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Author SHA1 Message Date
宋文武 39eefcee97 gnu: weechat: Update to 1.4. 
* gnu/packages/weechat.scm (weechat): Update to 1.4.
 2016-01-31 17:12:46 +08:00
Efraim Flashner 692bb77da9 gnu: pumpa: Update to 0.9.2. 
* gnu/packages/pumpio.scm (pumpa): Update to 0.9.2.
[source]: Add 'file-name' field.
 2016-01-30 22:39:05 +02:00
Alex Kost 171a0a13a4 Rename 'dmd' to 'shepherd' in comments and strings. 
* build-aux/hydra/demo-os.scm (operating-system)[issue]: Point to
  shepherd instead of dmd.
* ROADMAP: Likewise.
* gnu/build/install.scm (directives): Adjust comment.
 2016-01-29 20:21:54 +03:00
Alex Kost d4053c710b services: Rename 'dmd' services to 'shepherd'. 
* gnu/services/shepherd.scm (dmd-root-service-type, %dmd-root-service)
  (dmd-service-type, <dmd-service>, dmd-service, dmd-service?)
  (make-dmd-service, dmd-service-documentation, dmd-service-provision)
  (dmd-service-requirement, dmd-service-respawn, dmd-service-start)
  (dmd-service-stop, dmd-service-auto-start?, dmd-service-modules)
  (dmd-service-imported-modules, dmd-service-file-name, dmd-service-file)
  (dmd-service-back-edges): Rename to...
  (shepherd-root-service-type, %shepherd-root-service, shepherd-service-type)
  (<shepherd-service>, shepherd-service, shepherd-service?)
  (make-shepherd-service, shepherd-service-documentation)
  (shepherd-service-provision, shepherd-service-requirement)
  (shepherd-service-respawn, shepherd-service-start)
  (shepherd-service-stop, shepherd-service-auto-start?)
  (shepherd-service-modules, shepherd-service-imported-modules)
  (shepherd-service-file-name, shepherd-service-file)
  (shepherd-service-back-edges): ...this
* gnu/services.scm: Adjust comments.
* gnu/services/avahi.scm (avahi-dmd-service): Rename to...
  (avahi-shepherd-service): ... this.
* gnu/services/base.scm (%root-file-system-dmd-service)
  (file-system->dmd-service-name, mapped-device->dmd-service-name)
  (dependency->dmd-service-name, file-system-dmd-service)
  (mingetty-dmd-service, nscd-dmd-service, guix-dmd-service)
  (guix-publish-dmd-service, udev-dmd-service, gpm-dmd-service): Rename to...
  (%root-file-system-shepherd-service)
  (file-system->shepherd-service-name, mapped-device->shepherd-service-name)
  (dependency->shepherd-service-name, file-system-shepherd-service)
  (mingetty-shepherd-service, nscd-shepherd-service, guix-shepherd-service)
  (guix-publish-shepherd-service, udev-shepherd-service)
  (gpm-shepherd-service): ... this.
* gnu/services/databases.scm (postgresql-dmd-service): Rename to...
  (postgresql-shepherd-service): ... this.
* gnu/services/desktop.scm (upower-dmd-service, elogind-dmd-service):
  Rename to...
  (upower-shepherd-service, elogind-shepherd-service): ... this.
* gnu/services/dbus.scm (dbus-dmd-service): Rename to...
  (dbus-shepherd-service): ... this.
* gnu/services/lirc.scm (lirc-dmd-service): Rename to...
  (lirc-shepherd-service): ... this.
* gnu/services/mail.scm (dovecot-dmd-service): Rename to...
  (dovecot-shepherd-service): ... this.
* gnu/services/networking.scm (ntp-dmd-service, tor-dmd-service)
  (bitlbee-dmd-service, wicd-dmd-service, network-manager-dmd-service): Rename to...
  (dbus-shepherd-service): ... this.
* gnu/services/ssh.scm (lsh-dmd-service): Rename to...
  (lsh-shepherd-service): ... this.
* gnu/services/web.scm (nginx-dmd-service): Rename to...
  (nginx-shepherd-service): ... this.
* gnu/services/xorg.scm (slim-dmd-service): Rename to...
  (slim-shepherd-service): ... this.
* gnu/system.scm (essential-services): Use '%shepherd-root-service'.
* gnu/system/install.scm (cow-store-service-type): Adjust accordingly.
* guix/scripts/system.scm (dmd-service-node-label, dmd-service-node-type)
  (export-dmd-graph): Likewise.
* tests/guix-system.sh: Likewise.
* tests/services.scm ("dmd-service-back-edges"): Rename to...
  ("shepherd-service-back-edges"): Adjust accordingly.
* doc/guix.texi: Likewise.
* doc/images/service-graph.dot: Use 'shepherd' service name.
 2016-01-29 20:21:53 +03:00
Alex Kost 26b94866ad services: xorg: Use 'shepherd' instead of 'dmd'. 
* gnu/services/xorg.scm (slim-configuration-dmd): Rename to...
  (slim-configuration-shepherd): ... this.
  (slim-shepherd-service): Adjust accordingly.
  (slim-service): Take 'shepherd' keyword argument.
 2016-01-29 20:21:53 +03:00
Alex Kost fe1ad5f5db services: shepherd: Rename shepherd configuration file. 
* gnu/services/shepherd.scm (dmd-configuration-file): Rename to...
  (shepherd-configuration-file): ... this.  Use "shepherd.conf" name.
  (dmd-boot-gexp): Use it.
 2016-01-29 20:21:53 +03:00
Alex Kost 0190c1c02f Rename (gnu services dmd) to (gnu services shepherd). 
* gnu/services/dmd.scm: Rename to...
* gnu/services/shepherd.scm: ... this.
* gnu/system.scm: Use it.
* gnu/system/install.scm: Likewise.
* gnu/services/xorg.scm: Likewise.
* gnu/services/web.scm: Likewise.
* gnu/services/ssh.scm: Likewise.
* gnu/services/networking.scm: Likewise.
* gnu/services/mail.scm: Likewise.
* gnu/services/lirc.scm: Likewise.
* gnu/services/desktop.scm: Likewise.
* gnu/services/dbus.scm: Likewise.
* gnu/services/databases.scm: Likewise.
* gnu/services/base.scm: Likewise.
* gnu/services/avahi.scm: Likewise.
* guix/scripts/system.scm: Likewise.
* tests/services.scm: Likewise.
* tests/guix-system.sh: Likewise.
* doc/guix.texi (Shepherd Services): Adjust accordingly.
* gnu-system.am (GNU_SYSTEM_MODULES): Likewise.
* po/guix/POTFILES.in: Likewise.
 2016-01-29 20:21:53 +03:00
Alex Kost b8c02c18b4 Rename '/root/etc/dmd' directory and 'do-not-kill' file. 
* gnu/services/base.scm (%do-not-kill-file): Rename to
  "/etc/shepherd/do-not-kill".
* gnu/build/linux-boot.scm (mount-root-file-system): Rename
  "/root/etc/dmd" to "/root/etc/shepherd".
 2016-01-29 20:20:19 +03:00
Alex Kost 34044d551f Use 'shepherd' instead of 'dmd' as init system. 
* gnu/services/dmd.scm (dmd-boot-gexp): Use binary from 'shepherd' package.
  (dmd-root-service-type): Use 'shepherd' package.
  (%default-modules): Use (shepherd service) module.
* gnu/services/base.scm (%root-file-system-dmd-service): Use
  'stop-logging' procedure to close shepherd log.
 2016-01-29 12:07:32 +03:00
Alex Kost d312a8328d gnu: elogind: Use 'shepherd' input. 
* gnu/packages/freedesktop.scm (elogind)[inputs]: Replace 'dmd' with
  'shepherd'.
 2016-01-29 12:07:32 +03:00
Federico Beffa 13fe4891fa gnu: emacs: Find packages in "~/.guix-profile". 
* gnu/packages/emacs.scm (emacs)[inputs]: Add 'guix-src' input.
  [arguments]: Add 'install-site-start' phase.

Co-authored-by: Alex Kost <alezost@gmail.com>
 2016-01-29 11:13:15 +03:00
Alex Kost 2c776157ad gnu: guix: Update development snapshot to c3f29bc. 
* gnu/packages/package-management.scm (guix-devel): Update to c3f29bc.
 2016-01-29 11:13:15 +03:00
Rene Saavedra c3f29bc928 gnu: Add gtk-vnc. 
* gnu/packages/gnome.scm (gtk-vnc): New variable.

