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Author SHA1 Message Date
Ben Woodcroft bcadaf0050 gnu: Add sortmerna. 
* gnu/packages/bioinformatics.scm (sortmerna): New variable.
 2016-01-25 08:35:11 +10:00
Andreas Enge 447f3ae7c1 gnu: calibre: Update to 2.49.0. 
* gnu/packages/ebook.scm (calibre): Update to 2.49.0.
 2016-01-24 20:12:05 +01:00
Ricardo Wurmus 541ed7b030 gnu: cross-gcc-arguments: Enable C++, disable building of libstdc++-v3. 
* gnu/packages/cross-base.scm (cross-gcc-arguments)[arguments]: Disable
  building libstdc++-v3 and enable building C++ compiler.
 2016-01-24 14:25:20 +01:00
Ricardo Wurmus a763ce7da9 gnu: Add Qtractor. 
* gnu/packages/music.scm (qtractor): New variable.
 2016-01-24 14:20:52 +01:00
Ricardo Wurmus 8ddc5d5723 gnu: yoshimi: Update to 1.3.8.2. 
* gnu/packages/music.scm (yoshimi): Update to 1.3.8.2.
 2016-01-24 14:19:29 +01:00
Efraim Flashner 6b6a62dd05 gnu: privoxy: Update to 3.0.24. 
* gnu/packages/tor.scm (privoxy): Update to 3.0.24.
 2016-01-24 09:20:55 +02:00
Efraim Flashner be866fb13e gnu: tor: Update to 0.2.7.6. 
* gnu/packages/tor.scm (tor): Update to 0.2.7.6.
 2016-01-24 07:21:33 +02:00
Efraim Flashner 17206f72ed gnu: myrepos: Update to 1.20160123. 
* gnu/packages/version-control.scm (myrepos): Update to 1.20160123.
 2016-01-24 07:04:05 +02:00
Efraim Flashner 4c73302739 gnu: nano: Update to 2.5.1. 
* gnu/packages/nano.scm (nano): Update to 2.5.1.
 2016-01-24 06:46:01 +02:00
Mark H Weaver c5184468f5 build: container: Make 'unprivileged-user-namespace-supported?' more robust. 
* gnu/build/linux-container.scm (unprivileged-user-namespace-supported?): Only
  read and check the first character, to cope with a possible newline in the
  (pseudo-)file.
 2016-01-23 18:44:03 -05:00
Leo Famulari fe17fb4a2c gnu: letsencrypt and acme: Update to 0.2.0. 
These packages should be updated together.

* gnu/packages/tls.scm (letsencrypt): Update to 0.2.0.
(acme): Update to 0.2.0.
 2016-01-23 17:39:08 -05:00
Efraim Flashner 21565719e5 gnu: claws-mail: Update to 3.13.2. 
* gnu/packages/mail.scm (claws-mail): Update to 3.13.2.
 2016-01-23 20:13:31 +02:00
Ricardo Wurmus 3a40a92c73 gnu: Add cufflinks. 
* gnu/packages/bioinformatics.scm (cufflinks): New variable.
 2016-01-23 09:15:11 +01:00
Ricardo Wurmus 94ce537eac gnu: Add TopHat. 
* gnu/packages/bioinformatics.scm (tophat): New variable.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
 2016-01-23 08:53:10 +01:00
Ricardo Wurmus 3062d750b4 gnu: star: Update to 2.5.1b. 
* gnu/packages/bioinformatics.scm (star): Update to 2.5.1b.
[source]: Remove bundled htslib sources and pre-built binaries.
[arguments]: Add phase "do-not-use-bundled-htslib".
[inputs]: Add "htslib".
 2016-01-23 08:40:14 +01:00
Ricardo Wurmus c0266e8d03 gnu: star: Use "modify-phases" syntax. 
* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases"
  syntax.
 2016-01-23 08:40:14 +01:00
Efraim Flashner ebf89f134c gnu: fuse: Update to 2.9.5 [fixes CVE-2016-1233]. 
* gnu/packages/linux.scm (fuse): Update to 2.9.5.
 2016-01-22 09:00:34 +02:00
宋文武 6871628999 gnu: mozjs: Make milestone.pl compatible with Perl 5.22+. 
* gnu/packages/gnuzilla.scm (mozjs, mozjs-24)[source]: Add snippet.
 2016-01-22 14:42:10 +08:00
Eric Bavier b6d937d99e gnu: american-fuzzy-lop: Update to 1.96b. 
* gnu/packages/debug.scm (american-fuzzy-lop): Update to 1.96b.
  [arguments]: Create symbolic link to custom qemu, rather than copying.
 2016-01-21 23:54:48 -06:00
Eric Bavier 2d8211ab30 gnu: american-fuzzy-lop: Fix qemu configure flags. 
Fixes regression introduced in 06da1a6.

* gnu/packages/debug.scm (american-fuzzy-lop)[qemu]: Override inherited
  #:configure-flags.
 2016-01-21 23:54:48 -06:00
Eric Bavier 1022da10e1 gnu: texi2html: Disable tests. 
