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10677 Commits

Author SHA1 Message Date
Andy Patterson
8d0489aeb6
gnu: sbcl: Honour XDG_DATA_DIRS/sbcl-bundle-systems. 
* gnu/packages/lisp.scm (asdf-substitutions): New variable.
(sbcl)[source]: Add snippet.
[native-search-paths]: Add XDG_DATA_DIRS.

Signed-off-by: 宋文武 <iyzsong@gmail.com>
 2016-10-06 20:33:55 +08:00
Ricardo Wurmus
eb0ff8a382
gnu: Add ghc-pandoc-citeproc. 
* gnu/packages/haskell.scm (ghc-pandoc-citeproc): New variable.
 2016-10-06 14:18:25 +02:00
Ricardo Wurmus
bfdfb0f63f
gnu: Add ghc-xml-conduit. 
* gnu/packages/haskell.scm (ghc-xml-conduit): New variable.
 2016-10-06 14:18:25 +02:00
Ricardo Wurmus
e9ef2c51d5
gnu: Add ghc-xml-types. 
* gnu/packages/haskell.scm (ghc-xml-types): New variable.
 2016-10-06 14:18:25 +02:00
Ricardo Wurmus
1aa45bbf6f
gnu: Add ghc-conduit-extra. 
* gnu/packages/haskell.scm (ghc-conduit-extra): New variable.
 2016-10-06 14:18:25 +02:00
Ricardo Wurmus
9ce764b689
gnu: Add ghc-rfc5051. 
* gnu/packages/haskell.scm (ghc-rfc5051): New variable.
 2016-10-06 14:18:24 +02:00
Ricardo Wurmus
37e02bf65b
gnu: Add ghc-hs-bibutils. 
* gnu/packages/haskell.scm (ghc-hs-bibutils): New variable.
 2016-10-06 14:18:24 +02:00
Ricardo Wurmus
b376463552
gnu: ghc-streaming-commons: Remove standard packages from inputs. 
The "directory" and "transformers" modules are part of GHC and should
not be among the inputs to avoid conflicts.

* gnu/packages/haskell.scm (ghc-streaming-commons)[inputs]: Remove
"ghc-directory" and "ghc-transformers".
 2016-10-06 14:18:21 +02:00
Ricardo Wurmus
fc47c7d635
gnu: Add r-bsgenome-celegans-ucsc-ce10. 
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce10): New
variable.
 2016-10-06 10:33:43 +02:00
Leo Famulari
6a4cbc6f12
gnu: nss-certs and nss: Update to 3.27.1. 
* gnu/packages/certs.scm (nss-certs): Update to 3.27.1.
* gnu/packages/gnuzilla.scm (nss): Update to 3.27.1.
 2016-10-05 20:04:50 -04:00
Leo Famulari
22f08f0605
gnu: libxvmc: Update to 1.0.10. 
* gnu/packages/xorg.scm (libxvmc): Update to 1.0.10.
[replacement]: Remove field.
(libxvmc/fixed): Remove variable.
* gnu/packages/patches/libxvmc-CVE-2016-7953.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2016-10-05 19:36:26 -04:00
Leo Famulari
62ad505603
gnu: libxv: Update to 1.0.11. 
* gnu/packages/xorg.scm (libxv): Update to 1.0.11.
[replacement]: Remove field.
(libxv/fixed): Remove variable.
* gnu/packages/patches/libxv-CVE-2016-5407.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2016-10-05 19:36:25 -04:00
Leo Famulari
82e6a4341b
gnu: libxtst: Update to 1.2.3. 
* gnu/packages/xorg.scm (libxtst): Update to 1.2.3.
[replacement]: Remove field.
(libxtst/fixed): Remove variable.
* gnu/packages/patches/libxtst-CVE-2016-7951-CVE-2016-7952.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2016-10-05 19:36:25 -04:00
Leo Famulari
9eb76bd3e5
gnu: libxrender: Update to 0.9.10. 
* gnu/packages/xorg.scm (libxrender): Update to 0.9.10.
[replacement]: Remove field.
(libxrender/fixed): Remove variable.
* gnu/packages/patches/libxrender-CVE-2016-7949.patch,
gnu/packages/patches/libxrender-CVE-2016-7950.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
 2016-10-05 19:36:25 -04:00
Leo Famulari
2e81b0b5bf
gnu: libxrandr: Update to 1.5.1. 
* gnu/packages/xorg.scm (libxrandr): Update to 1.5.1.
[replacement]: Remove field.
(libxrandr/fixed): Remove variable.
* gnu/packages/patches/libxrandr-CVE-2016-7947-CVE-2016-7948.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2016-10-05 19:36:24 -04:00
Leo Famulari
571fa535cd
gnu: libxi: Update to 1.7.7. 
* gnu/packages/xorg.scm (libxi): Update to 1.7.7.
[replacement]: Remove field.
(libxi/fixed): Remove variable.
* gnu/packages/patches/libxi-CVE-2016-7945-CVE-2016-7946.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2016-10-05 19:36:24 -04:00
Leo Famulari
3e1ed70f74
gnu: libxfixes: Update to 5.0.3. 
* gnu/packages/xorg.scm (libxfixes): Update to 5.0.3.
[replacement]: Remove field.
(libxfixes/fixed): Remove variable.
* gnu/packages/patches/libxfixes-CVE-2016-7944.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2016-10-05 19:36:24 -04:00
Leo Famulari
4dd841c1dc
gnu: libx11: Update to 1.6.4. 
* gnu/packages/xorg.scm (libx11): Update to 1.6.4.
[replacement]: Remove field.
(libx11/fixed): Remove variable.
* gnu/packages/patches/libx11-CVE-2016-7942.patch,
gnu/packages/patches/libx11-CVE-2016-7943.patch: Remove files.
* gnu/local.mk (dist_patch_DATA): Remove them.
 2016-10-05 19:36:24 -04:00
Leo Famulari
b19c7989b7
Merge branch 'master' into core-updates 2016-10-05 19:15:25 -04:00
Leo Famulari
1459476089
gnu: e2fsprogs: Fix typo in comment. 
* gnu/packages/linux.scm (e2fsprogs)[arguments]: Fix typo in comment.
 2016-10-05 18:59:29 -04:00
Leo Famulari
7d45365684
gnu: e2fsprogs: Disable parallel build. 
* gnu/packages/linux.scm (e2fsprogs)[arguments]: Add #:parallel-build? #f.
 2016-10-05 17:41:44 -04:00
Leo Famulari
87312f8aa1
gnu: json-c: Update to 0.12.1. 
* gnu/packages/web.scm (json-c): Update to 0.12.1.
 2016-10-05 17:38:48 -04:00
Leo Famulari
813062a5f7
gnu: libxvmc: Fix CVE-2016-7953. 
* gnu/packages/patches/libxvmc-CVE-2016-7953.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/xorg.scm (libxvmc)[replacement]: New field.
(libxvmc/fixed): New variable.
 2016-10-05 17:37:23 -04:00
Leo Famulari
e73631a906
gnu: libxv: Fix CVE-2016-5407. 
* gnu/packages/patches/libxv-CVE-2016-5407.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/xorg.scm (libxv)[replacement]: New field.
(libxv/fixed): New variable.
 2016-10-05 17:37:22 -04:00
Leo Famulari
1f90b80f8b
gnu: libxtst: Fix CVE-2016-{7951,7952}. 
* gnu/packages/patches/libxtst-CVE-2016-7951-CVE-2016-7952.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/xorg.scm (libxtst)[replacement]: New field.
(libxtst/fixed): New variable.
 2016-10-05 17:37:22 -04:00
Leo Famulari
666d40193c
gnu: libxrender: Fix CVE-2016-{7949,7950}. 
* gnu/packages/patches/libxrender-CVE-2016-7949.patch,
gnu/packages/patches/libxrender-CVE-2016-7950.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/xorg.scm (libxrender)[replacement]: New field.
(libxrender/fixed): New variable.
 2016-10-05 17:37:22 -04:00
Leo Famulari
a300db1c7f
gnu: libxrandr: Fix CVE-2016-{7947,7948}. 
* gnu/packages/patches/libxrandr-CVE-2016-7947-CVE-2016-7948.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/xorg.scm (libxrandr)[replacement]: New field.
(libxrandr/fixed): New variable.
 2016-10-05 17:37:21 -04:00
Leo Famulari
b78ba2274f
gnu: libxi: Fix CVE-2016-{7945,7946}. 
* gnu/packages/patches/libxi-CVE-2016-7945-CVE-2016-7946.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/xorg.scm (libxi)[replacement]: New field.
(libxi/fixed): New variable.
 2016-10-05 17:37:21 -04:00
Leo Famulari
b50c6bf2a8
gnu: libxfixes: Fix CVE-2016-7944. 
* gnu/packages/patches/libxfixes-CVE-2016-7944.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/xorg.scm (libxfixes)[replacement]: New field.
(libxfixes/fixed): New variable.
 2016-10-05 17:37:21 -04:00
Leo Famulari
13c10b4ca4
gnu: libx11: Fix CVE-2016-{7942,7943}. 
* gnu/packages/patches/libx11-CVE-2016-7942.patch,
gnu/packages/patches/libx11-CVE-2016-7943.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/xorg.scm (libx11)[replacement]: New field.
(libx11/fixed): New variable.
 2016-10-05 17:37:15 -04:00
ng0
81d5a62fb1
gnu: Remove lispf4. 
The package in its current state is unusable and documentation with unclear
licenses is included.