Co-authored-by: 宋文武 <iyzsong@gmail.com>
 2016-01-29 08:36:07 +08:00
Efraim Flashner f88f0d20e4 gnu: ffmpeg: Add hardware acceleration, opengl support. 
* gnu/packages/video.scm (ffmpeg)[inputs]: Add libvdpau, libx11, mesa.
[arguments]: Add configure-flags '--enable-opengl' '--enable-x11grab'.
 2016-01-28 18:14:58 +02:00
Leo Famulari 03675cad53 gnu: icedtea-7: Update to 2.6.4. 
Fixes CVE-2015-{7575, 8126, 8472} and CVE-2016-{0402, 0448, 0466, 0483,
0494}.

* gnu/packages/java.scm (icedtea-7): Update to 2.6.4.
 2016-01-28 08:48:35 -05:00
Leo Famulari 559239af7a gnu: icedtea-6: Update to 1.13.10. 
Fixes CVE-2015-{8126, 8472} and CVE-2016-{0402, 0448, 0466, 0483, 0494}.

* gnu/packages/java.scm (icedtea-6): Update to 1.13.10.
 2016-01-28 08:48:35 -05:00
Mark H Weaver 593c366bde Merge branch 'core-updates' 2016-01-28 07:29:13 -05:00
Ludovic Courtès 133056bd74 gnu: shepherd: Update to 0.3. 
* gnu/packages/admin.scm (shepherd): Update to 0.3.
 2016-01-28 11:45:03 +01:00
Mark H Weaver 29a780147d gnu: icecat: Add fixes for CVE-2016-{1930,1935} and other bugs. 
* gnu/packages/patches/icecat-CVE-2016-1930-pt01.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt02.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt03.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt04.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt05.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt06.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt07.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt08.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt09.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt10.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt11.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt12.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt13.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt14.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt15.patch,
  gnu/packages/patches/icecat-CVE-2016-1935.patch,
  gnu/packages/patches/icecat-bug-1146335-pt1.patch,
  gnu/packages/patches/icecat-bug-1146335-pt2.patch,
  gnu/packages/patches/icecat-limit-max-buffers-size-for-ANGLE.patch: New
  files.
* gnu-system.am (dist_patch_DATA): Add them.
* gnu/packages/gnuzilla.scm (icecat)[source]: Add patches.
 2016-01-28 00:34:20 -05:00
Ludovic Courtès 9a8b9eb8de services: guix: Provide Guix via 'profile-service-type'. 
* gnu/services/base.scm (guix-service-type): Extend
PROFILE-SERVICE-TYPE.
* gnu/system.scm (%base-packages): Remove GUIX.
 2016-01-27 15:48:35 +01:00
Ludovic Courtès c273d81bfa services: dmd: Provide dmd via 'profile-service-type'. 
* gnu/services/dmd.scm (dmd-root-service-type): Extend
PROFILE-SERVICE-TYPE.
* gnu/system.scm (%base-packages): Remove dmd.
 2016-01-27 15:48:35 +01:00
Ludovic Courtès e932d371e5 gnu: Add snapshot of the GNU Shepherd. 
* gnu/packages/admin.scm (shepherd): New variable.
 2016-01-27 15:48:35 +01:00
Ben Woodcroft d114ceebac gnu: Add ruby-http-cookie. 
* gnu/packages/ruby.scm (ruby-http-cookie): New variable.
 2016-01-28 00:08:32 +10:00
Ben Woodcroft 5799aadde4 gnu: Add ruby-domain-name. 
* gnu/packages/ruby.scm (ruby-domain-name): New variable.
 2016-01-28 00:08:32 +10:00
Ben Woodcroft 3b44bcdfcd gnu: Add ruby-unf. 
* gnu/packages/ruby.scm (ruby-unf): New variable.
 2016-01-28 00:08:32 +10:00
Ben Woodcroft 6f390716b6 gnu: Add ruby-shoulda. 
* gnu/packages/ruby.scm (ruby-shoulda): New variable.
 2016-01-28 00:08:32 +10:00
Ben Woodcroft 3885c58b25 gnu: Add ruby-shoulda-matchers-2. 
* gnu/packages/ruby.scm (ruby-shoulda-matchers-2): New variable.
 2016-01-28 00:08:32 +10:00
Ben Woodcroft e4fea00896 gnu: Add ruby-shoulda-matchers. 
* gnu/packages/ruby.scm (ruby-shoulda-matchers): New variable.
 2016-01-28 00:08:32 +10:00
Ben Woodcroft 4dfa39cc67 gnu: Add ruby-shoulda-context. 
* gnu/packages/ruby.scm (ruby-shoulda-context): New variable.
 2016-01-28 00:08:32 +10:00
Ben Woodcroft 4fea500bb1 gnu: Add ruby-sqlite3. 
* gnu/packages/ruby.scm (ruby-sqlite3): New variable.
 2016-01-28 00:08:32 +10:00
Ben Woodcroft d39b606c88 gnu: Add ruby-mime-types. 
* gnu/packages/ruby.scm (ruby-mime-types): New variable.
 2016-01-28 00:08:32 +10:00
Ben Woodcroft eb5e0bd96e gnu: Add ruby-fivemat. 
* gnu/packages/ruby.scm (ruby-fivemat): New variable.
 2016-01-28 00:08:32 +10:00
Ben Woodcroft 32d1c06ffa gnu: Add ruby-mime-types-data. 
* gnu/packages/ruby.scm (ruby-mime-types-data): New variable.
 2016-01-28 00:08:32 +10:00
Ben Woodcroft e582fa93a8 gnu: Add ruby-minitest-rg. 
* gnu/packages/ruby.scm (ruby-minitest-rg): New variable.
 2016-01-28 00:08:32 +10:00
Ben Woodcroft e07ef1d625 gnu: Add ruby-minitest-bonus-assertions. 
* gnu/packages/ruby.scm (ruby-minitest-bonus-assertions): New variable.
 2016-01-28 00:08:32 +10:00
Ben Woodcroft 685d0d2fbe gnu: Add ruby-minitest-moar. 
* gnu/packages/ruby.scm (ruby-minitest-moar): New variable.
 2016-01-28 00:08:32 +10:00
Ben Woodcroft 99fc5cd577 gnu: Add ruby-minitest-pretty-diff. 
* gnu/packages/ruby.scm (ruby-minitest-pretty-diff): New variable.
 2016-01-28 00:08:32 +10:00
Ben Woodcroft 39dc0eb502 gnu: Add ruby-minitest-focus. 
* gnu/packages/ruby.scm (ruby-minitest-focus): New variable.
 2016-01-28 00:08:32 +10:00
Ben Woodcroft 8092e33376 gnu: Add ruby-turn. 
* gnu/packages/ruby.scm (ruby-turn): New variable.
 2016-01-28 00:08:32 +10:00
Efraim Flashner f66842dccc gnu: Add aria2. 
* gnu/packages/bittorrent.scm (aria2): New variable.
 2016-01-27 14:39:31 +02:00
Efraim Flashner cd44f1c1b0 gnu: c-ares: Move to adns.scm. 
* gnu/packages/aria2.scm (c-ares): Move to...
* gnu/packages/adns.scm (c-ares): ... here.
* gnu/packages/aria2.scm: Remove file.
* gnu-system.am (GNU_SYSTEM_MODULES): Remove aria2.scm.
 2016-01-27 14:13:45 +02:00
Andreas Enge bb2120cd1d gnu: libressl: Update to 2.2.5. 
* gnu/packages/tls.scm (libressl): Update to 2.2.5.
 2016-01-26 21:40:35 +01:00
Leo Famulari 7432386adb gnu: nginx: Update to 1.8.1 [fixes CVE-2016-{0742,0746,0747}]. 
* gnu/packages/web.scm (nginx): Update to 1.8.1.
 2016-01-26 15:27:58 -05:00
Ricardo Wurmus 61eecd71cc gnu: alsa-modular-synth: Update to 2.1.2. 
* gnu/packages/audio.scm (alsa-modular-synth): Update to 2.1.2.
 2016-01-26 18:46:54 +01:00
Andreas Enge a394c60aa3 gnu: hop: Add input avahi. 
gnu/packages/scheme.scm (hop)[inputs]: Add avahi.
 2016-01-26 15:10:23 +01:00
Ben Woodcroft edf8caae6d gnu: Add ruby-ttfunk. 
* gnu/packages/ruby.scm (ruby-ttfunk): New variable.
 2016-01-26 16:27:40 +10:00
Ben Woodcroft acb6be4298 gnu: Add ruby-ascii85. 
* gnu/packages/ruby.scm (ruby-ascii85): New variable.
 2016-01-26 16:25:11 +10:00
Ben Woodcroft f3e085a8d5 gnu: Add ruby-afm. 
* gnu/packages/ruby.scm (ruby-afm): New variable.
 2016-01-26 16:22:17 +10:00
Ben Woodcroft 1f1d71e09f gnu: Add ruby-rc4. 
* gnu/packages/ruby.scm (ruby-rc4): New variable.
 2016-01-26 16:21:05 +10:00
Ben Woodcroft 72ccbfe314 gnu: Add ruby-hashery. 
* gnu/packages/ruby.scm (ruby-hashery): New variable.
 2016-01-26 16:19:41 +10:00
Ben Woodcroft 0832804ed5 gnu: Add ruby-rubytest-cli. 
* gnu/packages/ruby.scm (ruby-rubytest-cli): New variable.
 2016-01-26 16:17:01 +10:00
Ben Woodcroft 78bb471f37 gnu: Add ruby-lemon. 
* gnu/packages/ruby.scm (ruby-lemon): New variable.
 2016-01-26 16:15:24 +10:00
Ben Woodcroft 9273ee8f44 gnu: Add ruby-ae. 
* gnu/packages/ruby.scm (ruby-ae): New variable.
 2016-01-26 16:11:49 +10:00
Ben Woodcroft 120fc74b21 gnu: Add ruby-qed. 
* gnu/packages/ruby.scm (ruby-qed): New variable.
 2016-01-26 16:06:10 +10:00
Ben Woodcroft 90fcedf220 gnu: Add ruby-brass. 
* gnu/packages/ruby.scm (ruby-brass): New variable.
 2016-01-26 16:02:15 +10:00
Ben Woodcroft 7c8131c76b gnu: Add ruby-rubytest. 
* gnu/packages/ruby.scm (ruby-rubytest): New variable.
 2016-01-26 15:59:39 +10:00
Ben Woodcroft a78d62f432 gnu: sra-tools: Update to 2.5.7. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.7.
 2016-01-26 10:59:13 +10:00
Ben Woodcroft fe91666b79 gnu: ncbi-vdb: Update to 2.5.7. 
gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.7.
 2016-01-26 10:59:13 +10:00
Ben Woodcroft d3b39bc231 gnu: ngs-sdk: Update to 1.2.3. 
gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.3.
 2016-01-26 10:59:13 +10:00
Andreas Enge 46854e99ca gnu: webkitgtk-2.4, webkitgtk/gtk+-2, qt: Disable parallel builds. 
* gnu/packages/webkit.scm (webkitgtk-2.4, webkitgtk/gtk+-2):
  Disable parallel builds as suggested in
  https://lists.gnu.org/archive/html/guix-devel/2016-01/msg00837.html .
* gnu/packages/qt.scm (qt): Likewise.
 2016-01-25 23:33:54 +01:00
Alex Kost 0833d0c025 gnu: aspell-dict-en: Update to 2016.01.19-0. 
* gnu/packages/aspell.scm (aspell-dict-en): Update to 2016.01.19-0.
 2016-01-25 22:11:47 +03:00
Efraim Flashner 8581f4c195 gnu: Add python-efl. 
* gnu/packages/enlightenment.scm (python-efl, python2-efl): New variables.
 2016-01-25 11:41:23 +02:00
Efraim Flashner 2259442b15 gnu: cmocka: New variable. 
* gnu/packages/check.scm (cmocka): New variable.
 2016-01-25 11:39:42 +02:00
Ben Woodcroft 23f3cbb8de gnu: Add pixz. 
* gnu/packages/compression.scm (pixz): New variable.
 2016-01-25 18:45:33 +10:00
Mark H Weaver 412bee5e29 Merge branch 'master' into core-updates 2016-01-24 21:04:54 -05:00
Ludovic Courtès f6afc48008 gnu: grue-hunter: Use 'https' URL. 
* gnu/packages/grue-hunter.scm (grue-hunter): Use 'https' URL.
 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 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
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 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
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 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
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
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
Christopher Allan Webber 16966d5b4d gnu: fdm: Adjust license link to point to web-accessible copy of command.c 
* gnu/packages/mail.scm (fdm): Adjusted license field
 2016-01-19 07:54:18 -08:00
Christopher Allan Webber 34dd26af49 gnu: Add fdm. 
* gnu/packages/mail.scm (fdm): New variable.
 2016-01-18 21:51:45 -08:00
Mark H Weaver afe9f40949 Merge branch 'master' into core-updates 2016-01-19 00:18:37 -05:00
Christopher Allan Webber 1348185ac2 gnu: Add linux-libre-4.2.5 
* gnu/packages/linux.scm (linux-libre-4.2.5): New variable.
 2016-01-18 15:10:38 -08:00
Efraim Flashner 26da7c2606 gnu: mpv: Update to 0.15.0. 
* gnu/packages/video.scm (mpv): Update to 0.15.0.
 2016-01-18 22:26:56 +02:00
Alex Kost 60edbe2297 gnu: magit: Update to 2.4.0. 
* gnu/packages/emacs.scm (magit): Update to 2.4.0.
 2016-01-18 22:40:33 +03:00
Alex Kost d44d60d211 gnu: sxiv: Update to 1.3.2. 
* gnu/packages/sxiv.scm (sxiv): Update to 1.3.2.
 2016-01-18 22:40:33 +03:00
Alex Kost 4c896c9195 gnu: manaplus: Update to 1.6.1.16. 
* gnu/packages/games.scm (manaplus): Update to 1.6.1.16.
 2016-01-18 22:40:33 +03:00
Efraim Flashner 264ae686fa python2-jsonschema: Add python2-functools32 to inputs. 
* gnu/packages/python.scm (python2-jsonschema)[inputs]: Add
python2-functools32.
(python2-wheel)[native-inputs]: Specify python2-jsonschema. Add
python2-functools32.
(python2-requests)[propagated-inputs]: Specify python2-wheel.
(python2-ipython)[inputs]: Specify python2-jsonschema, python2-requests.
(python2-rauth)[propagated-inputs]: Specify python2-requests.
* gnu/packages/openstack.scm (python2-requests-mock)[propagated-inputs]:
Specify python2-requests.
(python2-tempest-lib)[propagated-inputs]: Specify python2-jsonschema.
(python2-oslosphinx)[propagated-inputs]: Specify python2-requests.
(python2-keystoneclient)[porpagated-inputs]: Specify python2-requests.
[native-inputs]: Specify python2-oslosphinx, python2-requests-mock,
python2-tempest-lib.
(python2-swiftclient)[propagated-inputs]: Specify python2-requests,
python2-oslosphinx.
 2016-01-18 17:23:37 +02:00
Efraim Flashner 058247efff gnu: datamash: Update to 1.1.0. 
* gnu/packages/datamash.scm (datamash): Update to 1.1.0.
 2016-01-18 12:14:20 +02:00
Mark H Weaver 8047d13dcf gnu: mariadb: Update to 10.0.23. 
* gnu/packages/databases.scm (mariadb): Update to 10.0.23.
 2016-01-18 01:43:07 -05:00
Mark H Weaver 51a277d8e8 gnu: rsync: Update to 3.1.2. 
* gnu/packages/rsync.scm (rsync): Update to 3.1.2.
 2016-01-17 21:44:31 -05:00
Ricardo Wurmus e8309291a7 gnu: solfege: Build scores with Lilypond. 
* gnu/packages/music.scm (solfege)[inputs]: Add "lilypond".
 2016-01-17 22:57:58 +01:00
Ricardo Wurmus 18ef998bfc gnu: bristol: Remove SSE flags on platforms other than x86_64 and i686. 
* gnu/packages/music.scm (bristol)[arguments]: Add phase
"remove-sse-flags" to remove unsupported optimizations on platforms
other than x86_64 and i686.
 2016-01-17 22:57:58 +01:00
Ludovic Courtès b153f9f0a9 linux-initrd: Remove "usbkbd" from the default set of modules. 
Reported by Ricardo Wurmus <rekado@elephly.net>
at <http://debbugs.gnu.org/cgi/bugreport.cgi?bug=20433#39>.