* gnu/packages/texinfo.scm (texi2html): New 'arguments' field.
 2016-01-21 22:09:42 -06:00
Leo Famulari 765973cd65 gnu: Add iftop. 
* gnu/packages/admin.scm (iftop): New variable.
 2016-01-21 20:21:19 -05:00
Leo Famulari c2af02602a Revert "gnu: Add iftop." 
This reverts commit 45da8c6dd1.
 2016-01-21 20:11:21 -05:00
Leo Famulari 45da8c6dd1 gnu: Add iftop. 
* gnu/packages/admin.scm (iftop): New variable.
 2016-01-21 18:11:12 -05:00
Ludovic Courtès 6b779207ee system: grub: Search root device by label or UUID if possible. 
Fixes <http://bugs.gnu.org/22281>.
Reported by Christopher Allan Webber <cwebber@dustycloud.org>.

* gnu/system/grub.scm (eye-candy): Add 'root-fs' parameter.  Replace
'search --file' command in the output with whatever 'grub-root-search'
returns.
(grub-root-search): New procedure.
(grub-configuration-file): Add 'store-fs' parameter.  Use
'grub-root-search' instead of hard-coded 'search --file' commands.
* gnu/system.scm (store-file-system,
operating-system-store-file-system): New procedures.
(operating-system-grub.cfg): Use it, and adjust call to
'grub-configuration-file'.
* tests/system.scm: New file.
* Makefile.am (SCM_TESTS): Add it.
 2016-01-22 00:02:52 +01:00
Mark H Weaver 3738d8700f gnu: ffmpeg: Update to 2.8.5. 
* gnu/packages/video.scm (ffmpeg): Update to 2.8.5.
 2016-01-21 10:30:21 -05:00
Mark H Weaver 0c0207a93b gnu: gajim: Update to 0.16.5 [fixes CVE-2015-8688]. 
* gnu/packages/messaging.scm (gajim): Update to 0.16.5.
  [arguments]: Disable tests.
 2016-01-21 10:24:44 -05:00
Ricardo Wurmus 6c92d8dd35 gnu: bind-utils: Build and install "nsupdate". 
* gnu/packages/dns.scm (bind-utils)[arguments]: Build and install
  "nsupdate" executable.
 2016-01-21 15:53:35 +01:00
Ricardo Wurmus bd0eb6672b gnu: bind-utils: Generalize "build" and "install" phases. 
* gnu/packages/dns.scm (bind-utils)[arguments]: Generalize "build" and
  "install" phases.
 2016-01-21 15:53:35 +01:00
Ricardo Wurmus b2844d8f14 gnu: bind-utils: Use "modify-phases" syntax. 
* gnu/packages/dns.scm (bind-utils): Use "modify-phases" syntax.
 2016-01-21 15:53:35 +01:00
Pjotr Prins 897092875e gnu: r-qtl: Update to 1.38-4. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4.
 2016-01-21 11:16:12 +01:00
Mark H Weaver 1207a0c33e gnu: libxmp: Update to 4.3.10. 
* gnu/packages/audio.scm (libxmp): Update to 4.3.10.
 2016-01-21 00:44:46 -05:00
Mark H Weaver 86fa2ea92f gnu: libtiff: Update to 4.0.6. Add fixes for CVE-2015-{8665,8683}. 
* gnu/packages/patches/libtiff-CVE-2015-8665+CVE-2015-8683.patch,
  gnu/packages/patches/libtiff-oob-accesses-in-decode.patch,
  gnu/packages/patches/libtiff-oob-write-in-nextdecode.patch: New files.
* gnu-system.am (dist_patch_DATA): Add them.
* gnu/packages/image.scm (libtiff): Update to 4.0.6.
  [source]: Add patches.
 2016-01-21 00:30:15 -05:00
Eric Bavier 7ed0145712 gnu: Add NQC. 
* gnu/packages/lego.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
 2016-01-20 22:06:27 -06:00
Leo Famulari feb767b23c gnu: Add transmission-remote-cli. 
* gnu/packages/bittorrent.scm (transmission-remote-cli): New variable.
 2016-01-20 20:19:46 -05:00
Eric Bavier a2190cccc2 gnu: Add dependencies on Perl modules as needed. 
This is a follow-on to bb8afbf5.

* gnu/packages/language.scm (perl-lingua-en-inflect, perl-lingua-stem)
  (perl-snowball-norwegian, perl-snowball-swedish): Add 'native-inputs'
  field.
* gnu/packages/perl.scm (perl-aliased, perl-class-accessor-chained)
  (perl-datetime-set, perl-datetime-format-ical, perl-datetime-locale)
  (perl-error, perl-module-runtime, perl-module-runtime-conflicts)
  (perl-path-class, perl-posix-strftime-compiler, perl-readonly)
  (perl-test-differences, perl-test-pod, perl-test-trap)
  (perl-text-aligner, perl-text-glob, perl-text-table, perl-tie-ixhash)
  (perl-time-mock): Ditto.
  (perl-config-any): Add 'propagated-inputs' field.
