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5535 Commits

Author SHA1 Message Date
Ricardo Wurmus 191c710139 gnu: Add crossmap. 
* gnu/packages/bioinformatics.scm (crossmap): New variable.
* gnu/packages/patches/crossmap-allow-system-pysam.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
 2015-03-02 17:23:56 +01:00
Ludovic Courtès 7e75a6739b gexp: Make sure 'gexp-outputs' removes duplicate outputs. 
Fixes a regression introduced in f9efe56.

* guix/gexp.scm (gexp-outputs): Add call to 'delete-duplicates'.
* tests/gexp.scm ("output list, combined gexps, duplicate output"): New
  test.
 2015-03-02 16:26:13 +01:00
宋文武 1385d37a6e gnu: gtk-xfce-engine: Update to 2.10.0. 
* gnu/packages/xfce.scm (gtk-xfce-engine): Update to 2.10.0.
 2015-03-02 21:27:42 +08:00
Ricardo Wurmus 810cff8557 gnu: Add CLIPper. 
* gnu/packages/bioinformatics.scm (clipper): New variable.
 2015-03-02 14:11:54 +01:00
Ricardo Wurmus 240ca4aae7 gnu: Add Scikit-learn. 
* gnu/packages/python.scm (python-scikit-learn, python2-scikit-learn): New
  variables.
 2015-03-02 14:09:10 +01:00
宋文武 b283679951 gnu: xfconf: Re-enable tests. 
* gnu/packages/xfce.scm (xfconf)[arguments]: Add #:phases.
 2015-03-02 20:37:21 +08:00
Ricardo Wurmus d57e6d0f8e gnu: Add MACS. 
* gnu/packages/bioinformatics.scm (macs): New variable.
 2015-03-02 11:33:13 +01:00
Ricardo Wurmus a2fb1492af gnu: Add pybedtools. 
* gnu/packages/bioinformatics.scm (python2-pybedtools): New variable.
 2015-03-02 11:32:10 +01:00
Ricardo Wurmus 8d12be1eb1 gnu: Add pyyaml. 
* gnu/packages/python.scm (python-pyyaml, python2-pyyaml): New variables.
 2015-03-02 11:31:14 +01:00
Mark H Weaver 649b5e1bd4 gnu: libotr: Update to 4.1.0. 
* gnu/packages/messaging.scm (libotr): Update to 4.1.0.
 2015-03-02 00:09:09 -05:00
Mark H Weaver 9515b74554 Revert "services: xorg: Fix file descriptor leak from SLiM/xinitrc." 
This reverts commit ec4a4c46ef,
because it broke XFCE.
 2015-03-01 23:57:23 -05:00
Mark H Weaver e013220eb6 gnu: xfconf: Update to 4.12.0. 
* gnu/packages/xfce.scm (xfconf): Update to 4.12.0.  Disable tests.
 2015-03-01 20:16:45 -05:00
Mark H Weaver f6176e7870 gnu: gnu-pw-mgr: Update to 1.3. 
* gnu/packages/gnu-pw-mgr.scm (gnu-pw-mgr): Update to 1.3.
 2015-03-01 19:44:13 -05:00
Mark H Weaver 0a5c308782 gnu: sharutils: Update to 4.15. 
* gnu/packages/compression.scm (sharutils): Update to 4.15.
 2015-03-01 19:42:57 -05:00
Mark H Weaver 5245251eaa gnu: gdb: Update to 7.9. 
* gnu/packages/gdb.scm (gdb): Update to 7.9.
 2015-03-01 19:35:46 -05:00
Mark H Weaver 3820d39739 Merge branch 'master' into core-updates 
Conflicts:
	gnu/packages/gnupg.scm
 2015-03-01 19:05:29 -05:00
Mark H Weaver afff9058a0 gnu: gnupg: Update to 2.0.27. 
* gnu/packages/gnupg.scm (gnupg): Update to 2.0.27.
 2015-03-01 19:02:49 -05:00
Mark H Weaver 751be9a056 gnu: libgcrypt: Update to 1.6.3. 
* gnu/packages/gnupg.scm (libgcrypt): Update to 1.6.3.
 2015-03-01 18:52:02 -05:00
Ludovic Courtès 6b9540bcff gnu: wget: Update to 1.16.2. 
* gnu/packages/wget.scm (wget): Update to 1.16.2.
  [inputs]: Add PKG-CONFIG.
 2015-03-01 22:22:43 +01:00
Ludovic Courtès ec35d36495 gnu: libpsl: Fix link flag in 'libpsl.pc'. 
* gnu/packages/web.scm (libpsl)[source]: Add 'snippet' and 'modules'
  fields.
 2015-03-01 22:22:43 +01:00
Ludovic Courtès 9041d935c4 gnu: gnupg-1: Update to 1.4.19. 
* gnu/packages/gnupg.scm (gnupg-1): Update to 1.4.19.
 2015-03-01 22:22:43 +01:00
Taylan Ulrich Bayırlı/Kammer cb03a9b6a2 gnu: ecl: Update to version 15.2.21. 
* gnu/packages/lisp.scm (ecl): Update to version 15.2.21, and disable the test
  suite because ECL now fails to initialize during 'make check'.
 2015-03-01 21:29:33 +01:00
Mathieu Lirzin 76212b57f6 gnu: Add xbindkeys. 
* gnu/packages/xdisorg.scm (xbindkeys): New variable.
 2015-03-01 11:22:19 -05:00
Ricardo Wurmus eb0fb087b9 gnu: Add AlsaModularSynth. 
* gnu/packages/audio.scm (alsa-modular-synth): New variable.
 2015-03-01 17:07:51 +01:00
Ricardo Wurmus 631ac903b6 gnu: Add clalsadrv. 
* gnu/packages/audio.scm (clalsadrv): New variable.
 2015-03-01 17:07:44 +01:00
Ludovic Courtès bbe7a2ce0c Revert "build-system/gnu: Keep the sloppy conversion strategy during bootstrap." 
This reverts commit b479c3ddaf.
This commit was the result of an incorrect characterization of the
problem; see the log of commit 87c8b92 for details.
 2015-03-01 17:05:41 +01:00
Ludovic Courtès 87c8b92f50 gnu: commencement: Make UTF-8 locales available right after 'guile-final'. 
In <http://hydra.gnu.org/build/263170>, we see:

