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10896 Commits (736f9ffce22f994e6141fa81c4dd9f2997ab1049)

Author SHA1 Message Date
Ludovic Courtès 736f9ffce2 gnu: Add missing import in bioinformatics.scm. 
This is a followup to 1baee94.

* gnu/packages/bioinformatics.scm: Add missing import.
 2016-02-25 12:48:08 +01:00
Ludovic Courtès cfd503205e guix system: Restore load path after running the activation script. 
Fixes <http://bugs.gnu.org/22753>.
Reported by Mark H Weaver <mhw@netris.org>.

* guix/scripts/system.scm (save-load-path-excursion): New variable.
(upgrade-shepherd-services): Add comment about the issue.
(switch-to-system): Use 'save-load-path-excursion' around
'primitive-load' call.
 2016-02-25 12:44:41 +01:00
Ludovic Courtès 06b76acceb store: Clarify documentation of 'valid-path?'. 
* guix/store.scm (valid-path?): Improve docstring.
* doc/guix.texi (The Store): Update accordingly.
 2016-02-25 12:44:41 +01:00
Ludovic Courtès 0043558082 publish: Do not publish nars for invalid store items. 
Before that, /nar requests could succeed if the requested store item
exists but is invalid (although such requests were unlikely because the
corresponding narinfo request would have failed.)

* guix/scripts/publish.scm (render-nar): Add 'store' parameter.  Use
'valid-path?' instead of 'file-exists?'.
(make-request-handler): Adjust 'render-nar' call accordingly.
* tests/publish.scm ("/nar/invalid"): New test.
 2016-02-25 12:44:41 +01:00
Nils Gillmann a65e2a02fc gnu: Add kyotocabinet. 
* gnu/packages/databases.scm (kyotocabinet): New variable.
 2016-02-25 11:56:00 +01:00
Ricardo Wurmus 1baee943ca gnu: Add libBigWig. 
* gnu/packages/bioinformatics.scm (libbigwig): New variable.
 2016-02-25 11:43:44 +01:00
Jan Nieuwenhuizen 1644f0cd87 gnu: guile-json: Update to 0.5.0. 
* gnu/packages/guile.scm (guile-json): Update to 0.5.0.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2016-02-25 09:19:30 +01:00
Ricardo Wurmus b16043a361 gnu: ardour: Update to 4.7. 
* gnu/packages/audio.scm (ardour): Update to 4.7.
 2016-02-25 09:17:35 +01:00
宋文武 f072e9adf5 gnu: xdg-utils: Propagate xprop and xset. 
Fixes <http://bugs.gnu.org/22755>.

* gnu/packages/freedesktop.scm (xdg-utils): Propagate xprop and xset.
 2016-02-25 08:54:42 +08:00
Ludovic Courtès bf98aea9b2 doc: Improve recent changes in "Binary Installation". 
This amends part of c8e2688.

* doc/guix.texi (Binary Installation): Improve wording of some parts.
Fix Upstart example.  Remove incorrect paragraph about locales.
Reinstate bit about reproducing the binary tarball.
 2016-02-24 23:24:33 +01:00
Ludovic Courtès cb05108a5d doc: Clarify who can run 'guix pull'. 
Suggested by Chris Marusich <cmmarusich@gmail.com>.

* doc/guix.texi (Invoking guix pull): Add paragraph explaining that any
user can run 'guix pull'.
 2016-02-24 23:24:33 +01:00
Leo Famulari 85267efb2a gnu: libssh: Update to 0.7.3 [fixes CVE-2016-0739]. 
* gnu/packages/patches/libssh-CVE-2014-0017.patch: Delete file.
* gnu/packages/patches/libssh-0.6.5-CVE-2016-0739.patch: New file.
* gnu-system.am (dist_patch_DATA): Adjust accordingly.
* gnu/packages/ssh.scm (libssh): Update to 0.7.3.
  (libssh-0.5): Rename to...
  (libssh-0.6): ... this.  Update to 0.6.5.
  [source]: Add patch for CVE-2016-0739.
  (guile-ssh)[inputs]: Use libssh-0.6.

Modified-By: Mark H Weaver <mhw@netris.org>
 2016-02-24 16:32:09 -05:00
Leo Famulari 78d80c5c6a gnu: libssh2: Update to 1.7.0 [fixes CVE-2016-0787]. 
* gnu/packages/ssh.scm (libssh2): Update to 1.7.0.
  (libssh2-1.4): New variable.
* gnu/packages/curl.scm (curl)[inputs]: Use libssh4-1.4.