  (perl-data-page, perl-datetime, perl-datetime-format-natural)
  (perl-moosex-getopt, perl-moosex-role-parameterized)
  (perl-moosex-types, perl-namespace-autoclean, perl-params-validate)
  (perl-tree-simple-visitorfactory)[native-inputs]: Add PERL-MODULE-BUILD.
  (perl-file-changenotify)[native-inputs]: Ditto.
  [propagated-inputs]: Add PERL-MODULE-PLUGGABLE.
  (perl-datetime-format-flexible, perl-test-writevariants)
  [propagated-inputs]: Ditto.
  (perl-test-mockobject): Add 'arguments' field.
* gnu/packages/mail.scm (perl-email-abstract)[propagated-inputs]: Ditto.
* gnu/packages/web.scm (perl-datetime-format-http, perl-io-socket-ip)
  (perl-plack-middleware-methodoverride, perl-uri-find)
  (perl-www-mechanize): Add 'native-inputs' field.
  (perl-html-template, perl-http-server-simple): Add 'propagated-inputs'
  field.
  (perl-apache-logformat-compiler, perl-html-tree)[native-inputs]:
  Add PERL-MODULE-BUILD.
  (perl-catalyst-runtime)[propagated-inputs]: Add PERL-MODULE-PLUGGABLE.
  (perl-finance-quote)[propagated-inputs]: Add PERL-CGI.
 2016-01-20 17:45:31 -06:00
Eric Bavier 97b07aaa41 gnu: Add perl-module-pluggable. 
This Perl module was moved out of Perl core in v5.19.0.

* gnu/packages/perl.scm (perl-module-pluggable): New variable.
* gnu/packages/patches/perl-module-pluggable-search.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.
 2016-01-20 17:45:31 -06:00
Eric Bavier 7b158c4ee2 gnu: Add perl-cgi. 
The CGI module was removed from Perl core in v5.21.0.

* gnu/packages/web.scm (perl-cgi): New variable.
 2016-01-20 17:45:31 -06:00
Ludovic Courtès 893106cbbf services: avahi: Export service type. 
* gnu/services/avahi.scm: Export 'avahi-service-type'.
 2016-01-21 00:22:34 +01:00
Mark H Weaver 80b64ee2d8 gnu: isc-dhcp: Update bundled bind to 9.9.8-P3 [fixes CVE-2015-8704]. 
* gnu/packages/admin.scm (isc-dhcp): Update bundled bind to 9.9.8-P3.
 2016-01-20 14:58:40 -05:00
Mark H Weaver d912db5bc0 gnu: bind-utils: Update to 9.10.3-P3 [fixes CVE-2015-8704]. 
* gnu/packages/dns.scm (bind-utils): Update to 9.10.3-P3.
 2016-01-20 14:57:06 -05:00
Mark H Weaver beed3af565 gnu: linux-libre: Add fix for CVE-2016-0728. 
* gnu/packages/patches/linux-libre-CVE-2016-0728.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/linux.scm (linux-libre)[source]: Add patch.
 2016-01-20 13:23:42 -05:00
David Thompson d4df203292 gnu: obs: Add support for webcams. 
* gnu/packages/video.scm (obs)[inputs]: Add v4l-utils.
 2016-01-20 11:46:45 -05:00
David Thompson 945d985aab gnu: Add v4l-utils. 
* gnu/packages/video.scm (v4l-utils): New variable.
 2016-01-20 11:46:45 -05:00
Andreas Enge f32ee38fcd gnu: arb: Correct patch. 
* gnu/packages/patches/arb-ldconfig.patch: Correct erroneously committed file.

This is a follow-up to commit ffc8f34511.
 2016-01-20 16:57:17 +01:00
Andreas Enge ffc8f34511 gnu: arb: Update to 2.8.1. 
* gnu/packages/algebra.scm (arb)[source]: Update to 2.8.1. Add patch.
* gnu/packages/patches/arb-ldconfig.patch: New file.
* gnu-system.am (dist_patch_DATA): Register patch.
 2016-01-20 16:33:34 +01:00
Andreas Enge 05944b3aa6 gnu: doxygen: Drop propagated input graphviz. 
* gnu/packages/doxygen.scm (doxygen)[propagated-inputs]: Drop graphviz.
 2016-01-20 13:23:25 +01:00
Andreas Enge 7c853c02b8 gnu: doxygen: Update to 1.8.11. 
* gnu/packages/doxygen.scm (doxygen)[source]: Update to 1.8.11.
  Drop one patch.
  [build-system]: Switch to cmake-build-system, since gnu-build-system
  is not supported any more.
  [arguments]: Adapt.
  [native-inputs]: Drop unused perl.
* gnu/packages/patches/doxygen-tmake.patch: Remove file.
* gnu/packages/patches/doxygen-test.patch: Adapt.
* gnu-system.am (dist_patch_DATA): Unregister patch.
 2016-01-20 13:19:48 +01:00
Efraim Flashner 4c3d2b2a8f gnu: enlightenment: Update to 0.20.3. 
* gnu/packages/enlightenment.scm (enlightenment): Update to 0.20.3.