   153: 12 [patch-usr-bin-file #:native-inputs #f ...]

  [...]

     ?: 1 [regexp-exec # ...]
  In ice-9/boot-9.scm:
   106: 0 [#<procedure 1998ec0 at ice-9/boot-9.scm:97:6 (thrown-k . args)> encoding-error ...]

  ice-9/boot-9.scm:106:20: In procedure #<procedure 1998ec0 at ice-9/boot-9.scm:97:6 (thrown-k . args)>:
  ice-9/boot-9.scm:106:20: Throw to key `encoding-error' with args `("scm_to_stringn" "cannot convert narrow string to output locale" 84 #f #f)'.

This is due to that fact that 'patch-/usr/bin/file' read a line
containing a byte sequence with bytes > 127 (namely a copyright sign.)
But this build was running with a C locale, and so those bytes cannot be
represented in that locale, hence this error.

This commit makes the UTF-8 locales available earlier such that
everything can be represented in locale encoding.

* gnu/packages/commencement.scm (glibc-utf8-locales-final): Move
  earlier; change "gzip" input to GZIP built with %BOOT4-INPUTS.
  (%boot5-inputs): Define to %BOOT4-INPUTS plus
  GLIBC-UTF8-LOCALES-FINAL.
  (gnu-make-final, coreutils-final, grep-final): Use it instead of
  %BOOT4-INPUTS.
  (gzip-final): Remove.
  (%boot6-inputs): New variable.
  (%final-inputs): Use it instead of %BOOT5-INPUTS.  Don't rely on
  GZIP-FINAL.
 2015-03-01 17:03:04 +01:00
宋文武 8ccf68f9e0 gnu: xfwm4: Add inputs libdrm and libxdamage. 
* gnu/packages/xfce.scm (xfwm4): Add libdrm and libxdamage to inputs.
 2015-03-01 18:41:57 +08:00
宋文武 39a4d761c7 gnu: xfwm4: Update to 4.12.0. 
* gnu/packages/xfce.scm (xfwm4): Update 4.12.0.
 2015-03-01 18:41:02 +08:00
宋文武 046bcf2952 gnu: xfdesktop: Update to 4.12.0. 
* gnu/packages/xfce.scm (xfdesktop): Update to 4.12.0.
 2015-03-01 18:38:52 +08:00
宋文武 ad1540062b gnu: thunar-volman: Update to 0.8.1. 
* gnu/packages/xfce.scm (thunar-volman): Update to 0.8.1.
 2015-03-01 18:38:39 +08:00
宋文武 78daf79be1 gnu: thunar: Update to 1.6.6. 
* gnu/packages/xfce.scm (thunar): Update to 1.6.6.
 2015-03-01 18:38:22 +08:00
宋文武 2998f7181f gnu: xfce4-settings: Update to 4.12.0. 
* gnu/packages/xfce.scm (xfce4-settings): Update to 4.12.0.
 2015-03-01 18:38:06 +08:00
宋文武 3d75c320fa gnu: xfce4-session: Update to 4.12.0. 
* gnu/packages/xfce.scm (xfce4-session): Update to 4.12.0.
 2015-03-01 18:37:54 +08:00
宋文武 be3db25a52 gnu: xfce4-appfinder: Update to 4.12.0. 
* gnu/packages/xfce.scm (xfce4-appfinder): Update to 4.12.0.
 2015-03-01 18:37:37 +08:00
宋文武 bcd54994f0 gnu: xfce4-panel: Update to 4.12.0. 
* gnu/packages/xfce.scm (xfce4-panel): Update to 4.12.0.