Also, the file 'lispf42.c' (and possible others) is generated C code and
thus not "source code" as we define it.

* gnu/packages/lisp.scm (lispf4): Delete variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-10-05 16:23:56 -04:00
Tobias Geerinckx-Rice
151df6ab3d
gnu: btrfs-progs: Update to 4.8. 
* gnu/packages/linux.scm (btrfs-progs): Update to 4.8.
 2016-10-05 22:07:21 +02:00
Leo Famulari
bda45da336
gnu: libass: Update to 0.13.4 [fixes CVE-2016-{7969,7970,7972}. 
* gnu/packages/video.scm (libass): Update to 0.13.4.
 2016-10-05 16:04:26 -04:00
Efraim Flashner
a4796b29e1
gnu: gnucash: Update to 2.6.14. 
* gnu/packages/gnucash.scm (gnucash): Update to 2.6.14.
 2016-10-05 20:42:49 +03:00
Danny Milosavljevic
b04ca7a12b
gnu: Add sunxi-tools. 
* gnu/packages/admin.scm (sunxi-tools): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-10-05 18:50:52 +02:00
Leo Famulari
517318adf0
gnu: Add Vc. 
* gnu/packages/maths.scm (vc): New variable.
 2016-10-05 12:49:41 -04:00
Ludovic Courtès
9d50da7060
gnu: wordnet: Make sure the self-reference is visible to the GC. 
Before that, "guix gc --references $(guix build wordnet)" would not show
WordNet itself, erroneously so.

* gnu/packages/wordnet.scm (wordnet)[arguments]: Add -fno-builtin-strcpy
  to #:configure-flags.
 2016-10-05 18:35:55 +02:00
Ludovic Courtès
939f87438c
gnu: wordnet: Compile with optimizations. 
* gnu/packages/wordnet.scm (wordnet)[arguments]: Add -O2 to
  #:configure-flags.
 2016-10-05 18:35:55 +02:00
Kei Kebreau
cd1869cdbd
gnu: Add hyperrogue. 
* gnu/packages/games.scm (hyperrogue): New variable.
 2016-10-05 10:10:36 -04:00
Ludovic Courtès
358db0041f
gnu: grub: Make dependency on mdadm explicit. 
* gnu/packages/grub.scm (grub)[arguments]: Path getroot.c in
'patch-stuff' phase.
[inputs]: Add MDADM.
 2016-10-05 15:11:08 +02:00
Ludovic Courtès
ab2cc5cde1
gnu: gsl: Disable failing tests on i686. 
* gnu/packages/patches/gsl-test-i686.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/maths.scm (gsl)[source](patches): New field.
 2016-10-05 15:11:08 +02:00
Leo Famulari
50948a9026
gnu: git: Update to 2.10.1. 
* gnu/packages/version-control.scm (git): Update to 2.10.1.
 2016-10-05 01:57:51 -04:00
Ludovic Courtès
acbf2c4f60
gnu: guix: Honor the user's 'GUILE_LOAD_PATH'. 
* gnu/packages/package-management.scm (guix-0.11.0)[arguments]: Use
'prefix' when wrapping 'guix' for 'GUILE_LOAD_PATH'.
 2016-10-04 22:40:46 +02:00
Ludovic Courtès
8cecd22e4a
gnu: Add GoAccess. 
* gnu/packages/web.scm (goaccess): New variable.
 2016-10-04 17:44:27 +02:00
Ludovic Courtès
a9764b7d2e
gnu: pies: Update to 1.3. 
* gnu/packages/admin.scm (pies): Update to 1.3.
[arguments]: New field.
 2016-10-04 16:38:00 +02:00
Ludovic Courtès
9d3425f24a
gnu: global: Update to 6.5.5. 
* gnu/packages/code.scm (global): Update to 6.5.5.
 2016-10-04 16:37:59 +02:00
Ludovic Courtès
8c82e1c9d3
gnu: gsl: Update to 2.2.1. 
* gnu/packages/maths.scm (gsl): Update to 2.2.1.
 2016-10-04 16:37:59 +02:00
Ludovic Courtès
bac67a5a5c
gnu: direvent: Update to 5.1. 
* gnu/packages/admin.scm (direvent): Update to 5.1.
[arguments]: Augment 'patch-/bin/sh' phase to patch 'progman.c' and
'testsuite'.
 2016-10-04 16:37:59 +02:00
Ludovic Courtès
d35f8c7cb6
gnu: gnu-c-manual: Update to 0.2.5. 
* gnu/packages/gcc.scm (gnu-c-manual): Update to 0.2.5.
 2016-10-04 16:37:59 +02:00
Ludovic Courtès
a884fa2141
gnu: rush: Update to 1.8. 
* gnu/packages/rush.scm (rush): Update to 1.8.
[source]: Remove 'patches'.
* gnu/packages/patches/cpio-gets-undeclared.patch,
gnu/packages/patches/rush-CVE-2013-6889.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
 2016-10-04 16:37:59 +02:00
Leo Famulari
491dbac415
gnu: cryptsetup: Update to 1.7.2. 
* gnu/packages/cryptsetup.scm (cryptsetup): Update to 1.7.2.
[source]: Use kernel mirror.
[home-page]: Update URL.
 2016-10-04 10:24:46 -04:00
Ben Woodcroft
2c3eb4b85b
gnu: metabat: Update to 0.32.4-1.cbdca756. 
* gnu/packages/bioinformatics.scm (metabat): Update to 0.32.4-1.cbdca756.
* gnu/packages/patches/metabat-remove-compilation-date.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-10-04 22:02:52 +10:00
Ludovic Courtès
47c14714a4
gnu: fish: Do not use the bundled PCRE2. 
* gnu/packages/shells.scm (fish)[inputs]: Add PCRE2.
 2016-10-04 11:26:45 +02:00
Arun Isaac
a8d3bc473d
gnu: fish: Add input bc. 
Fixes <http://bugs.gnu.org/24433>.