 2016-01-20 12:37:21 +02:00
Efraim Flashner 0568dbabe0 gnu: libshout: Update to 2.4.1. 
* gnu/packages/xiph.scm (libshout): Update to 2.4.1.
 2016-01-20 02:12:23 +02:00
Efraim Flashner 1c3d37e648 gnu: opusfile: Update to 0.7. 
* gnu/packages/xiph.scm (opusfile): Update to 0.7.
 2016-01-20 02:12:23 +02:00
Efraim Flashner 275cc09280 gnu: opus: Update to 1.1.2. 
* gnu/packages/xiph.scm (opus): Update to 1.1.2.
 2016-01-20 02:12:23 +02:00
Ludovic Courtès 55ca5e8095 gnu: lilypond: Double 'max-silent-time'. 
Suggested by Mark H Weaver <mhw@netris.org>.

* gnu/packages/music.scm (lilypond)[properties]: New field.
 2016-01-19 22:14:15 +01:00
Christopher Allan Webber 16966d5b4d gnu: fdm: Adjust license link to point to web-accessible copy of command.c 
* gnu/packages/mail.scm (fdm): Adjusted license field
 2016-01-19 07:54:18 -08:00
Christopher Allan Webber 34dd26af49 gnu: Add fdm. 
* gnu/packages/mail.scm (fdm): New variable.
 2016-01-18 21:51:45 -08:00
Mark H Weaver afe9f40949 Merge branch 'master' into core-updates 2016-01-19 00:18:37 -05:00
Christopher Allan Webber 1348185ac2 gnu: Add linux-libre-4.2.5 
* gnu/packages/linux.scm (linux-libre-4.2.5): New variable.
 2016-01-18 15:10:38 -08:00
Efraim Flashner 26da7c2606 gnu: mpv: Update to 0.15.0. 
* gnu/packages/video.scm (mpv): Update to 0.15.0.
 2016-01-18 22:26:56 +02:00
Alex Kost 60edbe2297 gnu: magit: Update to 2.4.0. 
* gnu/packages/emacs.scm (magit): Update to 2.4.0.
 2016-01-18 22:40:33 +03:00
Alex Kost d44d60d211 gnu: sxiv: Update to 1.3.2. 
* gnu/packages/sxiv.scm (sxiv): Update to 1.3.2.
 2016-01-18 22:40:33 +03:00
Alex Kost 4c896c9195 gnu: manaplus: Update to 1.6.1.16. 
* gnu/packages/games.scm (manaplus): Update to 1.6.1.16.
 2016-01-18 22:40:33 +03:00
Efraim Flashner 264ae686fa python2-jsonschema: Add python2-functools32 to inputs. 
* gnu/packages/python.scm (python2-jsonschema)[inputs]: Add
python2-functools32.
(python2-wheel)[native-inputs]: Specify python2-jsonschema. Add
python2-functools32.
(python2-requests)[propagated-inputs]: Specify python2-wheel.
(python2-ipython)[inputs]: Specify python2-jsonschema, python2-requests.
(python2-rauth)[propagated-inputs]: Specify python2-requests.
* gnu/packages/openstack.scm (python2-requests-mock)[propagated-inputs]:
Specify python2-requests.
(python2-tempest-lib)[propagated-inputs]: Specify python2-jsonschema.
(python2-oslosphinx)[propagated-inputs]: Specify python2-requests.
(python2-keystoneclient)[porpagated-inputs]: Specify python2-requests.
[native-inputs]: Specify python2-oslosphinx, python2-requests-mock,
python2-tempest-lib.
(python2-swiftclient)[propagated-inputs]: Specify python2-requests,
python2-oslosphinx.
 2016-01-18 17:23:37 +02:00
Efraim Flashner 058247efff gnu: datamash: Update to 1.1.0. 
* gnu/packages/datamash.scm (datamash): Update to 1.1.0.
 2016-01-18 12:14:20 +02:00
Mark H Weaver 8047d13dcf gnu: mariadb: Update to 10.0.23. 
* gnu/packages/databases.scm (mariadb): Update to 10.0.23.
 2016-01-18 01:43:07 -05:00
Mark H Weaver 51a277d8e8 gnu: rsync: Update to 3.1.2. 
* gnu/packages/rsync.scm (rsync): Update to 3.1.2.
 2016-01-17 21:44:31 -05:00
Ricardo Wurmus e8309291a7 gnu: solfege: Build scores with Lilypond. 
* gnu/packages/music.scm (solfege)[inputs]: Add "lilypond".
 2016-01-17 22:57:58 +01:00
Ricardo Wurmus 18ef998bfc gnu: bristol: Remove SSE flags on platforms other than x86_64 and i686. 
* gnu/packages/music.scm (bristol)[arguments]: Add phase
"remove-sse-flags" to remove unsupported optimizations on platforms
other than x86_64 and i686.
 2016-01-17 22:57:58 +01:00
Ludovic Courtès b153f9f0a9 linux-initrd: Remove "usbkbd" from the default set of modules. 
Reported by Ricardo Wurmus <rekado@elephly.net>
at <http://debbugs.gnu.org/cgi/bugreport.cgi?bug=20433#39>.