Modified-By: Mark H Weaver <mhw@netris.org>
 2016-02-24 16:32:08 -05:00
George Clemmer c8e26887ed doc: Add details for binary installation. 
* doc/guix.texi (Binary Installation): Provide some more details for binary
  installation, in particular automatic starting of the daemon.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2016-02-24 22:00:07 +01:00
Chris Marusich a40424bd11 doc: Fix minor typos and add missing words. 
* doc/guix.texi (Shepherd Services): Add missing words.
  (Invoking guix system): Fix typo.
  (Service Types and Services): Fix typo.
* doc/contributing.texi (Submitting Patches): Fix typo.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2016-02-24 21:34:30 +01:00
Efraim Flashner a49332a0c0 gnu: gdb: Update to 7.11. 
* gnu/packages/gdb.scm (gdb): Update to 7.11.
 2016-02-24 20:52:12 +02:00
Efraim Flashner c73210d7a9 gnu: kde-frameworks: Update to 5.19.0. 
* gnu/packages/kde-frameworks.scm (kwindowsystem): Update to 5.19.0.
(extra-cmake-modules): Update to 5.19.0.
 2016-02-24 20:25:25 +02:00
Ricardo Wurmus 6d415db23d gnu: r-topgo: Add missing input. 
* gnu/packages/bioinformatics.scm (r-topgo)[propagated-inputs]: Add
  "r-graph".
 2016-02-24 17:36:55 +01:00
Ricardo Wurmus d1dbde6ac1 gnu: Add r-graph. 
* gnu/packages/bioinformatics.scm (r-graph): New variable.
 2016-02-24 17:36:55 +01:00
Ricardo Wurmus e761beb9a9 gnu: Add r-org-mm-eg-db. 
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): New variable.
 2016-02-24 17:26:39 +01:00
Ricardo Wurmus 16c53a1e26 gnu: Add r-org-dm-eg-db. 
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): New variable.
 2016-02-24 17:26:39 +01:00
Ricardo Wurmus fefedf98cb gnu: Add r-org-ce-eg-db. 
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): New variable.
 2016-02-24 17:26:39 +01:00
Ricardo Wurmus 486da49143 gnu: Add r-org-hs-eg-db. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): New variable.
 2016-02-24 17:26:39 +01:00
Alex Kost 6caa4dfa37 Do not check package freshness during upgrade. 
Fixes <http://bugs.gnu.org/22740>.
Reported by Andreas Enge <andreas@enge.fr>.

* gnu/packages.scm (waiting, ftp-open*, check-package-freshness): Remove.
* guix/scripts/package.scm (options->installable): Adjust accordingly.
* emacs/guix-main.scm (package->manifest-entry*): Likewise.
 2016-02-24 18:24:16 +03:00
Ludovic Courtès 4d459d8734 publish: Move 'query-path-info' call where it belongs. 
* guix/scripts/publish.scm (narinfo-string): Remove 'path-info'
parameter and add 'store' parameter.  Call 'query-path-info'.
(render-narinfo): Adjust accordingly.
 2016-02-24 13:11:50 +01:00
Ludovic Courtès da35acf91d gnu: lsh: lshd now supports X11 forwarding. 
Reported by myglc2 <myglc2@gmail.com>.

* gnu/packages/lsh.scm (lsh)[inputs]: Add XAUTH.
[arguments]: Modify 'XAUTH_PROGRAM' macro in 'server_x11.c'.
 2016-02-24 13:11:50 +01:00
Ludovic Courtès 03b93ed70e gnu: lsh: Use 'modify-phases'. 
* gnu/packages/lsh.scm (lsh)[arguments]: Use 'modify-phases' instead of
'alist-cons-before'.
 2016-02-24 13:11:50 +01:00
Andy Wingo ea84bd88da gnu: services: Install policies for polkit service. 
* gnu/services/desktop.scm (polkit-etc-files): Add the polkit package
  itself to the list of packages to scan for .policy files.  This add
  support for pkexec.
 2016-02-24 10:16:54 +01:00
Efraim Flashner ebde7c7a9b mplayer: Use 'modify-phases'. 
* gnu/packages/video.scm (mplayer)[arguments]: Use 'modify-phases'.
[source]: Use https.
[home-page]: Use https.
 2016-02-24 10:33:05 +02:00
Efraim Flashner 778a6a8bf0 gnu: mplayer: Add codecs. 
* gnu/packages/video.scm (mplayer)[inputs]: Add libass, libmpeg2,
  libvdpau, libx264, opus.
 2016-02-24 09:43:51 +02:00
Efraim Flashner dec3e015eb gnu: dropbear: Update to 2015.71. 
* gnu/packages/ssh.scm (dropbear): Update to 2015.71.
 2016-02-24 09:18:14 +02:00
David Thompson dd90ed892a gnu: guile-next: Set correct native search paths. 
* gnu/packages/guile.scm (guile-next): Use the "2.2" directory for the
  load paths.
 2016-02-23 19:39:56 -05:00
Ludovic Courtès f2d8faff04 services: herd: Add missing newlines in error messages. 
* gnu/services/herd.scm (report-action-error): Add missing newlines in
messages.
 2016-02-23 13:03:23 +01:00
Ludovic Courtès 305b58c05c refresh: Remove unneeded import. 
Reported by Leo Famulari <leo@famulari.name>
and Ben Woodcroft <b.woodcroft@uq.edu.au>
at <http://bugs.gnu.org/22752>.

