3969fcd gnu: Add Test::Deep. 
* gnu/packages/perl.scm (perl-test-deep): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-17 00:11:28 +01:00
Ricardo Wurmus
9dc8a1577f gnu: Add Test::NoWarnings. 
* gnu/packages/perl.scm (perl-test-nowarnings): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-17 00:11:28 +01:00
Ricardo Wurmus
ea0a52d7d6 gnu: Add Test::Tester. 
* gnu/packages/perl.scm (perl-test-tester): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-17 00:11:27 +01:00
Federico Beffa
6a84316848 Revert "gnu: python-numpy-bootstrap: Reduce matrix size in failing test." 
This reverts commit 31557440c2 as it did not
provide the desired effect.  The test is still failing.
 2014-12-16 18:37:13 +01:00
Ricardo Wurmus
81de56479a gnu: Add bedtools 
* gnu/packages/bioinformatics.scm (bedtools): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-16 18:17:15 +01:00
Tomáš Čech
b336da21e9 gnu: tmux: Update to 1.9a. 
* gnu/packages/tmux.scm (tmux): Update to 1.9a

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-16 18:17:15 +01:00
Ricardo Wurmus
f3cd952b45 gnu: samtools: disable tests for non-64-bit systems 
* gnu/packages/bioinformatics.scm (samtools): disable tests for all non-64-bit
  systems because of an upstream bug in the test data.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-16 18:17:15 +01:00
Mark H Weaver
a142e38e9d gnu: groff: Disable parallel builds. 
* gnu/packages/groff.scm (groff): Disable parallel builds.
 2014-12-16 11:16:54 -05:00
Mark H Weaver
dec7ab5953 gnu: groff: Update to 1.22.3. 
* gnu/packages/groff.scm (groff): Update to 1.22.3.
 2014-12-16 03:28:06 -05:00
Mark H Weaver
a6e818586b gnu: ghostscript: Update to 9.14.0. 
* gnu/packages/ghostscript.scm (ghostscript): Update to 9.14.0.
  Change license to agpl3+.
 2014-12-16 03:08:00 -05:00
Mark H Weaver
6b282cc9fb gnu: lcms: Update to 2.6. 
* gnu/packages/ghostscript.scm (lcms): Update to 2.6.
 2014-12-16 03:07:57 -05:00
Mark H Weaver
9f8552fab5 gnu: icecat: Apply security updates for CVE-2014-{1587,1590,1592,1593,1594}. 
* gnu/packages/patches/icecat-CVE-2014-1587-bug-1042567.patch,
  gnu/packages/patches/icecat-CVE-2014-1587-bug-1072847.patch,
  gnu/packages/patches/icecat-CVE-2014-1587-bug-1079729.patch,
  gnu/packages/patches/icecat-CVE-2014-1587-bug-1080312.patch,
  gnu/packages/patches/icecat-CVE-2014-1587-bug-1089207.patch,
  gnu/packages/patches/icecat-CVE-2014-1590.patch,
  gnu/packages/patches/icecat-CVE-2014-1592.patch,
  gnu/packages/patches/icecat-CVE-2014-1593.patch,
  gnu/packages/patches/icecat-CVE-2014-1594.patch: New files.
* gnu-system.am (dist_patch_DATA): Add them.
* gnu/packages/gnuzilla.scm (icecat): Add them.
 2014-12-15 20:42:53 -05:00
Ludovic Courtès
bea26837e8 profiles: Fix removal of the next-to-last item in a profile. 
Fixes a bug whereby removing the next-to-last item in a profile would
lead to an obscure error, as shown at
<http://lists.gnu.org/archive/html/guix-devel/2014-12/msg00292.html>.
Reported by Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>.

* guix/profiles.scm (profile-derivation)[inputs]: Use (list info-dir
  "out") instead of just INFO-DIR.
 2014-12-15 23:01:56 +01:00