* gnu/system/linux-initrd.scm (base-initrd): Remove "usbkbd".
 2016-01-17 22:01:47 +01:00
Efraim Flashner e8d2168c27 gnu: Add git-annex-remote-hubic. 
* gnu/packages/version-control.scm (git-annex-remote-hubic): New variable.
 2016-01-17 22:37:04 +02:00
Efraim Flashner c18f636823 gnu: Add python-urllib3. 
* gnu/packages/python.scm (python-urllib3, python2-urllib3): New variables.
 2016-01-17 22:37:04 +02:00
Efraim Flashner e1ba074999 gnu: python-wheel: Clarify description. 
* gnu/packages/python.scm (python-wheel): Do it.
 2016-01-17 22:37:04 +02:00
Efraim Flashner 10468636ff gnu: python-pytest-cov: Clarify description. 
* gnu/packages/python.scm (python-pytest-cov): Do it.
 2016-01-17 22:37:04 +02:00
Efraim Flashner 1abe448d56 gnu: Add python2-functools32. 
* gnu/packages/python.scm (python2-functools32): New variable.
 2016-01-17 22:37:04 +02:00
Efraim Flashner 5988c299c4 gnu: Add python-pyasn1-modules. 
* gnu/packages/python.scm (python-pyasn1-modules)
(python2-pyasn1-modules): New variables.
 2016-01-17 22:37:04 +02:00
Efraim Flashner 81f7f29752 gnu: Add python-rauth. 
* gnu/packages/python.scm (python-rauth, python2-rauth): New variables.
 2016-01-17 22:37:04 +02:00
Efraim Flashner 8f0cc2ffce gnu: Add python-swiftclient. 
* gnu/packages/openstack.scm (python-swiftclient, python2-swiftclient):
New variables.
 2016-01-17 22:37:04 +02:00
Efraim Flashner 7a5b944eb5 gnu: Add python-futures. 
* gnu/packages/python.scm (python-futures, python2-futures): New variables.
 2016-01-17 22:37:04 +02:00
Efraim Flashner c9e330d001 gnu: Add python-keystoneclient. 
* gnu/packages/openstack.scm (python-keystoneclient)
(python2-keystoneclient): New variables.
 2016-01-17 22:37:04 +02:00
Ricardo Wurmus fb492b9a64 gnu: vmpk: Update to 0.6.2a. 
* gnu/packages/music.scm (vmpk): Update to 0.6.2a.
 2016-01-17 19:57:07 +01:00
Ricardo Wurmus cfac12723a gnu: drumstick: Update to 1.0.2. 
* gnu/packages/music.scm (drumstick): Update to 1.0.2.
 2016-01-17 19:57:00 +01:00
Efraim Flashner 81c29cccaa gnu: mpv: Add features. 
* gnu/packages/video.scm (mpv)[inputs]: Add libvdpau.
[arguments]: Add gpl3 and zsh completion flags.
 2016-01-17 20:43:51 +02:00
Efraim Flashner 3161d32d37 gnu: Add vdpauinfo. 
* gnu/packages/video.scm (vdpauinfo): New variable.
 2016-01-17 20:43:51 +02:00
Efraim Flashner d5650f86a7 gnu: Add libvdpau. 
* gnu/packages/video.scm (libvdpau): New variable.
 2016-01-17 20:43:51 +02:00
Ludovic Courtès bb8afbf5a1 gnu: Add dependency on Perl's 'Module::Build' as needed. 
'Module::Build' was deprecated in Perl 5.20 and removed in 5.22.
Some packages need to explicitly depend on it now.

* gnu/packages/perl.scm (perl-class-factory-util):
(perl-date-manip, perl-devel-checkbin): Add 'native-inputs' field.
(perl-module-build)[description]: Mention that it used to be in Perl.
* gnu/packages/web.scm (perl-cgi-simple)[native-inputs]: Add
PERL-MODULE-BUILD.
 2016-01-17 18:41:20 +01:00
Eric Bavier 2328b47c64 gnu: Add autojump. 
* gnu/packages/admin.scm (autojump): New variable.
 2016-01-17 01:44:15 -06:00
Eric Bavier f5a8491b69 gnu: hevea: Update to 2.28. 
* gnu/packages/ocaml.scm (hevea): Update to 2.28.
  [arguments]: Add 'patch-/bin/sh phase.
 2016-01-17 01:04:43 -06:00
Eric Bavier 90907a22bc gnu: unison: Add "doc" output. 
* gnu/packages/ocaml.scm (unison)[source]: Use svn-fetch with snippet.
  [outputs]: New field.
  [native-inputs]: Add ghostscript, texlive, hevea, and lynx.
  [arguments]: Add 'install-doc phase.
 2016-01-17 01:04:43 -06:00
Ricardo Wurmus 2309ed6862 gnu: samtools-0.1: Adapt to changes in "samtools" variable. 
* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add
  "LIBCURSES" make flag; delete "configure" phase; disable tests outside
  of "substitute-keyword-arguments".
 2016-01-16 15:50:51 +01:00
Ludovic Courtès 7ba903b6db linux-modules: Support 'modprobe.blacklist' on the command line. 