* guix/scripts/refresh.scm: Remove unneeded and harmful import of (guix
import gem).
 2016-02-23 12:58:25 +01:00
Ludovic Courtès 561360a589 doc: Add example of VCS-snapshot version numbers. 
* doc/guix.texi (Version Numbers): Add example for VCS version numbers.
 2016-02-23 12:45:25 +01:00
Andreas Enge 5a179844e7 gnu: Add xfce4-xkb-plugin. 
* gnu/packages/xfce.scm (xfce4-xkb-plugin): New variable.
  (xfce)[propagated-inputs]: Add it.
 2016-02-23 11:53:03 +01:00
Leo Famulari 8758efe0b0 gnu: telepathy-logger: Disable parallel tests. 
* gnu/packages/freedesktop.scm (telepathy-logger)[arguments]: Disable parallel
tests.
 2016-02-23 01:53:47 -05:00
Roel Janssen c1fc7a67e4 gnu: Add rdmd. 
* gnu/packages/ldc.scm (rdmd): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-02-23 01:27:19 -05:00
Leo Famulari e9f68a647d gnu: modem-manager: Use HTTPS URL. 
* gnu/packages/freedesktop.scm (modem-manager)[source]: Use HTTPS URL.
 2016-02-23 00:15:05 -05:00
Leo Famulari fae58fe1d1 gnu: mpd: Update to 0.19.12. 
* gnu/packages/mpd.scm (mpd): Update t0 0.19.12.
 2016-02-22 20:16:25 -05:00
Leo Famulari a4c7c57c2c gnu: ncmpcpp: Udate to 0.7.3. 
* gnu/packages/mpd.scm (ncmpcpp): Update to 0.7.3.
[inputs]: Add icu4c.
 2016-02-22 20:16:25 -05:00
Leo Famulari 9913c78a09 gnu: ncmpcpp: Use 'modify-phases'. 
* gnu/packages/mpd.scm (ncmpcpp)[arguments]: Use 'modify-phases'.
 2016-02-22 20:16:25 -05:00
Christopher Allan Webber 944d2b17b5 vm: Only pass "-enable-kvm" to qemu if /dev/kvm is present. 
Fixes <http://bugs.gnu.org/22633>.

* gnu/build/vm.scm (load-in-linux-vm): Only pass "-enable-kvm" flag to qemu
  if "/dev/kvm" is present.
* gnu/system/vm.scm (common-kvm-options): Same as above.
 2016-02-22 13:28:58 -08:00
Ludovic Courtès 8b16a5e199 gnu: pkg-config: Add non-HTTPS alternate URL. 
* gnu/packages/pkg-config.scm (%pkg-config)[source]: Add non-HTTPS URL.
 2016-02-22 22:11:37 +01:00
Ludovic Courtès b0fef4d660 grafts: 'name' parameter of 'graft-derivation' is now optional. 
* guix/grafts.scm (graft-derivation): Name 'name' a keyword parameter.
* guix/packages.scm (package-derivation, package-cross-derivation):
Adjust accordingly.
* tests/grafts.scm ("graft-derivation"): Likewise.
* tests/packages.scm ("package-derivation, indirect grafts"): Likewise.
 2016-02-22 22:11:37 +01:00
Ludovic Courtès 7adf9b8469 derivations: Move grafts to (guix grafts). 
* guix/derivations.scm (<graft>, graft-derivation, %graft?)
(set-grafting): Move to...
* guix/grafts.scm: ... here.  New file.
* guix/gexp.scm, guix/packages.scm, tests/packages.scm,
guix/scripts/build.scm: Use it.
* Makefile.am (MODULES): Add it.
(SCM_TESTS): Add tests/grafts.scm.
* tests/derivations.scm ("graft-derivation"): Move to...
* tests/grafts.scm: ... here.  New file.
 2016-02-22 22:11:37 +01:00
Andreas Enge 3297deedd1 gnu: Remove python2-pyqt-4. 
* gnu/packages/qt.scm (python2-pyqt-4): Delete variable. It depends on Qt 4,
  which does not receive security updates any more.
 2016-02-22 21:33:29 +01:00
Andreas Enge dbbb45dd73 gnu: Remove KDE 4. 
* gnu/packages/kde.scm (qjson): Move from here...
* gnu/packages/qt.scm (qjson): ...to here.
* gnu/packages/pumpio.scm: Drop inclusion of (gnu packages kde).
* gnu/packages/kde.scm: Delete file.
* gnu-system.am (GNU_SYSTEM_MODULES): Unregister it.
* gnu/packages/rdf.scm (soprano): Delete variable.

KDE 4 relies on Qt 4, which does not receive security updates any more.
 2016-02-22 21:30:56 +01:00
Efraim Flashner 5ad87e5bb5 gnu: python-patsy: Define 'python2-variant'. 
* gnu/packages/statistics.scm (python-patsy)[properties]: New field.
(python2-patsy): Use 'strip-python2-variant'.
 2016-02-22 21:59:02 +02:00
Efraim Flashner f4cd2ceabd gnu: python-patsy: Update to 0.4.1. 
* gnu/packages/statistics.scm (python-patsy, python2-patsy): Update to 0.4.1.
 2016-02-22 21:59:02 +02:00