* gnu/packages/shells.scm (fish)[inputs]: Add bc.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-10-04 11:26:45 +02:00
Ricardo Wurmus
c5d17d50d0
gnu: warzone2100: Update to 3.2.1. 
* gnu/packages/games.scm (warzone2100): Update to 3.2.1.
[arguments]: Remove phase "set-sdl-paths", add phase
"link-tests-with-qt", add phase "remove-reference-to-missing-file".
[inputs]: Replace "qt-4" with "qt", replace "sdl-union" with
"sdl2", add "openssl".
 2016-10-04 10:21:38 +02:00
Ricardo Wurmus
5c31e981bb
gnu: ruby-nokogumbo: Move "build-gemspec" phase after "unpack". 
* gnu/packages/ruby.scm (ruby-nokogumbo)[arguments]: Move
"build-gemspec" phase after "unpack".
 2016-10-04 08:54:55 +02:00
Ricardo Wurmus
92a312dc86
gnu: python-pathlib: Disable tests. 
* gnu/packages/python.scm (python-pathlib)[arguments]: Disable tests.
 2016-10-04 08:54:55 +02:00
Ricardo Wurmus
ced12a7bff
gnu: ghmm: Run tests after install. 
* gnu/packages/machine-learning.scm (ghmm)[arguments]: Move "check"
phase after "install"; add phase "fix-PYTHONPATH".
 2016-10-04 08:54:55 +02:00
Ricardo Wurmus
4262d178a7
gnu: raincat: Add missing input. 
* gnu/packages/games.scm (raincat)[inputs]: Add freeglut.
 2016-10-04 08:48:55 +02:00
Ricardo Wurmus
d910d584b7
gnu: supertux: Update to 0.5.0. 
* gnu/packages/games.scm (supertux): Update to 0.5.0.
[arguments]: Add flag to disable static boost libraries.
 2016-10-04 08:38:09 +02:00
Leo Famulari
c88cd83b71
gnu: parallel: Update to 20160922. 
* gnu/packages/parallel.scm (parallel): Update to 20160922.
 2016-10-03 23:59:29 -04:00
Mark H Weaver
1927839dcb
gnu: linux-libre: Update to 4.8. 
* gnu/packages/linux.scm (linux-libre): Update to 4.8.
* gnu/packages/linux-libre-4.7-x86_64.conf,
gnu/packages/linux-libre-4.7-i686.conf: Delete files.
* gnu/packages/linux-libre-4.8-x86_64.conf,
gnu/packages/linux-libre-4.8-i686.conf: New files.
* Makefile.am (KCONFIGS): Update accordingly.
 2016-10-03 22:05:51 -04:00
Mark H Weaver
e9b718a05a
gnu: nss: Increase build timeout to 60 hours. 
* gnu/packages/gnuzilla.scm (nss)[properties]: Increase build timeout to
60 hours.
 2016-10-03 22:05:32 -04:00
ng0
6adda006be
gnu: gnunet: Add inputs. 
* gnu/packages/gnunet.scm (gnunet)[inputs]: Add perl, jansson, nss, gmp, bluez,
glib, libogg.
[native-inputs]: Move python-2 from here ...
[inputs]: ... to here.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-10-03 17:43:23 -04:00
Ludovic Courtès
0f7cd95b81
gnu: gctp: 'license' field now has a <license> value. 
* gnu/packages/maths.scm (gctp)[license]: Change to a <license> record.
 2016-10-03 23:20:23 +02:00
Ludovic Courtès
b1cb9f281a
gnu: libgcrypt@1.7: Replacement now has an accurate 'version' field. 
* gnu/packages/gnupg.scm (libgcrypt-1.7.3)[version]: New field.
 2016-10-03 23:16:48 +02:00
Ludovic Courtès
8389e6f06e
gnu: openssl@1.0: Replacement now has an accurate 'version' field. 
* gnu/packages/tls.scm (openssl-1.0.2j)[name, version]: New fields.
 2016-10-03 23:16:48 +02:00
Leo Famulari
6524c1cfcf
gnu: libarchive: Incorporate grafted security patches. 
* gnu/packages/backup.scm (libarchive)[source]: Add patches from
libarchive/fixed.
[replacement]: Remove field.
(libarchive/fixed): Remove variable.
 2016-10-03 17:08:23 -04:00
Leo Famulari
9c2130757c
Merge branch 'master' into core-updates 2016-10-03 17:08:05 -04:00
Leo Famulari
b38e97e03b
gnu: libarchive: Fix several security issues. 
* gnu/packages/backup.scm (libarchive)[replacement]: New field.
(libarchive/fixed): New variable.
* gnu/packages/patches/libarchive-7zip-heap-overflow.patch,
gnu/packages/patches/libarchive-fix-symlink-check.patch,
gnu/packages/patches/libarchive-fix-filesystem-attacks.patch,
gnu/packages/patches/libarchive-safe_fprintf-buffer-overflow.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
 2016-10-03 16:52:28 -04:00
Leo Famulari
85358aef8e
gnu: perl-dbd-mysql: Update to 4.037 [fixes CVE-2016-1246]. 
* gnu/packages/databases.scm (perl-dbd-mysql): Update to 4.037.
 2016-10-03 14:39:11 -04:00
Ricardo Wurmus
d79e8f65b5
gnu: ghc-process: Replace reference to /bin/sh. 
* gnu/packages/haskell.scm (ghc-process)[arguments]: Add phases
"patch-reference-to-/bin/sh" to replace reference to /bin/sh.
 2016-10-02 17:31:40 +02:00
Ricardo Wurmus
2d47cee25b
gnu: Do not propagate inputs in haskell.scm. 
* gnu/packages/haskell.scm
(ghc-streaming-commons)[propagated-inputs]: Move ghc-random...
[inputs]: ...to here; remove ghc-async, add ghc-directory, add
ghc-transformers; move ghc-quickcheck, ghc-hspec...
[native-inputs]: ...to here; add hspec-discover.

(ghc-test-framework)[propagated-inputs]: Move all from here...
[inputs]: ...to here; move ghc-hunit and ghc-quickcheck...
[native-inputs]: ...to here.

(ghc-attoparsec)[propagated-inputs]: Move ghc-scientific...
[inputs]: ...to here; move ghc-quickcheck, ghc-quickcheck-unicode,
ghc-test-framework, ghc-test-framework-quickcheck2, ghc-vector...
[native-inputs]: ...to here.

(ghc-zip-archive)[propagated-inputs]: Move all inputs from here...
[inputs]: ...to here; move ghc-hunit from here...
[native-inputs]: ...to here.

(ghc-network-uri)[inputs]: Add ghc-parsec; move ghc-hunit from here...
[native-inputs]: ...to here.
[propagated-inputs]: Remove.

(ghc-wai)[propagated-inputs]: Move all inputs from here...
[inputs]: ...to here; move ghc-quickcheck, ghc-hunit, and ghc-hspec from
here...
[native-inputs]: ...to here.  Add hspec-discover.

(ghc-wai-extra)[propagated-inputs]: Remove ghc-hspec and ghc-hunit; move
all other inputs from here...
[inputs]: ...to here.
[native-inputs]: Add hspec-discover, ghc-hspec, and ghc-hunit.

(ghc-resourcet, ghc-xss-sanitize, ghc-parsec, ghc-vector, ghc-http,
ghc-base-compat, ghc-base-orphans, ghc-word8)[inputs]: Move all inputs
from here...
[native-inputs]: ...to here.