* gnu/build/linux-modules.scm (file-name->module-name)
(module-black-list): New procedure.
* gnu/build/linux-modules.scm (load-linux-module*): Add #:black-list
parameter.
[black-listed?, load-dependencies]: New procedures.
Use them.
 2016-01-16 14:45:47 +01:00
Alex Kost b8300494c0 Move <boot-parameters> to (gnu system). 
* guix/scripts/system.scm (previous-grub-entries)
  (display-system-generation): Use accessors instead of matching
  <boot-parameters>.
  (boot-parameters, boot-parameters?, boot-parameters-label)
  (boot-parameters-root-device, boot-parameters-kernel)
  (boot-parameters-kernel-arguments, read-boot-parameters): Move to...
* gnu/system.scm: ... here. Export them.
 2016-01-16 13:02:21 +03:00
宋文武 c3e919d7a0 gnu: Add python-hy. 
* gnu/packages/python.scm (python-hy, python2-hy): New variables.
 2016-01-16 08:18:37 +08:00
宋文武 e224b7d0bd gnu: Add python-rply. 
* gnu/packages/python.scm (python-rply, python2-rply): New variables.
 2016-01-16 08:18:37 +08:00
宋文武 4ecdeef8ae gnu: Add python-astor. 
* gnu/packages/python.scm (python-astor, python2-astor): New variables.
 2016-01-16 08:18:37 +08:00
宋文武 c06a3de93a gnu: Add python-clint. 
* gnu/packages/python.scm (python-clint, python2-clint): New variables.
 2016-01-16 08:17:04 +08:00
宋文武 2216e15cc3 gnu: Add python-args. 
* gnu/packages.scm (python-args, python2-args): New variables.
 2016-01-16 08:16:51 +08:00
Mark H Weaver ca3f9952d7 gnu: ffmpeg: Update to 2.8.5. 
* gnu/packages/video.scm (ffmpeg): Update to 2.8.5.
 2016-01-15 18:20:21 -05:00
Mark H Weaver 8d9bae4ed7 gnu: librsvg: Update to 2.40.13 [fixes CVE-2015-7558]. 
* gnu/packages/patches/librsvg-tests.patch: Delete file.
* gnu-system.am (dist_patch_DATA): Remove it.
* gnu/packages/gnome.scm (librsvg): Update to 2.40.13.
  [source]: Remove patch.
 2016-01-15 18:03:02 -05:00
Leo Famulari 78e6c4a862 gnu: Add khal. 
* gnu/packages/calendar.scm (khal): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari b97c1bfd56 gnu: python-urwid: Disable failing test test_remove_watch_file. 
* gnu/packages/python.scm (python-urwid)[arguments]: Add
'disable-failing-test' phase.
[source]: Use pypi-uri.
 2016-01-15 16:45:24 -05:00
Leo Famulari 226d333103 gnu: Update python-tzlocal to 1.2. 
* gnu/packages/python.scm (python-tzlocal): Update to 1.2.
[source]: Use pypi-uri.
[arguments]: Remove the custom 'unpack phase.
[native-inputs]: Remove unzip, python-setuptools.
[propagated-inputs]: Add python-pytz.
 2016-01-15 16:45:24 -05:00
Leo Famulari 6bbbb53eeb gnu: Add python-sphinxcontrib-newsfeed. 
* gnu/packages/python.scm (python-sphinxcontrib-newsfeed): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari 5c299bf016 gnu: Add python-icalendar. 
* gnu/packages/python.scm (python-icalendar): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari a2f6a3d502 gnu: Add vdirsyncer. 
* gnu/packages/dav.scm (vdirsyncer): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari f75bbb028a gnu: Add radicale. 
* gnu/packages/dav.scm (radicale): New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
 2016-01-15 16:45:24 -05:00
Leo Famulari 89b8a5516f gnu: Add python-pytest-xprocess. 
* gnu/packages/python.scm (python-pytest-xprocess): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari 28cecbb7cc gnu: Add python-wsgi-intercept. 
* gnu/packages/python.scm (python-wsgi-intercept): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari d7e729fe08 gnu: Add python-pytest-localserver. 
* gnu/packages/python.scm (python-pytest-localserver): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari 6720dbb49f gnu: Add python-pytest-cache. 
* gnu/packages/python.scm (python-pytest-cache): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari 848964fe11 gnu: Add python-execnet. 
* gnu/packages/python.scm (python-execnet): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari 7b3a4ee4c3 gnu: Add python-apipkg. 
* gnu/packages/python.scm (python-apipkg): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari 7b17cab902 gnu: Add python-click-log. 
* gnu/packages/python.scm (python-click-log): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari d1deb90b3f gnu: Add python-click-threading. 
* gnu/packages/python.scm (python-click-threading): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari 561bb3cb1a gnu: Add python-requests-toolbelt. 
* gnu/packages/python.scm (python-requests-toolbelt): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari 5c6eea2ad1 gnu: Add python-atomicwrites. 
* gnu/packages/python.scm (python-atomicwrites): New variable.