* gnu/system/linux-initrd.scm (base-initrd): Remove "usbkbd".
 2016-01-17 22:01:47 +01:00
Efraim Flashner e8d2168c27 gnu: Add git-annex-remote-hubic. 
* gnu/packages/version-control.scm (git-annex-remote-hubic): New variable.
 2016-01-17 22:37:04 +02:00
Efraim Flashner c18f636823 gnu: Add python-urllib3. 
* gnu/packages/python.scm (python-urllib3, python2-urllib3): New variables.
 2016-01-17 22:37:04 +02:00
Efraim Flashner e1ba074999 gnu: python-wheel: Clarify description. 
* gnu/packages/python.scm (python-wheel): Do it.
 2016-01-17 22:37:04 +02:00
Efraim Flashner 10468636ff gnu: python-pytest-cov: Clarify description. 
* gnu/packages/python.scm (python-pytest-cov): Do it.
 2016-01-17 22:37:04 +02:00
Efraim Flashner 1abe448d56 gnu: Add python2-functools32. 
* gnu/packages/python.scm (python2-functools32): New variable.
 2016-01-17 22:37:04 +02:00
Efraim Flashner 5988c299c4 gnu: Add python-pyasn1-modules. 
* gnu/packages/python.scm (python-pyasn1-modules)
(python2-pyasn1-modules): New variables.
 2016-01-17 22:37:04 +02:00
Efraim Flashner 81f7f29752 gnu: Add python-rauth. 
* gnu/packages/python.scm (python-rauth, python2-rauth): New variables.
 2016-01-17 22:37:04 +02:00
Efraim Flashner 8f0cc2ffce gnu: Add python-swiftclient. 
* gnu/packages/openstack.scm (python-swiftclient, python2-swiftclient):
New variables.
 2016-01-17 22:37:04 +02:00
Efraim Flashner 7a5b944eb5 gnu: Add python-futures. 
* gnu/packages/python.scm (python-futures, python2-futures): New variables.
 2016-01-17 22:37:04 +02:00
Efraim Flashner c9e330d001 gnu: Add python-keystoneclient. 
* gnu/packages/openstack.scm (python-keystoneclient)
(python2-keystoneclient): New variables.
 2016-01-17 22:37:04 +02:00
Ricardo Wurmus fb492b9a64 gnu: vmpk: Update to 0.6.2a. 
* gnu/packages/music.scm (vmpk): Update to 0.6.2a.
 2016-01-17 19:57:07 +01:00
Ricardo Wurmus cfac12723a gnu: drumstick: Update to 1.0.2. 
* gnu/packages/music.scm (drumstick): Update to 1.0.2.
 2016-01-17 19:57:00 +01:00
Efraim Flashner 81c29cccaa gnu: mpv: Add features. 
* gnu/packages/video.scm (mpv)[inputs]: Add libvdpau.
[arguments]: Add gpl3 and zsh completion flags.
 2016-01-17 20:43:51 +02:00
Efraim Flashner 3161d32d37 gnu: Add vdpauinfo. 
* gnu/packages/video.scm (vdpauinfo): New variable.
 2016-01-17 20:43:51 +02:00
Efraim Flashner d5650f86a7 gnu: Add libvdpau. 
* gnu/packages/video.scm (libvdpau): New variable.
 2016-01-17 20:43:51 +02:00
Ludovic Courtès bb8afbf5a1 gnu: Add dependency on Perl's 'Module::Build' as needed. 
'Module::Build' was deprecated in Perl 5.20 and removed in 5.22.
Some packages need to explicitly depend on it now.