(ghc-haddock-library, ghc-hspec-contrib, ghc-base-compat,
ghc-base-orphans, ghc-fast-logger, ghc-word8, ghc-aeson-qq,
ghc-logging-facade, ghc-mockery, ghc-yaml, ghc-hslua)[native-inputs]:
Add hspec-discover.

(ghc-fast-logger)[inputs]: Move ghc-hspec from here...
[native-inputs]: ...to here.

(ghc-data-default,
ghc-data-default-instances-base,
ghc-data-default-instances-containers,
ghc-data-default-instances-dlist,
ghc-haddock-api,
ghc-happy,
ghc-haskell-src-exts,
ghc-resourcet,
ghc-xss-sanitize,
ghc-sdl-mixer,
ghc-sdl-image,
ghc-glut,
ghc-gluraw,
ghc-opengl,
cpphs,
ghc-old-time,
ghc-data-default-instances-old-locale,
cabal-install,
ghc-x11,
ghc-x11-xft,
ghc-hashable,
ghc-test-framework-hunit,
ghc-test-framework,
ghc-tf-random,
ghc-transformers-base,
ghc-unix-time,
ghc-http-types,
ghc-iproute,
ghc-regex-base,
ghc-regex-posix,
ghc-regex-tdfa-rc,
ghc-parsers,
ghc-trifecta,
ghc-distributive,
ghc-comonad,
ghc-polyparse,
ghc-profunctors,
ghc-reducers,
ghc-xml,
ghc-exceptions,
ghc-temporary,
ghc-temporary-rc,
ghc-smallcheck,
ghc-tasty-ant-xml,
ghc-quickcheck-instances,
ghc-quickcheck,
ghc-case-insensitive,
ghc-chasingbottoms,
ghc-unordererd-containers,
ghc-uniplate,
ghc-ansi-wl-pprint,
ghc-parsec,
ghc-vector,
ghc-vector-binary-instances,
ghc-http,
ghc-hspec,
ghc-hspec-contrib,
ghc-hspec-core,
ghc-hspec-meta,
ghc-vault,
ghc-monad-control,
ghc-blaze-builder,
ghc-blaze-markup,
ghc-blaze-html,
ghc-async,
ghc-optparse-applicative,
ghc-charset,
ghc-void,
ghc-kan-extensions,
ghc-statevar,
ghc-lens,
ghc-cheapskate,
ghc-semigroupoids,
ghc-contrvariant,
ghc-semigroups,
ghc-free,
ghc-adjunctions,
ghc-fast-logger,
ghc-doctest,
ghc-lifted-base,
ghc-tasty-quickcheck,
ghc-tasty-golden,
ghc-tasty,
ghc-cookie,
ghc-scientific,
ghc-aeson,
ghc-wai-logger,
ghc-pandoc-types,
ghc-texmath,
ghc-regex-pcre-builtin,
ghc-highlighting-kate,
ghc-cmark,
ghc-enclosed-exceptions,
ghc-th-lift,
ghc-th-expand-syns,
ghc-th-reify-many,
ghc-th-orphans,
ghc-haskell-src-meta,
ghc-aeson-qq,
ghc-conduit,
ghc-mockery,
ghc-yaml,
ghc-filemanip,
ghc-juicypixels,
ghc-hslua,
ghc-mime-types,
ghc-http-client,
ghc-hourglass,
ghc-pem,
ghc-asn1-types,
ghc-asn1-encoding,
ghc-asn1-parse,
ghc-tasty-kat,
ghc-cryptonite,
ghc-x509,
ghc-x509-store,
ghc-x509-validation,
ghc-x509-system,
ghc-tls,
ghc-socks,
ghc-connection,
ghc-http-client-tls,
ghc-pandoc)[propagated-inputs]: Move inputs from here...
[inputs]: ...to here.
 2016-10-02 17:31:39 +02:00
Ricardo Wurmus
88cf917b74
gnu: r-plotly: Update to 4.5.2. 
* gnu/packages/statistics.scm (r-plotly): Update to 4.5.2.
[propagated-inputs]: Remove r-plyr; remove r-viridis; add r-dplyr; add
r-lazyeval; add r-purrr; add r-tibble; add r-viridislite.
 2016-10-02 17:31:39 +02:00
Ricardo Wurmus
a3c6445be5
gnu: Add r-purrr. 
* gnu/packages/statistics.scm (r-purrr): New variable.
 2016-10-02 17:31:39 +02:00
Ricardo Wurmus
c6ab73e8ff
gnu: Add r-viridislite. 
* gnu/packages/statistics.scm (r-viridislite): New variable.
 2016-10-02 17:31:36 +02:00
Mark H Weaver
6a703976f4
gnu: libotf: Fix source URI. 
* gnu/packages/fontutils.scm (libotf)[source]: Fix suorce URI.
 2016-10-02 10:49:22 -04:00
Ludovic Courtès
e543c8a2c6
gnu: bash-minimal: Remove 'move-development-files' phase. 
* gnu/packages/bash.scm (bash-minimal)[arguments]: Delete
'move-development-files' phase.
(static-bash)[arguments]: Remove deletion of 'move-development-files'
phase.
 2016-10-02 15:16:21 +02:00
Ben Woodcroft
4bdc3df92d
gnu: vsearch: Update to 2.1.2. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.2.
 2016-10-02 22:25:39 +10:00
Efraim Flashner
10bc741619
gnu: ffmpeg: Update to 3.1.4. 
* gnu/packages/video.scm (ffmpeg): Update to 3.1.4.
 2016-10-02 11:38:32 +03:00
Mark H Weaver
79992a3e6f
gnu: linux-libre: Update to 4.7.6. 
* gnu/packages/linux.scm (linux-libre): Update to 4.7.6.
 2016-10-01 18:22:43 -04:00
Mark H Weaver
2bfa61c034
gnu: linux-libre@4.4: Update to 4.4.23. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.23.
 2016-10-01 18:20:28 -04:00
Ricardo Wurmus
09a86196e9
gnu: guitarix: Update to 0.35.1. 
* gnu/packages/audio.scm (guitarix): Update to 0.35.1.
 2016-10-01 22:31:10 +02:00
Ricardo Wurmus
89fa2219a7
gnu: eigen: Update to 3.2.9. 
* gnu/packages/algebra.scm (eigen): Update to 3.2.9.
 2016-10-01 21:36:36 +02:00
Ricardo Wurmus
d70f5139da
gnu: julia: Update to 0.5.0. 
* gnu/packages/julia.scm (libuv-julia): Update to commit
8d5131b6c1595920dd30644cd1435b4f344b46c8.
(libunwind-for-julia): New variable.
(julia): Update to 0.5.0.
[arguments]: Disable stripping of binaries; modify "prepare-deps" phase;
add "fix-llvm-flag" phase; add "set-home" phase; adjust
"hardcode-soname-map" phase; remove fix for "double-conversion" from
"fix-include-and-link-paths" phase; enable "repl" and "replcompletions"
tests; disable "backtrace", "compile", "replutil", and "cmdlineargs"
tests; remove USE_SYSTEM_RMATH flag; remove USE_SYSTEM_GRISU flag.
[inputs]: Replace "llvm-3.5" with "llvm"; replace "libunwind" with
"libunwind-for-julia"; remove "double-conversion"; remove "rmath-julia";
update "suitesparse" origin; replace "virtualenv" origin with
"python2-virtualenv".
[native-inputs]: Add "openssl".
 2016-10-01 21:36:36 +02:00
Ricardo Wurmus
9b72ce60fb
gnu: utf8proc: Update to 2.0.2. 
* gnu/packages/textutils.scm (utf8proc): Update to 2.0.2.
 2016-10-01 21:36:35 +02:00
Leo Famulari
917de2511b
gnu: gd: Fix CVE-2016-7568. 
* gnu/packages/patches/gd-CVE-2016-7568.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd)[source]: Use it.
 2016-10-01 12:27:37 -04:00
Ludovic Courtès
5bde29685b
gnu: perl: Make builds reproducible again. 
* gnu/packages/patches/perl-reproducible-build-date.patch: Add hunks to
set 'myuname', 'cf_time', and 'cf_by' in 'Configure'.
 2016-10-01 15:20:08 +02:00
Ben Woodcroft
156c0810e9
gnu: perl: Enable threading support. 
* gnu/packages/perl.scm (perl)[arguments]: Configure with '-Dusethreads'.
* gnu/packages/commencement.scm (perl-boot0)[arguments]: Omit inherited
'-Dusethreads' flag during configure.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2016-10-01 14:34:33 +02:00
Ben Woodcroft
56ee1d2015
gnu: perl: Use configure-flags. 
* gnu/packages/perl.scm (perl)[arguments]: Use configure-flags.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-10-01 14:34:31 +02:00
Ludovic Courtès
8d29bfa9fc
gnu: bash-minimal: Disable loadable module support. 
* gnu/packages/bash.scm (bash-minimal)[arguments]: Add
'ac_cv_func_dlopen=no' to #:configure-flags.
 2016-10-01 12:15:02 +02:00
Ludovic Courtès
712b62d8f7
gnu: make-boot0: Use 'install-file'. 
* gnu/packages/commencement.scm (gnu-make-boot0)[arguments]: Use
'install-file' in 'install' phase instead of 'copy-file' etc.
 2016-10-01 11:55:09 +02:00
Ludovic Courtès
8e5e8724d2
gnu: make-boot0: Use 'modify-phases'. 
* gnu/packages/commencement.scm (gnu-make-boot0)[arguments]: Use
'modify-phases'.
 2016-10-01 11:55:09 +02:00
Ivan Vilata i Balaguer
37356e0bf8
gnu: Add quickswitch-i3. 
* gnu/packages/wm.scm (quickswitch-i3): New variable.
* gnu/packages/patches/quickswitch-fix-dmenu-check.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.