 2016-01-15 16:45:24 -05:00
Ricardo Wurmus f5ca44b86e gnu: glade: Update to 3.18.5. 
* gnu/packages/gnome.scm (glade): Update to 3.18.5.
[arguments]: Disable tests; add "fix-docbook" phase.
[inputs]: Replace "gtk+-2" with "gtk+".
[native-inputs]: Add "itstool", "libxslt", "docbook-xml", "docbook-xsl";
replace "python" with "python-2".
 2016-01-15 22:29:37 +01:00
Ludovic Courtès 89b48232f8 gnu: automake: Adjust to deal with Perl 5.22. 
Fixes <http://bugs.gnu.org/22375>.

* gnu/packages/patches/automake-regexp-syntax.patch: New file.
* gnu/packages/autotools.scm (automake)[source]: Use it.
* gnu-system.am (dist_patch_DATA): Add it.
 2016-01-15 14:23:46 +01:00
Mark H Weaver 45f2ffb48c gnu: openssh: Update to 7.1p2. 
* gnu/packages/ssh.scm (openssh): Update to 7.1p2.
 2016-01-15 02:46:12 -05:00
Mark H Weaver 1beec63ac8 Revert "gnu: openssh: Update to 7.1p2 [fixes CVE-0216-0778]." 
This reverts commit 6d139e53b5.
 2016-01-15 02:45:58 -05:00
Mark H Weaver 6d139e53b5 gnu: openssh: Update to 7.1p2 [fixes CVE-0216-0778]. 
* gnu/packages/ssh.scm (openssh): Update to 7.1p2.
 2016-01-14 10:39:00 -05:00
David Thompson df1f1d6936 gnu: Add docker-compose. 
* gnu/packages/docker.scm (docker-compose): New variable.
 2016-01-14 09:17:12 -05:00
David Thompson b42c9c8124 gnu: Add python-dockerpty. 
* gnu/packages/docker.scm (python-dockerpty): New variable.
 2016-01-14 09:16:22 -05:00
David Thompson d020bfc2df gnu: Add python-docker-py. 
* gnu/packages/docker.scm: New file.
* Makefile.am (GNU_SYSTEM_MODULES): Add it.
 2016-01-14 09:16:22 -05:00
David Thompson 67c52bb3e7 gnu: Add python-websocket-client. 
* gnu/packages/python.scm (python-websocket-client): New variable.
 2016-01-14 09:12:23 -05:00
David Thompson 210bf49754 gnu: Add python-texttable. 
* gnu/packages/python.scm (python-texttable, python2-texttable): New
variables.
 2016-01-14 09:12:23 -05:00
David Thompson b3667afbd2 gnu: Update python-jsonschema to 2.5.1. 
* gnu/packages/python.scm (python-jsonschema): Update to 2.5.1.
[inputs]: Add python-vcversioner.
 2016-01-14 09:12:06 -05:00
David Thompson ea521b42c2 gnu: Add python-vcversioner. 
* gnu/packages/python.scm (python-vcversioner, python2-vcversioner): New
variables.
 2016-01-14 09:05:19 -05:00
David Thompson e90051808b gnu: Add version 2.7 variant of python-requests. 
* gnu/packages/python.scm (python-requests-2.7): New variable.
 2016-01-14 09:05:19 -05:00
Ricardo Wurmus 3141b83d4d gnu: r-go-db: Add missing input. 
* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add
  "r-annotationdbi".
 2016-01-14 14:43:59 +01:00
Ricardo Wurmus d7786ce9b0 gnu: r-sparsem: Add missing "gfortran" input. 
* gnu/packages/statistics.scm (r-sparsem)[inputs]: Add "gfortran".
 2016-01-14 14:43:59 +01:00
Ricardo Wurmus 0047d26a22 gnu: bowtie: Update to 2.2.6. 
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.6.
[source]: Remove patch; do not set CC and CPP variables.
[inputs]: Add "tbb".
[arguments]: Pass "prefix" and "WITH_TBB" make flags; remove custom
"install" phase.
* gnu/packages/patches/bowtie-fix-makefile.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove patch file.
 2016-01-14 14:43:25 +01:00
Efraim Flashner 2d12284d38 gnu: gnupg: Add TOFU support. 
* gnu/packages/gnupg.scm (gnupg)[inputs]: Add sqlite.
 2016-01-14 15:05:36 +02:00
Ludovic Courtès 76002e54f2 gnu: gawk: Protect against random failures of the 'fts' test. 
* gnu/packages/patches/gawk-fts-test.patch: New file.
* gnu/packages/gawk.scm (gawk)[source]: Use it.
* gnu-system.am (dist_patch_DATA): Add it.
 2016-01-14 10:43:08 +01:00
Ben Woodcroft 6b6f7d6a0e gnu: orfm: Update to 0.5.3. 
* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3.
[native-inputs]: Add inputs required for tests.
[description]: Add commas.
 2016-01-14 08:00:10 +10:00
Ben Woodcroft 3d84a99e73 gnu: Add ruby-bio-commandeer. 