* gnu/packages/perl.scm (perl-class-factory-util):
(perl-date-manip, perl-devel-checkbin): Add 'native-inputs' field.
(perl-module-build)[description]: Mention that it used to be in Perl.
* gnu/packages/web.scm (perl-cgi-simple)[native-inputs]: Add
PERL-MODULE-BUILD.
 2016-01-17 18:41:20 +01:00
Eric Bavier 2328b47c64 gnu: Add autojump. 
* gnu/packages/admin.scm (autojump): New variable.
 2016-01-17 01:44:15 -06:00
Eric Bavier f5a8491b69 gnu: hevea: Update to 2.28. 
* gnu/packages/ocaml.scm (hevea): Update to 2.28.
  [arguments]: Add 'patch-/bin/sh phase.
 2016-01-17 01:04:43 -06:00
Eric Bavier 90907a22bc gnu: unison: Add "doc" output. 
* gnu/packages/ocaml.scm (unison)[source]: Use svn-fetch with snippet.
  [outputs]: New field.
  [native-inputs]: Add ghostscript, texlive, hevea, and lynx.
  [arguments]: Add 'install-doc phase.
 2016-01-17 01:04:43 -06:00
Ricardo Wurmus 2309ed6862 gnu: samtools-0.1: Adapt to changes in "samtools" variable. 
* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add
  "LIBCURSES" make flag; delete "configure" phase; disable tests outside
  of "substitute-keyword-arguments".
 2016-01-16 15:50:51 +01:00
Ludovic Courtès 7ba903b6db linux-modules: Support 'modprobe.blacklist' on the command line. 
* gnu/build/linux-modules.scm (file-name->module-name)
(module-black-list): New procedure.
* gnu/build/linux-modules.scm (load-linux-module*): Add #:black-list
parameter.
[black-listed?, load-dependencies]: New procedures.
Use them.
 2016-01-16 14:45:47 +01:00
Alex Kost b8300494c0 Move <boot-parameters> to (gnu system). 
* guix/scripts/system.scm (previous-grub-entries)
  (display-system-generation): Use accessors instead of matching
  <boot-parameters>.
  (boot-parameters, boot-parameters?, boot-parameters-label)
  (boot-parameters-root-device, boot-parameters-kernel)
  (boot-parameters-kernel-arguments, read-boot-parameters): Move to...
* gnu/system.scm: ... here. Export them.
 2016-01-16 13:02:21 +03:00
宋文武 c3e919d7a0 gnu: Add python-hy. 
* gnu/packages/python.scm (python-hy, python2-hy): New variables.
 2016-01-16 08:18:37 +08:00
宋文武 e224b7d0bd gnu: Add python-rply. 
* gnu/packages/python.scm (python-rply, python2-rply): New variables.
 2016-01-16 08:18:37 +08:00
宋文武 4ecdeef8ae gnu: Add python-astor. 
* gnu/packages/python.scm (python-astor, python2-astor): New variables.
 2016-01-16 08:18:37 +08:00
宋文武 c06a3de93a gnu: Add python-clint. 
* gnu/packages/python.scm (python-clint, python2-clint): New variables.
 2016-01-16 08:17:04 +08:00
宋文武 2216e15cc3 gnu: Add python-args. 
* gnu/packages.scm (python-args, python2-args): New variables.
 2016-01-16 08:16:51 +08:00
Mark H Weaver ca3f9952d7 gnu: ffmpeg: Update to 2.8.5. 
* gnu/packages/video.scm (ffmpeg): Update to 2.8.5.
 2016-01-15 18:20:21 -05:00
Mark H Weaver 8d9bae4ed7 gnu: librsvg: Update to 2.40.13 [fixes CVE-2015-7558]. 
* gnu/packages/patches/librsvg-tests.patch: Delete file.
* gnu-system.am (dist_patch_DATA): Remove it.
* gnu/packages/gnome.scm (librsvg): Update to 2.40.13.
  [source]: Remove patch.
 2016-01-15 18:03:02 -05:00
Leo Famulari 78e6c4a862 gnu: Add khal. 
* gnu/packages/calendar.scm (khal): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari b97c1bfd56 gnu: python-urwid: Disable failing test test_remove_watch_file. 
* gnu/packages/python.scm (python-urwid)[arguments]: Add
'disable-failing-test' phase.
[source]: Use pypi-uri.
 2016-01-15 16:45:24 -05:00
Leo Famulari 226d333103 gnu: Update python-tzlocal to 1.2. 
* gnu/packages/python.scm (python-tzlocal): Update to 1.2.
[source]: Use pypi-uri.
[arguments]: Remove the custom 'unpack phase.
[native-inputs]: Remove unzip, python-setuptools.
[propagated-inputs]: Add python-pytz.
 2016-01-15 16:45:24 -05:00
Leo Famulari 6bbbb53eeb gnu: Add python-sphinxcontrib-newsfeed. 
* gnu/packages/python.scm (python-sphinxcontrib-newsfeed): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari 5c299bf016 gnu: Add python-icalendar. 
* gnu/packages/python.scm (python-icalendar): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari a2f6a3d502 gnu: Add vdirsyncer. 
* gnu/packages/dav.scm (vdirsyncer): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari f75bbb028a gnu: Add radicale. 
* gnu/packages/dav.scm (radicale): New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
 2016-01-15 16:45:24 -05:00
Leo Famulari 89b8a5516f gnu: Add python-pytest-xprocess. 
* gnu/packages/python.scm (python-pytest-xprocess): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari 28cecbb7cc gnu: Add python-wsgi-intercept. 
* gnu/packages/python.scm (python-wsgi-intercept): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari d7e729fe08 gnu: Add python-pytest-localserver. 
* gnu/packages/python.scm (python-pytest-localserver): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari 6720dbb49f gnu: Add python-pytest-cache. 
* gnu/packages/python.scm (python-pytest-cache): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari 848964fe11 gnu: Add python-execnet. 
* gnu/packages/python.scm (python-execnet): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari 7b3a4ee4c3 gnu: Add python-apipkg. 
* gnu/packages/python.scm (python-apipkg): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari 7b17cab902 gnu: Add python-click-log. 
* gnu/packages/python.scm (python-click-log): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari d1deb90b3f gnu: Add python-click-threading. 
* gnu/packages/python.scm (python-click-threading): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari 561bb3cb1a gnu: Add python-requests-toolbelt. 
* gnu/packages/python.scm (python-requests-toolbelt): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari 5c6eea2ad1 gnu: Add python-atomicwrites. 
* gnu/packages/python.scm (python-atomicwrites): New variable.
 2016-01-15 16:45:24 -05:00
Ricardo Wurmus f5ca44b86e gnu: glade: Update to 3.18.5. 
* gnu/packages/gnome.scm (glade): Update to 3.18.5.
[arguments]: Disable tests; add "fix-docbook" phase.
[inputs]: Replace "gtk+-2" with "gtk+".
[native-inputs]: Add "itstool", "libxslt", "docbook-xml", "docbook-xsl";
replace "python" with "python-2".
 2016-01-15 22:29:37 +01:00
Ludovic Courtès 89b48232f8 gnu: automake: Adjust to deal with Perl 5.22. 
Fixes <http://bugs.gnu.org/22375>.

