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Author SHA1 Message Date
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
c74f0cb2b8 tests: Prevent 'http_proxy' from breaking Web server tests. 
* tests/lint.scm: Add call to 'unsetenv' to remove 'http_proxy'.
* tests/publish.scm: Likewise.
 2016-01-22 00:02:52 +01:00
Ludovic Courtès
c4847f49b3 doc: Fix typo in "Locales". 
* doc/guix.texi (Locales): Add missing 's'.
 2016-01-22 00:02:52 +01:00
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
Eric Bavier
ea4a0e81cb gnu: licenses: Add Mozilla Public License 1.0. 
* guix/licenses.scm (mpl1.0): New variable.
 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
aca738f3c6 doc: Explain how to make the Info manual visible. 
Suggested by David Thompson <dthompson2@worcester.edu>
at <http://bugs.gnu.org/22402>.

* doc/guix.texi (Binary Installation): Explain how to make the Info
manual visible.
 2016-01-21 00:22:34 +01:00
Ludovic Courtès
5d94ac5192 doc: Explain how to remove services from a list. 
Suggested by <swedebugia@riseup.net>.

* doc/guix.texi (Using the Configuration System): Add
@unnumberedsubsubsec.  Explain how to remove services from a list.
Mention (gnu system).
 2016-01-21 00:22:34 +01:00
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
Ben Woodcroft
a132f7d68f tests: Move beatify-description tests to import-tests. 
Fixes <http://bugs.gnu.org/22391>.

* tests/cran.scm (beautify-description: use double spacing,
beautify-description: transform fragment into sentence). Move
from here ...
* tests/import-utils.scm: ... to here. New file.
* Makefile.am (SCM_TESTS): Add import-utils.
 2016-01-20 22:06:25 +10:00
Ben Woodcroft
e88d5fa9eb import: gem: Beautify only the description, not the synopsis. 
* guix/import/gem.scm (make-gem-sexp): Add synopsis argument.
(gem->guix-package): Pass unbeautified synopsis to make-gem-sexp.
* tests/gem.scm: Adapt it.
 2016-01-20 21:52:52 +10:00
Ricardo Wurmus
d0bd632f89 import: Add Bioconductor importer and updater. 
* guix/import/cran.scm (%bioconductor-updater,
latest-bioconductor-release, bioconductor-package?): New procedures.
(cran->guix-package): Support repositories other than CRAN.
(%bioconductor-url, %bioconductor-svn-url): New variables.
(description->package): Update signature to distinguish between packages
from different repositories.
(latest-release): Rename procedure ...
(latest-cran-release): ... to this.
(cran-package?): Do not assume all R packages are available on CRAN.
* tests/cran.scm: Update tests.
* guix/scripts/import/cran.scm: Add "--archive" option and default to
CRAN.
* guix/scripts/refresh.scm (%updaters): Add "%bioconductor-updater".
* doc/guix.texi: Document Bioconductor importer and updater.
 2016-01-20 12:41:28 +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
Eric Bavier
252ddedd4b build-system/haskell: Fix package.conf parsing. 
* guix/build/haskell-build-system.scm (register)[conf-depends]: Properly
  react to EOF while reading GHC package conf files.
 2016-01-19 18:01:07 -06:00
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