Signed-off-by: 宋文武 <iyzsong@gmail.com>
 2016-10-01 10:56:11 +08:00
Ivan Vilata i Balaguer
c165591d47
gnu: Add python-i3-py. 
* gnu/packages/wm.scm (python-i3-py, python2-i3-py): New variables.

Signed-off-by: 宋文武 <iyzsong@gmail.com>
 2016-10-01 10:44:44 +08:00
ng0
f1b61e26ae
gnu: Add emacs-rudel. 
* gnu/packages/emacs.scm (emacs-rudel): New variable.

Signed-off-by: 宋文武 <iyzsong@gmail.com>
 2016-10-01 10:22:31 +08:00
宋文武
df0e8a239b
gnu: shroud: Wrap 'shroud' with 'GUILE_LOAD_COMPILED_PATH'. 
* gnu/packages/password-utils.scm (shroud)[arguments]: New field.
 2016-10-01 08:50:48 +08:00
Leo Famulari
ebb9b9a60c
gnu: tmux: Update to 2.3. 
* gnu/packages/tmux.scm (tmux): Update to 2.3.
 2016-09-30 19:49:08 -04:00
Ludovic Courtès
c573f5a5a5
gnu: bash: Update to 4.4. 
* gnu/packages/bash.scm (%patch-series-4.3): Remove.
(%patch-series-4.4): New variable.
(bash)[source]: Update to 4.4.
[native-inputs]: Remove.
[arguments]: Remove (ice-9 regex) modules; add (srfi srfi-26).
Inline 'install-sh-symlink' phase.  Remove 'install-headers' phase.  Add
'move-development-files' phase.
[native-search-paths]: New field.
(static-bash)[outputs]: New field.
[arguments]: Delete 'move-development-files' phase.
* gnu/packages/commencement.scm (static-bash-for-glibc)
(bash-final): Remove 'native-inputs'.
 2016-10-01 00:00:03 +02:00
Ludovic Courtès
a7a1cf2948
gnu: bash-static: Use 'modify-phases'. 
* gnu/packages/bash.scm (static-bash)[arguments]: Use 'modify-phases'.
 2016-10-01 00:00:02 +02:00
Ludovic Courtès
0c64d8564f
gnu: readline: Update to 7.0. 
* gnu/packages/readline.scm (readline): Update to 7.0.
 2016-10-01 00:00:02 +02:00
Ludovic Courtès
42d1e525bc
gnu: texinfo: Update to 6.3. 
* gnu/packages/texinfo.scm (texinfo): Update to 6.3.
(texinfo-6.3): Remove.
 2016-09-30 12:06:46 +02:00
Ludovic Courtès
79355ae3e8
Merge branch 'master' into core-updates 2016-09-30 12:05:27 +02:00
Leo Famulari
bddf22b99e
gnu: libreoffice: Update to 5.1.5.2. 
* gnu/packages/libreoffice.scm (libreoffice): Update to 5.1.5.2.
 2016-09-30 01:17:24 -04:00
Danny Milosavljevic
cfb7e269e9
gnu: xonsh: Remove bundled PLY. 
* gnu/packages/shells.scm (xonsh)[source]: Add snippet to remove bundled
python-ply.
[inputs]: Add python-ply.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-09-29 17:13:05 -04:00
Julien Lepiller
86d8f6d3ef
services: Add 'openssh-service'. 
* gnu/packages/ssh.scm (openssh)[arguments]: Set sysconfdir to /etc/ssh.
* gnu/services/ssh.scm (<openssh-configuration>): New record type.
(%openssh-accounts): New variable.
(openssh-activation, openssh-config-file, openssh-shepherd-service)
(openssh-service): New procedures.
(openssh-service-type): New variable.
* doc/guix.texi (Networking Services): Document 'openssh-services'.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2016-09-29 23:11:48 +02:00
Arun Isaac
01c5c21a67
gnu: emacs: Build with m17n support. 
* gnu/packages/emacs.scm (emacs): Build with m17n support.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-09-29 17:54:33 +02:00
Arun Isaac
a80b60f484
gnu: Add m17n-lib. 
* gnu/packages/emacs.scm (m17n-lib): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-09-29 17:54:33 +02:00
Arun Isaac
154c71e003
gnu: Add m17n-db. 
* gnu/packages/emacs.scm (m17n-db): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-09-29 17:54:32 +02:00
Leo Famulari
0da1b7062a
gnu: c-ares: Update to 1.12.0 [fixes CVE-2016-5180]. 
* gnu/packages/adns.scm (c-ares): Update to 1.12.0.
[source]: Use HTTPS URL.
[home-page]: Use HTTPS URL.
 2016-09-29 11:18:52 -04:00
David Craven
b9f7895d39
Revert "gnu: %default-extra-linux-options: Remove redundant options." 
Options aren't redundant and are required for building the initrd.