* gnu/packages/patches/automake-regexp-syntax.patch: New file.
* gnu/packages/autotools.scm (automake)[source]: Use it.
* gnu-system.am (dist_patch_DATA): Add it.
 2016-01-15 14:23:46 +01:00
Mark H Weaver 45f2ffb48c gnu: openssh: Update to 7.1p2. 
* gnu/packages/ssh.scm (openssh): Update to 7.1p2.
 2016-01-15 02:46:12 -05:00
Mark H Weaver 1beec63ac8 Revert "gnu: openssh: Update to 7.1p2 [fixes CVE-0216-0778]." 
This reverts commit 6d139e53b5.
 2016-01-15 02:45:58 -05:00
Mark H Weaver 6d139e53b5 gnu: openssh: Update to 7.1p2 [fixes CVE-0216-0778]. 
* gnu/packages/ssh.scm (openssh): Update to 7.1p2.
 2016-01-14 10:39:00 -05:00
David Thompson df1f1d6936 gnu: Add docker-compose. 
* gnu/packages/docker.scm (docker-compose): New variable.
 2016-01-14 09:17:12 -05:00
David Thompson b42c9c8124 gnu: Add python-dockerpty. 
* gnu/packages/docker.scm (python-dockerpty): New variable.
 2016-01-14 09:16:22 -05:00
David Thompson d020bfc2df gnu: Add python-docker-py. 
* gnu/packages/docker.scm: New file.
* Makefile.am (GNU_SYSTEM_MODULES): Add it.
 2016-01-14 09:16:22 -05:00
David Thompson 67c52bb3e7 gnu: Add python-websocket-client. 
* gnu/packages/python.scm (python-websocket-client): New variable.
 2016-01-14 09:12:23 -05:00
David Thompson 210bf49754 gnu: Add python-texttable. 
* gnu/packages/python.scm (python-texttable, python2-texttable): New
variables.
 2016-01-14 09:12:23 -05:00
David Thompson b3667afbd2 gnu: Update python-jsonschema to 2.5.1. 
* gnu/packages/python.scm (python-jsonschema): Update to 2.5.1.
[inputs]: Add python-vcversioner.
 2016-01-14 09:12:06 -05:00
David Thompson ea521b42c2 gnu: Add python-vcversioner. 
* gnu/packages/python.scm (python-vcversioner, python2-vcversioner): New
variables.
 2016-01-14 09:05:19 -05:00
David Thompson e90051808b gnu: Add version 2.7 variant of python-requests. 
* gnu/packages/python.scm (python-requests-2.7): New variable.
 2016-01-14 09:05:19 -05:00
Ricardo Wurmus 3141b83d4d gnu: r-go-db: Add missing input. 
* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add
  "r-annotationdbi".
 2016-01-14 14:43:59 +01:00
Ricardo Wurmus d7786ce9b0 gnu: r-sparsem: Add missing "gfortran" input. 
* gnu/packages/statistics.scm (r-sparsem)[inputs]: Add "gfortran".
 2016-01-14 14:43:59 +01:00
Ricardo Wurmus 0047d26a22 gnu: bowtie: Update to 2.2.6. 
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.6.
[source]: Remove patch; do not set CC and CPP variables.
[inputs]: Add "tbb".
[arguments]: Pass "prefix" and "WITH_TBB" make flags; remove custom
"install" phase.
* gnu/packages/patches/bowtie-fix-makefile.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove patch file.
 2016-01-14 14:43:25 +01:00
Efraim Flashner 2d12284d38 gnu: gnupg: Add TOFU support. 
* gnu/packages/gnupg.scm (gnupg)[inputs]: Add sqlite.
 2016-01-14 15:05:36 +02:00
Ludovic Courtès 76002e54f2 gnu: gawk: Protect against random failures of the 'fts' test. 
* gnu/packages/patches/gawk-fts-test.patch: New file.
* gnu/packages/gawk.scm (gawk)[source]: Use it.
* gnu-system.am (dist_patch_DATA): Add it.
 2016-01-14 10:43:08 +01:00
Ben Woodcroft 6b6f7d6a0e gnu: orfm: Update to 0.5.3. 
* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3.
[native-inputs]: Add inputs required for tests.
[description]: Add commas.
 2016-01-14 08:00:10 +10:00
Ben Woodcroft 3d84a99e73 gnu: Add ruby-bio-commandeer. 
* gnu/packages/ruby.scm (ruby-bio-commandeer): New variable.
 2016-01-14 08:00:02 +10:00
Ben Woodcroft 7c033c4627 gnu: Add ruby-systemu. 
* gnu/packages/ruby.scm (ruby-systemu): New variable.
 2016-01-14 07:51:44 +10:00
Ricardo Wurmus ca7ef4d418 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.
 2016-01-13 22:32:37 +01:00
Ludovic Courtès 8c986ab120 Merge branch 'master' into core-updates 2016-01-13 18:18:48 +01:00
Ricardo Wurmus e5a19fed19 gnu: julia: Update to 0.4.3. 
* gnu/packages/julia.scm (julia): Update to 0.4.3.
(libuv-julia): Update to 07730c4bd595.
 2016-01-13 17:05:38 +01:00
Mark H Weaver 75418ae0fd gnu: isc-dhcp: Update to 4.3.3-P1 [fixes CVE-2015-8605]. 
* gnu/packages/admin.scm (isc-dhcp): Update to 4.3.3-P1.
 2016-01-13 09:38:57 -05:00
Ricardo Wurmus c44734115a gnu: samtools: Update to 1.3. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.
[arguments]: Enable tests for all architectures; set ncurses in
configure-flags instead of make-flags; simplify "patch-tests" phase;
restore "configure" phase.
 2016-01-13 15:12:22 +01:00
Ludovic Courtès 98f2339189 gnu: skribilo: Update to 0.9.3. 
* gnu/packages/skribilo.scm (skribilo): Update to 0.9.3.
[native-inputs]: New field.
 2016-01-13 11:13:34 +01:00
Eric Bavier c91d3fb7f4 gnu: boost: Update to 1.60.0. 
* gnu/packages/boost.scm (boost): Update to 1.60.0.
  [source]: Remove patch.
* gnu/packages/patches/boost-mips-avoid-m32.patch: Delete patch
* gnu-system.am (dist_patch_DATA): Remove patch.

Also fix dependent packages:

* gnu/packages/patches/csound-header-ordering.patch: New patch.
* gnu/packages/audio.scm (csound)[source]: Use it.
  [arguments]: Add 'set-flags phase.
* gnu/packages/patches/libcmis-fix-test-onedrive.patch: New patch.
* gnu/packages/libreoffice.scm (libcmis)[source]: Use it.
  (libreoffice)[arguments]: Add LDFLAGS to #:configure-flags.
  (librevenge)[inputs]: Move boost from here...
  [propogated-inputs]: to here.
  [arguments]: Add LDFLAGS to #:configure-flags.
* gnu/packages/patches/openimageio-boost-1.60.patch: New patch.
* gnu/packages/graphics.scm (openimageio): Use it.
* gnu-system.am (dist_patch_DATA): Add patches.
 2016-01-12 21:07:53 +01:00
Eric Bavier 3abe8136fd gnu: boost: Use modify-phases. 
* gnu/packages/boost.scm (boost)[arguments]: Use modify-phases.
 2016-01-12 20:53:14 +01:00
Mark H Weaver 203795acea gnu: perl: Add fix for CVE-2015-8607. 
* gnu/packages/patches/perl-CVE-2015-8607.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/perl.scm (perl)[source]: Add patch.
 2016-01-12 13:12:07 -05:00
Mark H Weaver ce3ac6670c gnu: perl: Update to 5.22.1. 
* gnu/packages/perl.scm (perl): Update to 5.22.1.
 2016-01-12 13:10:05 -05:00
Mark H Weaver 16aa649117 gnu: sudo: Add fix for CVE-2015-5602. 
* gnu/packages/patches/sudo-CVE-2015-5602.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/admin.scm (sudo)[source]: Add patch.
 2016-01-12 11:23:06 -05:00
Efraim Flashner 9d9951d6a6 gnu: global: Use modify-phases syntax. 
* gnu/packages/code.scm (global)[arguments]: Use modify-phases syntax.
 2016-01-12 14:47:10 +02:00
Efraim Flashner 94c3a6f1a6 gnu: global: Update to 6.5.2. 
* gnu/packages/code.scm (global): Update to 6.5.2.
 2016-01-12 14:39:15 +02:00
Ricardo Wurmus 9f40b1171b gnu: icedtea-6: Fix directory name in "unpack" phase. 
* gnu/packages/java.scm (icedtea-6)[arguments]: Change the directory
  prefix in the "unpack" phase to "icedtea6-".
 2016-01-12 11:39:21 +01:00
Mark H Weaver 6b0d24b17c gnu: linux-libre: Update to 4.4. 
* gnu/packages/linux.scm (linux-libre): Update to 4.4.
* gnu/packages/linux-libre-i686.conf,
  gnu/packages/linux-libre-x86_64.conf: Update from
  <https://jxself.org/git/kernel-configs.git>.
 2016-01-11 19:13:37 -05:00
Ben Woodcroft 81f3e0c1f3 gnu: Add fxtract. 
* gnu/packages/bioinformatics.scm (fxtract): New variable.
 2016-01-12 07:49:19 +10:00
Ben Woodcroft 65e84e3176 gnu: ruby: Update to 2.3.0. 
* gnu/packages/ruby.scm (ruby): Update to 2.3.0.
[source]: Remove bundled libffi.
[arguments]: Use parallel tests.
(ruby-2.2): New variable.
 2016-01-11 21:59:06 +10:00
Ben Woodcroft 9656b8bec5 gnu: ruby: Use modify-phases. 
* gnu/packages/ruby.scm (ruby)[arguments]: Use modify-phases.
 2016-01-11 21:59:06 +10:00
Ben Woodcroft 761e7042f6 ruby: Abstract out path to GEM_HOME. 
Previously paths to the GEM_HOME of certain Ruby packages were
hard-coded, so packages failed to build when Ruby was updated to 2.3.0.

* guix/build/ruby-build-system.scm (gem-home): New procedure.
* gnu/packages/ruby.scm (ruby-metaclass, ruby-instantiator,
ruby-introspection, ruby-mocha, ruby-minitest-tu-shim): Use it.
 2016-01-11 21:58:55 +10:00
Efraim Flashner ec70fec559 gnu: youtube-dl: Update to 2016.01.09. 
* gnu/packages/video.scm (youtube-dl): Update to 2016.01.09.
 2016-01-11 13:30:50 +02:00
Andreas Enge 4879d2ff66 gnu: gp2c: Update to 0.0.9pl5. 
* gnu/packages/algebra.scm (gp2c): Update to 0.0.9pl5.
 2016-01-11 11:24:52 +01:00
Andreas Enge 4a6635f353 gnu: texlive: Use modify-phases syntax. 
* gnu/packages/texlive.scm (texlive-bin, texlive-texmf): Use modify-phases
  syntax.
 2016-01-11 10:59:29 +01:00
Efraim Flashner a916c82649 gnu: man-pages: Update to 4.04. 
* gnu/packages/man.scm (man-pages): Update to 4.04.
[source]: Add alternate location.
 2016-01-11 09:37:50 +02:00
Ben Woodcroft 9b9b7ffd8e gnu: bedtools: Update to 2.25.0. 
* gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0.
[source]: Remove patch merged upstream.
[arguments]: Use 'modify-phases'.  Remove
'patch-makefile-SHELL-definition' phase.
* gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.
 2016-01-11 00:36:13 +10:00
Ben Woodcroft 6573ac82ad gnu: bedtools: Use modify-phases. 
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
 2016-01-11 00:36:13 +10:00
Ben Woodcroft 048036aee5 gnu: ruby-yard: Disable failing test. 
* gnu/packages/ruby.scm (ruby-yard)[arguments]: Disable test which fails on
Ruby 2.3.0.
 2016-01-10 21:10:29 +10:00
Ben Woodcroft 3918146b61 gnu: ruby-power-assert: Update to 0.2.7. 
* gnu/packages/ruby.scm (ruby-power-assert): Update to 0.2.7.
 2016-01-10 21:09:37 +10:00
Andreas Enge 695bea9803 gnu: r: Update to 3.2.3. 
* gnu/packages/statistics.scm (r): Update to 3.2.3.
 2016-01-09 23:18:28 +01:00
Andreas Enge 13035f5a03 gnu: icecat: Update to 38.5.2-gnu1. 
* gnu/packages/gnuzilla.scm (icecat): Update to 38.5.2-gnu1.
 2016-01-09 22:51:28 +01:00
Ben Woodcroft 4c40fa0229 gnu: ruby-2.1: Update to 2.1.8. 
* gnu/packages/ruby.scm (ruby-2.1): Update to 2.1.8.
 2016-01-09 14:53:58 +10:00
Leo Famulari f32274a71e gnu: i2c-tools: Update source and home-page URLs. 
* gnu/packages/linux.scm (i2c-tools)[source]: Update URL.
[home-page]: Update URL.
 2016-01-08 16:42:27 -05:00
Leo Famulari 3a04d5d4e4 gnu: lm-sensors: Update source and home-page URLs. 
* gnu/packages/linux.scm (lm-sensors)[source]: Update URL.
[home-page]: Update URL.
 2016-01-08 16:42:27 -05:00
Mark H Weaver bea25ae83c gnu: nss: Update to 3.21 [fixes CVE-2015-7575]. 
* gnu/packages/gnuzilla.scm (nss): Update to 3.21.
  [arguments]: In configure phase, setenv CC=gcc.
* gnu/packages/patches/nss-pkgconfig.patch: Adapt to NSS 3.21.
 2016-01-08 15:29:50 -05:00
Ludovic Courtès 195f557ed5 gnu: attr: Update to 2.4.47. 
* gnu/packages/attr.scm (attr): Update to 2.4.47.
 2016-01-08 16:45:32 +01:00
Ludovic Courtès 20c620d0a4 gnu: attr: Use 'modify-phases'. 
* gnu/packages/attr.scm (attr)[arguments]: Use 'modify-phases'.
 2016-01-08 16:45:28 +01:00
Mathieu Lirzin 2409f37f28 gnu: Add missing (gnu packages gcc) import. 
* gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is
required by 'r-impute' for 'gfortran'.
 2016-01-08 14:18:46 +01:00
Mathieu Lirzin 9ef824c10e gnu: xterm: Update to 322. 
* gnu/packages/xorg.scm (xterm): Update to 322.
 2016-01-08 14:12:29 +01:00
宋文武 a65e26f091 gnu: epiphany: Update to 3.18.2. 
* gnu/packages/gnome.scm (epiphany): Update to 3.18.2.
 2016-01-08 17:34:08 +08:00
宋文武 19e5258d84 gnu: webkitgtk: Update to 2.10.4. 
* gnu/packages/webkit.scm (webkitgtk): Update to 2.10.4.
 2016-01-08 17:34:08 +08:00
Efraim Flashner 209e09fa10 gnu: zlib: Update to 1.2.8. 
* gnu/packages/compression.scm (zlib): Update to 1.2.8.
 2016-01-08 06:39:12 +02:00
Pjotr Prins c8d969b58f gnu: Add Pfff. 
* gnu/packages/textutils.scm (pfff): New variable.
 2016-01-07 21:13:35 +01:00
Alex Kost fbbaa4dde8 gnu: mpv: Remove 'samba' input. 
This is a heavy-weight and uncommon feature.  See
<http://lists.gnu.org/archive/html/guix-devel/2015-12/msg00701.html>.

