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10333 Commits

Author SHA1 Message Date
Ludovic Courtès 9059b97dc3 doc: 'base-initrd' has #:virtio? default to #t. 
This is a followup to e26d507.

* doc/guix.texi (Initial RAM Disk): #:virtio? defaults to #t.
 2016-01-25 00:11:22 +01:00
Ben Woodcroft bcadaf0050 gnu: Add sortmerna. 
* gnu/packages/bioinformatics.scm (sortmerna): New variable.
 2016-01-25 08:35:11 +10:00
Andreas Enge 74273b6f2d doc: Fix typo in section on offloading. 
* doc/guix.texi (Daemon Offload Setup): Fix quoting typo in command.
 2016-01-24 23:25:38 +01:00
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
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
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
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
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
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