* gnu/packages/ruby.scm (ruby-bio-commandeer): New variable.
 2016-01-14 08:00:02 +10:00
Ben Woodcroft 7c033c4627 gnu: Add ruby-systemu. 
* gnu/packages/ruby.scm (ruby-systemu): New variable.
 2016-01-14 07:51:44 +10:00
Ricardo Wurmus ca7ef4d418 gnu: cross-gcc-arguments: Enable C++, disable building of libstdc++-v3. 
* gnu/packages/cross-base.scm (cross-gcc-arguments)[arguments]: Disable
  building libstdc++-v3 and enable building C++ compiler.
 2016-01-13 22:32:37 +01:00
Ludovic Courtès 8c986ab120 Merge branch 'master' into core-updates 2016-01-13 18:18:48 +01:00
Ricardo Wurmus e5a19fed19 gnu: julia: Update to 0.4.3. 
* gnu/packages/julia.scm (julia): Update to 0.4.3.
(libuv-julia): Update to 07730c4bd595.
 2016-01-13 17:05:38 +01:00
Mark H Weaver 75418ae0fd gnu: isc-dhcp: Update to 4.3.3-P1 [fixes CVE-2015-8605]. 
* gnu/packages/admin.scm (isc-dhcp): Update to 4.3.3-P1.
 2016-01-13 09:38:57 -05:00
Ricardo Wurmus c44734115a gnu: samtools: Update to 1.3. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.
[arguments]: Enable tests for all architectures; set ncurses in
configure-flags instead of make-flags; simplify "patch-tests" phase;
restore "configure" phase.
 2016-01-13 15:12:22 +01:00
Ludovic Courtès 98f2339189 gnu: skribilo: Update to 0.9.3. 
* gnu/packages/skribilo.scm (skribilo): Update to 0.9.3.
[native-inputs]: New field.
 2016-01-13 11:13:34 +01:00
Eric Bavier c91d3fb7f4 gnu: boost: Update to 1.60.0. 
* gnu/packages/boost.scm (boost): Update to 1.60.0.
  [source]: Remove patch.
* gnu/packages/patches/boost-mips-avoid-m32.patch: Delete patch
* gnu-system.am (dist_patch_DATA): Remove patch.

Also fix dependent packages:

* gnu/packages/patches/csound-header-ordering.patch: New patch.
* gnu/packages/audio.scm (csound)[source]: Use it.
  [arguments]: Add 'set-flags phase.
* gnu/packages/patches/libcmis-fix-test-onedrive.patch: New patch.
* gnu/packages/libreoffice.scm (libcmis)[source]: Use it.
  (libreoffice)[arguments]: Add LDFLAGS to #:configure-flags.
  (librevenge)[inputs]: Move boost from here...
  [propogated-inputs]: to here.
  [arguments]: Add LDFLAGS to #:configure-flags.
* gnu/packages/patches/openimageio-boost-1.60.patch: New patch.
* gnu/packages/graphics.scm (openimageio): Use it.
* gnu-system.am (dist_patch_DATA): Add patches.
 2016-01-12 21:07:53 +01:00
Eric Bavier 3abe8136fd gnu: boost: Use modify-phases. 
* gnu/packages/boost.scm (boost)[arguments]: Use modify-phases.
 2016-01-12 20:53:14 +01:00
Mark H Weaver 203795acea gnu: perl: Add fix for CVE-2015-8607. 
* gnu/packages/patches/perl-CVE-2015-8607.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/perl.scm (perl)[source]: Add patch.
 2016-01-12 13:12:07 -05:00
Mark H Weaver ce3ac6670c gnu: perl: Update to 5.22.1. 
* gnu/packages/perl.scm (perl): Update to 5.22.1.
 2016-01-12 13:10:05 -05:00
Mark H Weaver 16aa649117 gnu: sudo: Add fix for CVE-2015-5602. 
* gnu/packages/patches/sudo-CVE-2015-5602.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/admin.scm (sudo)[source]: Add patch.
 2016-01-12 11:23:06 -05:00
Efraim Flashner 9d9951d6a6 gnu: global: Use modify-phases syntax. 
* gnu/packages/code.scm (global)[arguments]: Use modify-phases syntax.
 2016-01-12 14:47:10 +02:00
Efraim Flashner 94c3a6f1a6 gnu: global: Update to 6.5.2. 
* gnu/packages/code.scm (global): Update to 6.5.2.
 2016-01-12 14:39:15 +02:00
Ricardo Wurmus 9f40b1171b gnu: icedtea-6: Fix directory name in "unpack" phase. 
* gnu/packages/java.scm (icedtea-6)[arguments]: Change the directory
  prefix in the "unpack" phase to "icedtea6-".
 2016-01-12 11:39:21 +01:00
Mark H Weaver 6b0d24b17c gnu: linux-libre: Update to 4.4. 
* gnu/packages/linux.scm (linux-libre): Update to 4.4.
* gnu/packages/linux-libre-i686.conf,
  gnu/packages/linux-libre-x86_64.conf: Update from
  <https://jxself.org/git/kernel-configs.git>.
 2016-01-11 19:13:37 -05:00