* gnu/packages/video.scm (mpv)[inputs]: Remove 'samba'.
 2016-01-07 22:30:18 +03:00
Ricardo Wurmus cb933df6da gnu: Add genomation. 
* gnu/packages/bioinformatics.scm (r-genomation): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus 03ea5a357e gnu: Add seqPattern. 
* gnu/packages/bioinformatics.scm (r-seqpattern): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus c43a011de3 gnu: Add impute. 
* gnu/packages/bioinformatics.scm (r-impute): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus c63cef6699 gnu: Add BSgenome. 
* gnu/packages/bioinformatics.scm (r-bsgenome): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus fbf6045e33 gnu: Add plotly. 
* gnu/packages/statistics.scm (r-plotly): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus a28d646b63 gnu: Add viridis. 
* gnu/packages/statistics.scm (r-viridis): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus d547ce5e70 gnu: Add topGO. 
* gnu/packages/bioinformatics.scm (r-topgo): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus e05c37da4a gnu: Add matrixStats. 
* gnu/packages/statistics.scm (r-matrixstats): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus 3703ffb41f gnu: Add R.rsp. 
* gnu/packages/statistics.scm (r-r-rsp): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus a63efbb453 gnu: Add R.cache. 
* gnu/packages/statistics.scm (r-r-cache): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus 9c94b53b5b gnu: Add R.utils. 
* gnu/packages/statistics.scm (r-r-utils): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus c8c75a8d88 gnu: Add R.oo. 
* gnu/packages/statistics.scm (r-r-oo): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus 8bfe007c9c gnu: Add R.methodsS3. 
* gnu/packages/statistics.scm (r-r-methodss3): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus a69a593595 gnu: Add base64enc. 
* gnu/packages/statistics.scm (r-base64enc): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus a8227e4ae9 gnu: Add DT. 
* gnu/packages/statistics.scm (r-dt): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus d706257b5b gnu: Add SparseM. 
* gnu/packages/statistics.scm (r-sparsem): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus fb25d8803f gnu: Add GO.db. 
* gnu/packages/bioinformatics.scm (r-go-db): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus 2fd7c04984 gnu: Add GenomicFeatures. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus 317755ff0f gnu: Add rtracklayer. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus d8a828af78 gnu: Add GenomicAlignments. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus 6e76dda2d0 gnu: Add SummarizedExperiment. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus f8d74f7018 gnu: Add Rsamtools. 
* gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus bf15935337 gnu: Add Biostrings. 
* gnu/packages/bioinformatics.scm (r-biostrings): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus e91d362e48 gnu: Add BiocParallel. 
* gnu/packages/bioinformatics.scm (r-biocparallel): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus c465fa72ed gnu: Add biomaRt. 
* gnu/packages/bioinformatics.scm (r-biomart): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus 8b7bce740d gnu: Add AnnotationDbi. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus 555e3399dc gnu: Add Biobase. 
* gnu/packages/bioinformatics.scm (r-biobase): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus bc899123e7 gnu: Add snow. 
* gnu/packages/statistics.scm (r-snow): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus 6b82f56cf9 gnu: Add futile.logger. 
* gnu/packages/statistics.scm (r-futile-logger): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus b9ff33b50e gnu: Add futile.options. 
* gnu/packages/statistics.scm (r-futile-options): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus ca65d387fd gnu: Add lambda.r. 
* gnu/packages/statistics.scm (r-lambda-r): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus 543ded3619 gnu: Add r-xml. 
* gnu/packages/statistics.scm (r-xml): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus cefaa79c9e gnu: Add RCurl. 
* gnu/packages/statistics.scm (r-rcurl): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus 21e4d6a9cf gnu: Add RSQLite. 
* gnu/packages/statistics.scm (r-rsqlite): New variable.
 2016-01-07 17:18:15 +01:00
Raimon Grau fe9451c50a gnu: Add xmlstarlet. 
* gnu/packages/xml.scm (xmlstarlet): New variable.
 2016-01-07 16:00:00 +01:00
宋文武 29e255ca83 gnu: zita-convolver: Drop the '-march=native' optimization. 
* gnu/packages/audio.scm (zita-convolver)[source]: Add snippet.
 2016-01-07 22:47:32 +08:00
宋文武 6dff495580 gnu: zita-resampler: Drop the '-march=native' optimization. 
* gnu/packages/audio.scm (zita-resampler)[source]: Add snippet.
 2016-01-07 22:47:32 +08:00
Ben Woodcroft 7d3a1a2dd2 gnu: Add ruby-ansi. 
* gnu/packages/ruby.scm (ruby-ansi): New variable.
 2016-01-07 15:36:05 +01:00
Efraim Flashner b24765139c gnu: sqlite: Update to 3.10.0. 
* gnu/packages/databases.scm (sqlite): Update to 3.10.0.
 2016-01-07 12:37:37 +02:00
Ricardo Wurmus 5dfd276602 gnu: edirect: Update to 3.50. 
* gnu/packages/bioinformatics.scm (edirect): Update to 3.50.
[native-inputs]: Remove "unzip".
 2016-01-07 11:25:24 +01:00
Leo Famulari 62339e2d49 gnu: w3m: Enable SSL, disable broken protocols and ciphers. 
Fixes <http://bugs.gnu.org/16791>.

* gnu/packages/patches/w3m-force-ssl_verify_server-on.patch: New file.
* gnu/packages/patches/w3m-disable-sslv2-and-sslv3.patch: New file.
* gnu/packages/patches/w3m-disable-weak-ciphers.patch: New file.
* gnu/packages/w3m.scm (w3m)[source]: Add patches.
* gnu-system.am (dist_patch_DATA): Add the new files.
 2016-01-07 02:35:38 -05:00
Leo Famulari e6352001c4 gnu: w3m: Update patch to use '-p1'. 
* gnu/packages/patches/w3m-fix-compile.patch: Rename this file...
* gnu/packages/patches/w3m-libgc.patch: ...to this, and adjust patch
prefix level to '-p1'.
* gnu-system.am (dist_patch_DATA): Update patch name.
* gnu/packages/w3m.scm (w3m)[source]: Update patch name.
[source]: Drop patch flag -p0.
 2016-01-07 02:35:38 -05:00
Efraim Flashner 93b3a8b0ee gnu: flex: Update to 2.6.0. 
* gnu/packages/flex.scm (flex): Update to 2.6.0.
[source]: Remove flex-bison-tests.patch.
* gnu-system.am (dist_patch_DATA): Remove flex-bison-tests.patch.
* gnu/packages/patches/flex-bison-tests.patch: Remove it.
 2016-01-07 08:42:15 +02:00
Ludovic Courtès d4aaf95401 build-system/gnu: Make 'package-with-explicit-inputs' idempotent. 
* guix/build-system/gnu.scm (package-with-explicit-inputs): Use
  'ensure-keyword-arguments' instead of appending to ARGS.
* gnu/packages/commencement.scm (static-bash-for-glibc): Add missing
  #:guile argument.
 2016-01-06 23:08:22 +01:00
Ludovic Courtès dff9141c5e gnu: guix: Update development snapshot to f888c0b. 
* gnu/packages/package-management.scm (guix-devel): Update to f888c0b.
 2016-01-06 23:08:22 +01:00
Efraim Flashner bfcb7bcb73 gnu: libffi: Update to 3.2.1. 
* gnu/packages/libffi.scm (libffi): Update to 3.2.1.
 2016-01-06 20:28:57 +02:00
Eric Bavier c7b08410de gnu: gmsh: Update to 2.11.0. 
* gnu/packages/maths.scm (gmsh): Update to 2.11.0.
  [arguments]: Replace 'check phase.
 2016-01-06 10:49:23 -06:00
Ludovic Courtès 7b78f359d1 gnu: sudo: Use /var/run/sudo instead of /run/sudo. 
* gnu/packages/admin.scm (sudo)[arguments]: Pass
--with-rundir=/var/run/sudo since /var/run is cleaned up at boot time on
GuixSD whereas /run is not.
 2016-01-06 15:51:31 +01:00
Ludovic Courtès 3c4c8c3e06 services: cleanup-service: Catch 'system-error' instead of everything. 
This makes sure that critical errors such as unbound-variable do not go
undetected.