This reverts commit 50dbc03647.
 2016-09-29 12:59:37 +02:00
Ludovic Courtès
d06ce0466f
gnu: dbus-c++: License has "or later" clause. 
* gnu/packages/glib.scm (dbus-c++)[license]: Change to LGPL2.1+.
 2016-09-29 09:01:22 +02:00
Ludovic Courtès
39d6b9c99f
gnu: linux-pam@1.2: Remove erroneous 'name' field. 
* gnu/packages/linux.scm (linux-pam-1.2)[name]: Remove.
 2016-09-28 23:03:00 +02:00
Rene Saavedra
411264c250
gnu: linux-pam: Allow compilation on GNU/Hurd. 
* gnu/packages/patches/linux-pam-no-setfsuid.patch: New file.
* gnu/packages/linux.scm (linux-pam)[source]: Use it.
(linux-pam-1.2)[source]: Likewise.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-09-28 23:01:49 +02:00
Ludovic Courtès
789f09a073
gnu: binutils: Work around Bash 4.2 bug. 
Fixes a 'binutils-cross-boot0' build failure on mips64el.

Reported at
<https://lists.gnu.org/archive/html/guix-devel/2016-09/msg01083.html>.

* gnu/packages/patches/binutils-mips-bash-bug.patch: New file.
* gnu/packages/base.scm (binutils)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-09-28 22:44:38 +02:00
Ricardo Wurmus
2320e76b82
gnu: sra-tools: Fix build on i686. 
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Pass
"VDB_LIBDIR" in make-flags; dynamically link libmagic.
 2016-09-28 22:30:41 +02:00
Efraim Flashner
37042a0fb4
gnu: tilda: Update to 1.3.3. 
* gnu/packages/terminals.scm (tilda): Update to 1.3.3.
 2016-09-28 21:38:38 +03:00
Stefan Reichoer
1d51585573
gnu: Add xonsh. 
* gnu/packages/shells.scm (xonsh): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-09-28 13:42:06 -04:00
Leo Famulari
b2fe918302
gnu: attic: Superseded by borg. 
* gnu/packages/backup.scm (attic)[properties]: New field.
 2016-09-28 13:07:06 -04:00
Taylan Ulrich Bayırlı/Kammer
415ee287fa
gnu: nestopia-ue: Update to version 1.47. 2016-09-28 17:00:35 +02:00
Taylan Ulrich Bayırlı/Kammer
dac65f90b6
gnu: higan: Update to version 101. 
* gnu/packages/games.scm (higan): Update to version 101.
 2016-09-28 17:00:12 +02:00
Alex Kost
9e01589469
gnu: gettext: Install Emacs tools. 
Fixes <http://bugs.gnu.org/24442>.
Reported by Ivan Vilata i Balaguer <ivan@selidor.net>.

* gnu/packages/gettext.scm (gnu-gettext)[native-inputs]: Add 'emacs'.
[arguments]: Add 'add-emacs-autoloads' phase.
 2016-09-28 17:54:50 +03:00
Alex Kost
b94a6ca074
gnu: Add and use gettext-minimal. 
* gnu/packages/gettext.scm (gnu-gettext): Rename to...
(gettext-minimal): ... this.  Adjust synopsis and description.
(gnu-gettext): Inherit from it.
(po4a): Use 'gettext-minimal' instead of 'gnu-gettext'.
* gnu/packages/acl.scm: Likewise.
* gnu/packages/admin.scm: Likewise.
* gnu/packages/apl.scm: Likewise.
* gnu/packages/attr.scm: Likewise.
* gnu/packages/audio.scm: Likewise.
* gnu/packages/base.scm: Likewise.
* gnu/packages/cdrom.scm: Likewise.
* gnu/packages/commencement.scm: Likewise.
* gnu/packages/crypto.scm: Likewise.
* gnu/packages/databases.scm: Likewise.
* gnu/packages/disk.scm: Likewise.
* gnu/packages/documentation.scm: Likewise.
* gnu/packages/education.scm: Likewise.
* gnu/packages/engineering.scm: Likewise.
* gnu/packages/enlightenment.scm: Likewise.
* gnu/packages/fcitx.scm: Likewise.
* gnu/packages/fontutils.scm: Likewise.
* gnu/packages/freedesktop.scm: Likewise.
* gnu/packages/games.scm: Likewise.
* gnu/packages/gkrellm.scm: Likewise.
* gnu/packages/glib.scm: Likewise.
* gnu/packages/gnome.scm: Likewise.
* gnu/packages/grub.scm: Likewise.
* gnu/packages/gtk.scm: Likewise.
* gnu/packages/guile.scm: Likewise.
* gnu/packages/ibus.scm: Likewise.
* gnu/packages/irc.scm: Likewise.
* gnu/packages/iso-codes.scm: Likewise.
* gnu/packages/kde-frameworks.scm: Likewise.
* gnu/packages/kodi.scm: Likewise.
* gnu/packages/linux.scm: Likewise.
* gnu/packages/man.scm: Likewise.
* gnu/packages/maths.scm: Likewise.
* gnu/packages/mono.scm: Likewise.
* gnu/packages/mp3.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/nano.scm: Likewise.
* gnu/packages/networking.scm: Likewise.
* gnu/packages/package-management.scm: Likewise.
* gnu/packages/pdf.scm: Likewise.
* gnu/packages/sawfish.scm: Likewise.
* gnu/packages/statistics.scm: Likewise.
* gnu/packages/terminals.scm: Likewise.
* gnu/packages/version-control.scm: Likewise.
* gnu/packages/vpn.scm: Likewise.
* gnu/packages/w3m.scm: Likewise.
* gnu/packages/webkit.scm: Likewise.
* gnu/packages/wicd.scm: Likewise.
* gnu/packages/wine.scm: Likewise.
* gnu/packages/xdisorg.scm: Likewise.
* gnu/packages/xorg.scm: Likewise.
 2016-09-28 17:54:50 +03:00
Thomas Danckaert
b411517a19
gnu: git: Add input perl-term-readkey for 'git-svn'. 
* gnu/packages/version-control.scm (git)[inputs]: Add perl-term-readkeys.
[arguments]: Add perl-term-readkeys to the PERL5LIB of `git-svn'.

Signed-off-by: 宋文武 <iyzsong@gmail.com>
 2016-09-28 21:23:47 +08:00
David Craven
7a0630035c
gnu: linux-libre-beagle-bone-black: Remove kernel variant. 
linux-libre-beagle-bone-black is misslabeled. This kernel variant is
for the original beagle board.

