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11022 Commits (97a08595930d429ed8ca3e1afa2d1274911481df)

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Ludovic Courtès 0043558082 publish: Do not publish nars for invalid store items.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
Mark H Weaver bf6996c9cf gnu: xf86-video-intel: Update to 2.99.917-1-d167280. 
* gnu/packages/xorg.scm (xf86-video-intel): Update to 2.99.917-1-d167280.
 2016-02-24 13:56:57 -05:00
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
Andy Wingo 79fd74facd gnu: services: Start X with -configdir. 
* gnu/services/xorg.scm (%default-xorg-modules): New public variable.
(xorg-configuration-directory): New function.
(xorg-start-command): Add #:modules keyword argument, defaulting to
%default-xorg-modules.  Build an xorg.conf.d directory from those
modules, and pass it to X via the -configdir parameter.
 2016-02-24 11:49:57 -05:00
Andy Wingo d0a6437f7d gnu: libxaw: Update to 1.0.13. 
* gnu/packages/xorg.scm (libxaw): Update to 1.0.13.
 2016-02-24 11:49:57 -05:00
Andy Wingo ea9763dae0 gnu: libxt: Update to 1.1.5. 
* gnu/packages/xorg.scm (libxt): Update to 1.1.5.
 2016-02-24 11:49:57 -05:00
Andy Wingo f1aeae762d gnu: libx11: Update to 1.6.3. 
* gnu/packages/xorg.scm (libx11): Update to 1.6.3.
 2016-02-24 11:49:57 -05:00
Andy Wingo 0eae6b2d91 gnu: xorg-server: Update to 1.18.1. 
* gnu/packages/xorg.scm (xorg-server): Update to 1.18.1.
 2016-02-24 11:49:57 -05:00
Andy Wingo 7606baa8f9 gnu: libxxf86vm: Update to 1.1.4. 
* gnu/packages/xorg.scm (libxxf86vm): Update to 1.1.4.
 2016-02-24 11:49:57 -05:00
Andy Wingo 9a5f739ef8 gnu: libxvmc: Update to 1.0.9. 
* gnu/packages/xorg.scm (libxvmc): Update to 1.0.9.
 2016-02-24 11:49:57 -05:00
Andy Wingo 61f29af1db gnu: libxrandr: Update to 1.5.0. 
* gnu/packages/xorg.scm (libxrandr): Update to 1.5.0.
 2016-02-24 11:49:57 -05:00
Andy Wingo d51b8529e6 gnu: libxi: Update to 1.7.6. 
* gnu/packages/xorg.scm (libxi): Update to 1.7.6.
 2016-02-24 11:49:57 -05:00
Andy Wingo 10d85db449 gnu: xproto: Update to 7.0.28. 
* gnu/packages/xorg.scm (xproto): Update to 7.0.28.
 2016-02-24 11:49:57 -05:00
Andy Wingo 6fad350498 gnu: libxrender: Update to 0.9.9. 
* gnu/packages/xorg.scm (libxrender): Update to 0.9.9.
 2016-02-24 11:49:57 -05:00
Andy Wingo 42ca6c8528 gnu: libxp: Update to 1.0.3. 
* gnu/packages/xorg.scm (libxp): Update to 1.0.3.
 2016-02-24 11:49:57 -05:00
Andy Wingo 97b6f9632e gnu: xvinfo: Update to 1.1.3. 
* gnu/packages/xorg.scm (xvinfo): Update to 1.1.3.
 2016-02-24 11:49:57 -05:00
Andy Wingo 625f4cae0a gnu: xmodmap: Update to 1.0.9. 
* gnu/packages/xorg.scm (xmodmap): Update to 1.0.9.
 2016-02-24 11:49:57 -05:00
Andy Wingo 85c64cb200 gnu: xlsatoms: Update to 1.1.2. 
* gnu/packages/xorg.scm (xlsatoms): Update to 1.1.2.
 2016-02-24 11:49:57 -05:00
Andy Wingo 379e1d875b gnu: xkeyboard-config: Update to 2.17. 
* gnu/packages/xorg.scm (xkeyboard-config): Update to 2.17.
 2016-02-24 11:49:57 -05:00
Andy Wingo ed7abe52e0 gnu: xkbevd: Update to 1.1.4. 
* gnu/packages/xorg.scm (xkbevd): Update to 1.1.4.
 2016-02-24 11:49:57 -05:00
Andy Wingo ab2d710cc2 gnu: xinput: Update to 1.6.2. 
* gnu/packages/xorg.scm (xinput): Update to 1.6.2.
 2016-02-24 11:49:57 -05:00
Andy Wingo 2e5a0b7850 gnu: xhost: Update to 1.0.7. 