 2015-03-01 18:37:20 +08:00
宋文武 3786be080f gnu: tumbler: Update to 0.1.31. 
* gnu/packages/xfce.scm (tumbler): Update to 0.1.31.
 2015-03-01 18:37:04 +08:00
宋文武 ea3fb8f183 gnu: garcon: Update to 0.4.0. 
* gnu/packages/xfce.scm (garcon): Update to 0.4.0.
 2015-03-01 18:36:48 +08:00
宋文武 9ade90ae52 gnu: exo: Update to 0.10.3. 
* gnu/packages/xfce.scm (exo): Update to 0.10.3.
 2015-03-01 18:36:26 +08:00
宋文武 7379ffc1a0 gnu: libxfce4ui: Update to 4.12.0. 
* gnu/packages/xfce.scm (libxfce4ui): Update to 4.12.0.
 2015-03-01 18:36:12 +08:00
宋文武 96fffedea0 gnu: libxfce4util: Update to 4.12.1. 
* gnu/packages/xfce.scm (libxfce4util): Update to 4.12.1.
 2015-03-01 18:35:14 +08:00
Ludovic Courtès ec4a4c46ef services: xorg: Fix file descriptor leak from SLiM/xinitrc. 
Previously processes started from the window manager would have a couple
of leaked file descriptors: writable /var/log/slim.log and readable
/gnu/store/…-xinitrc.

* gnu/services/xorg.scm (xinitrc)[builder]: Add 'close-all-fdes'.  Use
  it in 'exec-from-login-shell'.
 2015-03-01 00:25:30 +01:00
Ludovic Courtès b479c3ddaf build-system/gnu: Keep the sloppy conversion strategy during bootstrap. 
* guix/build/gnu-build-system.scm (gnu-build): Leave
  %DEFAULT-PORT-CONVERSION-STRATEGY unchanged when 'string->bytevector'
  fails to convert to ISO-8859-1.  This is an attempt to work around the
  build failures at <http://hydra.gnu.org/build/263002>.
 2015-03-01 00:23:07 +01:00
Ricardo Wurmus 74bbf89495 gnu: Add zita-alsa-pcmi. 
* gnu/packages/audio.scm (zita-alsa-pcmi): New variable.
 2015-02-28 22:30:19 +01:00
Ricardo Wurmus 8fb79e3dfb gnu: Add LV2 mda EPiano plugin. 
* gnu/packages/audio.scm (lv2-mdaepiano): New variable.
 2015-02-28 22:29:57 +01:00
Ricardo Wurmus 982471276b gnu: Add LV2 mda Piano plugin. 
* gnu/packages/audio.scm (lv2-mdapiano): New variable.
 2015-02-28 22:29:47 +01:00
Ricardo Wurmus dd6b54b846 gnu: Add txt2man. 
* gnu/packages/man.scm (txt2man): New variable.
 2015-02-28 21:54:29 +01:00
David Thompson 654b27e56e gnu: mpd: Export package variables using define-public. 
* gnu/packages/mpd.scm: Use define-public for package variables.  Remove
  #:exports from module declaration.
 2015-02-28 14:05:20 -05:00
Paul van der Walt 773b2792e1 gnu: Add mpd-mpc. 
* gnu/packages/mpd.scm (mpd-mpc): New variable.
 2015-02-28 13:10:32 -05:00
Paul van der Walt e42dc6249c gnu: ncmpcpp: Update to 0.6.2 
* gnu/packages/mpd.scm (ncmpcpp): Update to version 0.6.2.  Add boost,
  readline, autotools inputs.
 2015-02-28 09:54:12 -05:00