* gnu/packages/linux.scm (linux-libre-beagle-bone-black): Remove.
 2016-09-28 12:40:12 +02:00
David Craven
e4e9c0a083
gnu: make-linux-libre: Install device tree files. 
* gnu/packages/linux.scm (make-linux-libre): Install device tree files.
 2016-09-28 12:40:12 +02:00
David Craven
50dbc03647
gnu: %default-extra-linux-options: Remove redundant options. 
* gnu/packages/linux.scm (%default-extra-linux-options): Remove
  redundant options.
 2016-09-28 12:40:12 +02:00
David Craven
33619c3ae0
gnu: Add sdcc. 
* gnu/packages/sdcc.scm (sdcc): New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
 2016-09-28 12:40:12 +02:00
David Craven
a3af70aca8
gnu: Add picocom. 
* gnu/packages/terminals.scm (picocom): New variable.
 2016-09-28 12:40:12 +02:00
Lukas Gradl
615c999055
gnu: opendht: Propagate msgpack. 
* gnu/packages/crypto.scm (opendht)[inputs]: Remove msgpack.
[propagated-inputs]: Add it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-09-28 11:45:02 +02:00
Lukas Gradl
974aaf71e5
gnu: telephony: Add 'license:' prefix. 
* gnu/packages/telephony.scm (commoncpp) [license]: Add prefix.
(ucommon) [license]: Add prefix.
(ccrtp) [license]: Add prefix.
(osip) [license]: Add prefix.
(exosip) [license]: Add prefix.
(sipwitch) [license]: Add prefix.
(libsrtp) [license]: Add prefix.
(libiax2) [license]: Add prefix.
(seren) [license]: Add prefix.
(pjproject-sfl) [license]: Add prefix.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-09-28 11:25:34 +02:00
Lukas Gradl
9a4c032cc4
gnu: Add gsm. 
* gnu/packages/audio.scm (gsm): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-09-28 11:14:42 +02:00
Lukas Gradl
89eb7581a4
gnu: Add dbus-c++. 
* gnu/packages/glib.scm (dbus-c++): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-09-28 11:08:33 +02:00
Leo Famulari
a7c9b062ad
gnu: libressl: Update to 2.5.0. 
* gnu/packages/tls.scm (libressl): Update to 2.5.0.
 2016-09-27 20:40:39 -04:00
Tobias Geerinckx-Rice
ffabdc185c
gnu: encfs: Update to 1.9.1. 
* gnu/packages/crypto.scm (encfs): Update to 1.9.1.
 2016-09-28 00:20:30 +02:00
Tobias Geerinckx-Rice
9da3c49837
gnu: btrfs-progs: Update to 4.7.3. 
* gnu/packages/linux.scm (btrfs-progs): Update to 4.7.3.
 2016-09-28 00:20:30 +02:00
Tobias Geerinckx-Rice
8c120e4f3b
gnu: zip: Use 'modify-phases'. 
* gnu/packages/zip.scm (zip)[arguments]: Use 'modify-phases'.
 2016-09-28 00:20:30 +02:00
Leo Famulari
8be2428e85
gnu: isc-dhcp: Update bundled bind to 9.9.9-P3 [fixes CVE-2016-2776]. 
* gnu/packages/admin.scm (isc-dhcp)[inputs]: Update bundled bind to 9.9.9-P3.
 2016-09-27 15:19:14 -04:00
Leo Famulari
cc132e0f38
gnu: bind: Update to 9.10.4-P3 [fixes CVE-2016-2776]. 
* gnu/packages/dns.scm (bind): Update to 9.10.4-P3.
 2016-09-27 15:19:14 -04:00
Stefan Reichoer
e8c9b01090
gnu: Add python-q. 
* gnu/packages/python.scm (python-q, python2-q): New variables.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-09-27 14:54:58 -04:00
Leo Famulari
b9bc6e8420
gnu: expat: Fix regression caused by fix for CVE-2016-0718. 
* gnu/packages/xml.scm (expat)[replacement]: New field.
(expat/fixed): New variable.
* gnu/packages/patches/expat-CVE-2016-0718-fix-regression.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-09-27 13:49:49 -04:00
Thomas Danckaert
32f70e1f86
gnu: Add gctp. 
* gnu/packages/maths.scm (gctp): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-09-27 13:37:46 -04:00
ng0
3973e137f0
gnu: Add gloox. 
* gnu/packages/messaging.scm (gloox): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-09-27 13:31:18 -04:00
ng0
419fb3f1ac
gnu: femtolisp: Don't build on mips64el or armhf. 
* gnu/packages/lisp.scm (femtolisp)[supported-systems]: New field,
remove support for mips64el and armhf.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-09-27 12:29:35 -04:00
Andy Wingo
e9070933bf
gnu: Add gobby. 
* gnu/packages/gobby.scm (gobby): New variable.
 2016-09-27 14:46:10 +02:00
Andy Wingo
22a3cff3c8
gnu: Add obby. 
* gnu/packages/gobby.scm (obby): New variable.
 2016-09-27 14:46:10 +02:00
Andy Wingo
c8105e811b
gnu: Add libnet6. 
* gnu/packages/gobby.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add new file.
 2016-09-27 14:46:10 +02:00
Andy Wingo
b61d962723
gnu: Add libxml++-2. 
* gnu/packages/gnome.scm (libxml++-2): New variable.
 2016-09-27 14:46:10 +02:00
Efraim Flashner
a777535cd7
gnu: aria2: Update to 1.27.1. 
* gnu/packages/bittorrent.scm (aria2): Update to 1.27.1.
 2016-09-27 14:52:48 +03:00
Ben J Woodcroft
99caa6f75f
gnu: python-plastid: Update to 1.4.6. 
* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): Update to
1.4.6.
[propagated-inputs]: Add python-termcolor.
 2016-09-27 20:07:12 +10:00
Ben J Woodcroft
67f66812f5
gnu: Add python-termcolor. 
* gnu/packages/python.scm (python-termcolor, python2-termcolor): New
variables.
 2016-09-27 20:07:02 +10:00
Marius Bakke
f536dce522
gnu: python-pysam: Enable tests. 
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Change from
PyPi to source archive due to missing test data.
[arguments]: Add check phase after install.
[native-inputs]: Add python-nose, samtools and bcftools.
 2016-09-27 20:06:00 +10:00
Marius Bakke
dff26b2363
gnu: python-pysam: Delete bundled htslib. 
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Add snippet
to delete htslib.
[arguments]: Add htslib flags in 'set-flags phase.
[propagated-inputs]: New field. Add htslib.
 2016-09-27 20:06:00 +10:00
Marius Bakke
397d463a12
gnu: python-pysam: Use 'modify-phases'. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Use
'modify-phases'.
 2016-09-27 20:06:00 +10:00
Marius Bakke
bdc7be59eb
gnu: Add bcftools. 
* gnu/packages/bioinformatics.scm (bcftools): New variable.
 2016-09-27 20:06:00 +10:00
Marius Bakke
e301bfc886
gnu: python2-pbcore: Update to 1.2.10. 
* gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.10.
[propagated-inputs]: New field. Add python2-pyxb.
 2016-09-27 20:06:00 +10:00
Marius Bakke
c2efe1aea8
gnu: Add python-pyxb. 
* gnu/packages/xml.scm (python-pyxb, python2-pyxb): New variables.
 2016-09-27 20:06:00 +10:00
Marius Bakke
fd49eb213f
gnu: python-pysam: Update to 0.9.1.4. 
* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam): Update
to 0.9.1.4.
 2016-09-27 20:05:57 +10:00
Leo Famulari
9ad0965228
gnu: openssl-next: Update to 1.1.0b [fixes CVE-2016-6309]. 
* gnu/packages/tls.scm (openssl-next): Update to 1.1.0b.