* gnu/packages/xorg.scm (xhost): Update to 1.0.7.
 2016-02-24 11:49:57 -05:00
Andy Wingo 033a1ba373 gnu: xgamma: Update to 1.0.6. 
* gnu/packages/xorg.scm (xgamma): Update to 1.0.6.
 2016-02-24 11:49:57 -05:00
Andy Wingo 9177dbeb5f gnu: xf86-video-voodoo: Fix build. 
* gnu/packages/xorg.scm (xf86-video-voodoo): Add patch from upstream git
  to fix the build.
 2016-02-24 11:49:57 -05:00
Andy Wingo 2ae7a55062 gnu: xf86-video-vmware: Update to 13.1.0. 
* gnu/packages/patches/xf86-video-vmware-glibc-2.20.patch: Delete file.
* gnu-system.am (dist_patch_DATA): Remove it.
* gnu/packages/xorg.scm (xf86-video-vmware): Update to 13.1.0.
  [source]: Remove patch.
 2016-02-24 11:49:57 -05:00
Andy Wingo 937c13f220 gnu: xf86-video-vesa: Update to 2.3.4. 
* gnu/packages/xorg.scm (xf86-video-vesa): Update to 2.3.4.
 2016-02-24 11:49:57 -05:00
Andy Wingo bcd4a74039 gnu: xf86-video-trident: Update to 1.3.7. 
* gnu/packages/patches/xf86-video-trident-remove-mibstore.patch: Delete
  file.
* gnu-system.am (dist_patch_DATA): Remove it.
* gnu/packages/xorg.scm (xf86-video-trident): Update to 1.3.7.
  [source]: Remove patch.
 2016-02-24 11:49:57 -05:00
Andy Wingo 816decebf2 gnu: xf86-video-tdfx: Update to 1.4.6. 
* gnu/packages/patches/xf86-video-tdfx-remove-mibstore.patch: Delete
  file.
* gnu-system.am (dist_patch_DATA): Remove it.
* gnu/packages/xorg.scm (xf86-video-tdfx): Update to 1.4.6.
  [source]: Remove patch.
 2016-02-24 11:49:57 -05:00
Andy Wingo 5f59f5103a gnu: xf86-video-sis: Update to 0.10.8. 
* gnu/packages/patches/xf86-video-sis-fix-exa-crash.patch,
  gnu/packages/patches/xf86-video-sis-update-api.patch: Delete files.
* gnu-system.am (dist_patch_DATA): Remove them.
* gnu/packages/xorg.scm (xf86-video-sis): Update to 0.10.8.
  [source]: Remove patches.
 2016-02-24 11:49:57 -05:00
Andy Wingo fc1172f787 gnu: xf86-video-siliconmotion: Update to 1.7.8. 
* gnu/packages/patches/xf86-video-siliconmotion-remove-mibstore.patch:
  Delete file.
* gnu-system.am (dist_patch_DATA): Remove it.
* gnu/packages/xorg.scm (xf86-video-siliconmotion): Update to 1.7.8.
  [source]: Remove patch.
 2016-02-24 11:49:57 -05:00
Andy Wingo bfc0d8395e gnu: xf86-video-savage: Update to 2.3.8. 
* gnu/packages/xorg.scm (xf86-video-savage): Update to 2.3.8.
 2016-02-24 11:49:57 -05:00
Andy Wingo bfe27469b4 gnu: xf86-video-r128: Update to 6.10.1. 
* gnu/packages/patches/xf86-video-r128-glibc-2.20.patch: Delete file.
* gnu-system.am (dist_patch_DATA): Remove it.
* gnu/packages/xorg.scm (xf86-video-r128): Update to 6.10.1.
  [source]: Remove patch.
 2016-02-24 11:49:57 -05:00
Andy Wingo 9f9b89bcf2 gnu: xf86-video-nouveau: Update to 1.0.12. 
* gnu/packages/xorg.scm (xf86-video-nouveau): Update to 1.0.12.
 2016-02-24 11:49:57 -05:00
Andy Wingo bd714f8509 gnu: xf86-video-neomagic: Update to 1.2.9. 
* gnu/packages/xorg.scm (xf86-video-neomagic): Update to 1.2.9.
 2016-02-24 11:49:57 -05:00
Andy Wingo ea192db119 gnu: xf86-video-mga: Update to 1.6.4. 
* gnu/packages/patches/xf86-video-mga-glibc-2.20.patch: Delete file.
* gnu-system.am (dist_patch_DATA): Remove it.
* gnu/packages/xorg.scm (xf86-video-mga): Update to 1.6.4.
  [source]: Remove patch.
 2016-02-24 11:49:57 -05:00