 2016-09-26 17:09:08 -04:00
Leo Famulari
8be42e5daf
gnu: openssl: Update replacement to 1.0.2j [fixes CVE-2016-7052]. 
* gnu/packages/tls.scm (openssl): Update replacement to 1.0.2j.
(openssl-1.0.2i): Replace with...
(openssl-1.0.2j): ... new variable.
 2016-09-26 17:09:05 -04:00
Danny Milosavljevic
58478cc1cb
gnu: libftdi: Propagate the libusb input. 
* gnu/packages/libftdi.scm (libftdi): Change libusb from an input to a
propagated-input.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-09-26 14:30:37 -04:00
Ricardo Wurmus
675d7ae26f
gnu: ncbi-vdb: Only build on i686 and x86_64. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[supported-systems]: Only
build on i686 and x86_64.
[arguments]: Add mandatory "-msse2" flag to CFLAGS.
 2016-09-26 14:30:59 +02:00
Ricardo Wurmus
bc600b80a2
gnu: ghc-pandoc: Update to 1.17.2. 
* gnu/packages/haskell.scm (ghc-pandoc): Update to 1.17.2.
 2016-09-26 14:30:59 +02:00
Ricardo Wurmus
5a502d9abd
gnu: ghc-texmath: Update to 0.8.6.5. 
* gnu/packages/haskell.scm (ghc-texmath): Update to 0.8.6.5.
 2016-09-26 14:30:58 +02:00
Ricardo Wurmus
2e9b1276b7
gnu: ghc-cmark: Update to 0.5.3.1. 
* gnu/packages/haskell.scm (ghc-cmark): Update to 0.5.3.1.
 2016-09-26 14:30:58 +02:00
Ricardo Wurmus
8f1e2dca55
gnu: ghc-highlighting-kate: Update to 0.6.3. 
* gnu/packages/haskell.scm (ghc-highlighting-kate): Update to 0.6.3.
 2016-09-26 14:30:58 +02:00
Ricardo Wurmus
ae87e4fcde
gnu: ghc-pandoc-types: Update to 1.16.1.1. 
* gnu/packages/haskell.scm (ghc-pandoc-types): Update to 1.16.1.1.
 2016-09-26 14:30:58 +02:00
Ricardo Wurmus
1da48e4302
gnu: ghc-tagsoup: Update to 0.14. 
* gnu/packages/haskell.scm (ghc-tagsoup): Update to 0.14.
 2016-09-26 14:30:58 +02:00
Ricardo Wurmus
1a545a1e7c
gnu: tbb: Fail on test errors. 
* gnu/packages/tbb.scm (tbb)[arguments]: Add phase
"fail-on-test-errors".
 2016-09-26 14:30:58 +02:00
Ricardo Wurmus
ba4529c4f7
gnu: ghc-tls: Update to 1.3.8. 
* gnu/packages/haskell.scm (ghc-tls): Update to 1.3.8.
 2016-09-26 14:30:57 +02:00
Ricardo Wurmus
7f5ca399bf
gnu: tbb: Use modify-phases syntax. 
* gnu/packages/tbb.scm (tbb)[arguments]: Use "modify-phases" syntax.
 2016-09-26 14:30:57 +02:00
Ben Woodcroft
af8de20386
gnu: vsearch: Update to 2.1.1. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.1.
 2016-09-26 20:35:32 +10:00
Ricardo Wurmus
204adc3017
gnu: azr3: Fix libsigc++ build errors. 
* gnu/packages/audio.scm (azr3)[arguments]: Add "-std=gnu++11" flag.
[source]: Add patch.
* gnu/packages/patches/azr3.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-09-26 10:47:58 +02:00
Ricardo Wurmus
3ef08dceb3
gnu: qtractor: Update to 0.7.9. 
* gnu/packages/music.scm (qtractor): Update to 0.7.9.
 2016-09-26 08:16:13 +02:00
Ricardo Wurmus
f3cfe4515a
gnu: Add r-txdb-hsapiens-ucsc-hg19-knowngene. 
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene):
  New variable.
 2016-09-26 07:47:55 +02:00
Ricardo Wurmus
684f29bd2e
gnu: Add r-grohmm. 
* gnu/packages/bioinformatics.scm (r-grohmm): New variable.
 2016-09-26 07:47:55 +02:00
Ricardo Wurmus
7f903d7300
gnu: Add r-systempiper. 
* gnu/packages/bioinformatics.scm (r-systempiper): New variable.
 2016-09-26 07:47:55 +02:00
Ricardo Wurmus
cb99d457f0
gnu: Add r-shortread. 
* gnu/packages/bioinformatics.scm (r-shortread): New variable.
 2016-09-26 07:47:54 +02:00
Ricardo Wurmus
89f40c5e4e
gnu: Add r-gostats. 
* gnu/packages/bioinformatics.scm (r-gostats): New variable.
 2016-09-26 07:47:54 +02:00
Ricardo Wurmus
1a1931f7e0
gnu: Add r-category. 
* gnu/packages/bioinformatics.scm (r-category): New variable.
 2016-09-26 07:47:54 +02:00
Ricardo Wurmus
ad740ff818
gnu: Add r-gseabase. 
* gnu/packages/bioinformatics.scm (r-gseabase): New variable.
 2016-09-26 07:47:53 +02:00
Ricardo Wurmus
cd9e7dc7ff
gnu: Add r-rbgl. 
* gnu/packages/bioinformatics.scm (r-rbgl): New variable.
 2016-09-26 03:25:23 +02:00
Ricardo Wurmus
e816377374
gnu: Add r-annotationforge. 
* gnu/packages/bioinformatics.scm (r-annotationforge): New variable.
 2016-09-26 03:25:17 +02:00
Ricardo Wurmus
9e330278ee
gnu: Add r-batchjobs. 
* gnu/packages/statistics.scm (r-batchjobs): New variable.
 2016-09-26 03:25:11 +02:00
Ricardo Wurmus
dc4fb16d25
gnu: Add r-fail. 
* gnu/packages/statistics.scm (r-fail): New variable.
 2016-09-26 03:25:06 +02:00
Ricardo Wurmus
cd26ec3bbf
gnu: Add r-bbmisc. 
* gnu/packages/statistics.scm (r-bbmisc): New variable.
 2016-09-26 03:25:02 +02:00
Ricardo Wurmus
929d4aaea1
gnu: Add r-checkmate. 
* gnu/packages/statistics.scm (r-checkmate): New variable.
 2016-09-26 03:24:59 +02:00
Ricardo Wurmus
0d90462fa3
gnu: Add r-backports. 
* gnu/packages/statistics.scm (r-backports): New variable.
 2016-09-26 03:24:55 +02:00
Ricardo Wurmus
8e1bfc7e8c
gnu: Add r-sendmailr. 
* gnu/packages/statistics.scm (r-sendmailr): New variable.
 2016-09-26 03:24:50 +02:00
Ricardo Wurmus
0c77fd50f8
gnu: Add r-pheatmap. 
* gnu/packages/statistics.scm (r-pheatmap): New variable.
 2016-09-26 03:24:44 +02:00
Ricardo Wurmus
092197a548
gnu: Add r-matrix. 
* gnu/packages/statistics.scm (r-matrix): New variable.
 2016-09-26 03:21:32 +02:00
Ricardo Wurmus
ad34f0ac96
gnu: Add r-deseq2. 
* gnu/packages/bioinformatics.scm (r-deseq2): New variable.
 2016-09-26 03:21:27 +02:00
Ricardo Wurmus
2301fd3e4d
gnu: Add r-genefilter. 
* gnu/packages/bioinformatics.scm (r-genefilter): New variable.
 2016-09-26 03:21:19 +02:00
Ricardo Wurmus
2d21d44dbd
gnu: Add r-hmisc. 
* gnu/packages/statistics.scm (r-hmisc): New variable.
 2016-09-26 03:21:13 +02:00
Ricardo Wurmus
07a664cde0
gnu: Add r-geneplotter. 
* gnu/packages/bioinformatics.scm (r-geneplotter): New variable.
 2016-09-26 03:21:07 +02:00
Ricardo Wurmus
8c6de58849
gnu: Add r-annotate. 
* gnu/packages/bioinformatics.scm (r-annotate): New variable.
 2016-09-26 03:20:59 +02:00
Ricardo Wurmus
2213730c5b
gnu: Add r-rpart. 
* gnu/packages/statistics.scm (r-rpart): New variable.
 2016-09-26 03:20:52 +02:00
Ricardo Wurmus
356c6d61a6
gnu: Add r-rjson. 
* gnu/packages/web.scm (r-rjson): New variable.
 2016-09-26 03:20:44 +02:00
Ricardo Wurmus
bbed0ab6b4
gnu: Add r-hwriter. 
* gnu/packages/web.scm (r-hwriter): New variable.
 2016-09-26 03:20:19 +02:00
Ricardo Wurmus
57a31efb4b
gnu: tcc: Disable build on MIPS. 
* gnu/packages/c.scm (tcc)[supported-systems]: Disable build on
mips64el.
 2016-09-26 03:01:06 +02:00