* gnu/services.scm (cleanup-gexp): Introduce local 'fail-safe' macro and
use it.  Remove uses of 'false-if-exception'.
 2016-01-06 14:49:48 +01:00
Ludovic Courtès 341ae58213 gnu: ldc: Fix license. 
* gnu/packages/ldc.scm (ldc)[license]: Replace invalid use of
'license:x11-style' by LICENSE:BOOST1.0.
 2016-01-06 14:21:53 +01:00
Ricardo Wurmus a243e12aba gnu: icedtea7: Rename to icedtea-7. 
* gnu/packages/java.scm (icedtea7): Rename variable to...
(icedtea-7): ...this.
(icedtea): Refer to "icedtea-7".
 2016-01-06 11:38:50 +01:00
Ricardo Wurmus d028740622 gnu: icedtea6: Rename to icedtea-6. 
* gnu/packages/java.scm (icedtea6): Rename variable to...
(icedtea-6): ...this.
 2016-01-06 11:38:50 +01:00
Ricardo Wurmus 5452588c1a gnu: icedtea6, icedtea7: Rename package to "icedtea". 
* gnu/packages/java.scm (icedtea6): Change package name to "icedtea".
(icedtea7): Inherit package name.
 2016-01-06 11:38:50 +01:00
Ricardo Wurmus d2540f80c2 gnu: Add and use default IcedTea. 
* gnu/packages/java.scm (icedtea): New variable.
(swt)[native-inputs]: Replace "icedtea6" with "icedtea".
* gnu/packages/bioinformatics.scm (htsjdk)[native-inputs]: Likewise.
(ngs-java)[inputs]: Likewise.
* gnu/packages/kodi.scm (kodi)[native-inputs]: Replace "icedtea7" with
"icedtea".
* gnu/packages/ruby.scm (ruby-rjb)[native-inputs]: Replace "icedtea7"
with "icedtea".
 2016-01-06 11:38:50 +01:00
Ricardo Wurmus d91488908b gnu: icedtea6, icedtea7: Unpack to "openjdk.src". 
* gnu/packages/java.scm (icedtea6)[arguments]: Unpack OpenJDK sources to
"openjdk.src".
(icedtea7)[arguments]: Inherit "--with-openjdk-src-dir" flag; refer to
"openjdk.src" in build phases; simplify "unpack" phase.
[native-inputs]: Rename "openjdk-drop" to "openjdk-src".
 2016-01-06 11:38:50 +01:00
Ricardo Wurmus 43c565d2e7 gnu: Add Jellyfish. 
* gnu/packages/bioinformatics.scm (jellyfish): New variable.
 2016-01-06 11:10:46 +01:00
Andreas Enge 7d1f8d4f52 gnu: calibre: Update to 2.48.0. 
* gnu/packages/ebook.scm (calibre): Update to 2.48.0.
 2016-01-05 22:46:54 +01:00
Efraim Flashner e5f037624e gnu: gettext: Use "modify-phases" syntax. 
* gnu/packages/gettext.scm (gettext)[arguments]: Use "modify-phases" syntax.
 2016-01-05 21:13:57 +02:00
Efraim Flashner d99861d39d gnu: gettext: Update to 0.19.7. 
* gnu/packages/gettext.scm (gettext): Update to 0.19.7.
 2016-01-05 21:06:59 +02:00
Efraim Flashner 5a75865f9d gnu: gnutls: Update to 3.4.7. 
* gnu/packages/tls.scm (gnutls): Update to 3.4.7.
[source]: Remove gnutls-doc-fix.patch.
[arguments]: Remove delete-prebuilt-unfixed-info-file phase.
[native-inputs]: Remove texinfo.
* gnu-system.am (dist_patch_DATA): Remove gnutls-doc-fix.patch
 2016-01-05 21:06:59 +02:00
Efraim Flashner 3ea110b704 gnu: libtasn1: Update to 4.7. 
* gnu/packages/tls.scm (libtan1): Update to 4.7.
[native-inputs]: Remove texinfo.
 2016-01-05 21:06:59 +02:00
Roel Janssen a7ec569c98 gnu: Add LDC. 
* gnu/packages/ldc.scm: New file.
* gnu/packages/patches/ldc-disable-tests.patch: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add ldc.scm.
  (dist_patch_DATA): Add patch file.
 2016-01-05 16:24:57 +01:00
Ludovic Courtès e8e2e18b84 gnu: Read 'C_INCLUDE_PATH' instead of 'CPATH'. 
This is a followup to 009b53fd.

* gnu/packages/cmake.scm (cmake)[arguments]: Use (getenv
"C_INCLUDE_PATH") instead of (getenv "CPATH").
* gnu/packages/package-management.scm (rpm)[arguments]: Likewise.
* gnu/packages/video.scm (avidemux)[arguments]: Likewise.
* gnu/packages/webkit.scm (webkitgtk)[arguments]: Likewise.
* gnu/packages/cross-base.scm (cross-gcc-arguments): Likewise, and unset
'C_INCLUDE_PATH' and 'CPLUS_INCLUDE_PATH'.
 2016-01-05 14:11:54 +01:00
Ludovic Courtès a2ab82db9a gnu: python: Honor 'C_INCLUDE_PATH'. 
This is a followup to 009b53fd.

* gnu/packages/patches/python-3-search-paths.patch: Check
'C_INCLUDE_PATH' instead of 'CPATH'.
* gnu/packages/patches/python-2.7-search-paths.patch: Likewise.
 2016-01-05 13:13:17 +01:00
Dmitry Bogatov 1075b43737 gnu: Add emacs-undo-tree. 
* gnu/packages/emacs.scm (emacs-undo-tree): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-01-05 00:28:42 +01:00
Ludovic Courtès fe542b9762 gnu: emacs: Remove 'info.info'. 
* gnu/packages/emacs.scm (emacs)[arguments]: Use 'modify-phases'.  Add
'remove-info.info' phase.
 2016-01-05 00:28:42 +01:00
Ludovic Courtès fb74174958 linux-boot: Remove verbose output for module loads. 
* gnu/build/linux-boot.scm (boot-system): Leave
'current-module-debugging-port' unchanged.
* gnu/build/linux-modules.scm (load-linux-module*): Update comment about
'mmap'.
 2016-01-05 00:28:42 +01:00
Ludovic Courtès be7be9e8dd services: Move /tmp cleanup to a separate service. 
* gnu/services.scm (compute-boot-script): Remove /tmp and /var/run
deletion code from here.
(cleanup-gexp): New procedure with /tmp and /var/run deletion code
formerly in 'compute-boot-script'.
(cleanup-service-type): New variable.
* gnu/system.scm (essential-services): Add an instance of
CLEANUP-SERVICE-TYPE.
 2016-01-05 00:28:42 +01:00
Ludovic Courtès 94af9daa73 services: boot: Reinstate /tmp and /var/run deletion. 
For some time /tmp and /var/run were not being deleted because
'delete-file-recursively' was unbound.

* gnu/services.scm (compute-boot-script)[%modules, modules, compiled]:
New variables.  Use them to augment the module search path.
 2016-01-05 00:28:42 +01:00
Ricardo Wurmus 4828ff91ff gnu: gtk+: Add patch to support GUIX_GTK3_PATH. 
* gnu/packages/patches/gtk3-respect-GUIX_GTK3_PATH: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/gtk.scm (gtk+) [source]: Add patch.
[native-search-paths]: Add search path for GUIX_GTK3_PATH.
 2016-01-04 16:11:10 -05:00
Ricardo Wurmus 2a6afac905 gnu: gtk+-2: Add patch to support GUIX_GTK2_PATH. 
* gnu/packages/patches/gtk2-respect-GUIX_GTK2_PATH: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/gtk.scm (gtk+-2) [source]: Add patch.
[native-search-paths]: Add search path for GUIX_GTK2_PATH.
 2016-01-04 16:11:10 -05:00
Efraim Flashner 4f2ca23493 gnu: libgcrypt: Update to 1.6.4. 
* gnu/packages/gnupg.scm (libgcrypt): Update to 1.6.4.
 2016-01-04 22:29:08 +02:00
Manolis Ragkousis 4478dbd58c gnu: libgpg-error: Update to 1.21. 
* gnu/packages/gnupg.scm (libgpg-error): Update to 1.21.
 2016-01-04 18:23:29 +02:00
Efraim Flashner 82cb8519bc gnu: tzdata: Update to 2015g. 
* gnu/packages/base.scm (tzdata): Update to 2015g.
 2016-01-04 16:59:13 +02:00
Ricardo Wurmus c2e87caaa6 gnu: julia: Update to 0.4.2. 
* gnu/packages/patches/julia-0.3.10-fix-empty-array.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.
* gnu/packages/julia.scm (julia): Update to 0.4.2.
[arguments]: Remove phase "fix-building-with-mcjit-llvm"; replace phase
"patch-include-path" with "fix-include-and-link-paths"; add phase
"hardcode-paths"; add missing make-flags.
[inputs]: Replace "pcre" with "pcre2"; replace "git" with "libgit2"; add
"coreutils"; add "libuv-julia"; add "wget"; add "which".
[native-inputs]: Remove "which".
 2016-01-04 11:35:57 +01:00
Ricardo Wurmus 50b40d0709 gnu: Add libuv-julia. 
* gnu/packages/julia.scm (libuv-julia): New variable.
 2016-01-04 11:35:57 +01:00
Ricardo Wurmus f1e3a8aed2 gnu: utf8proc: Update to 1.3.1. 
* gnu/packages/textutils.scm (utf8proc): Update to 1.3.1.
[arguments]: Remove custom "install" phase.
 2016-01-04 11:35:57 +01:00
Leo Famulari 77553dff86 gnu: samba: Update to 4.3.3. 
Fixes CVE-2015-{3223,5252,5299,5296,8467,5330}.

* gnu/packages/samba.scm (samba): Update to 4.3.3.
 2016-01-03 14:59:49 -05:00
Leo Famulari f6cddbefcc gnu: ldb: Update to 1.1.24. 
Required for samba-4.3.3 in order to fix CVE-2015-5330 and
CVE-2015-3223.

* gnu/packages/samba.scm (ldb): Update to 1.2.24.
 2016-01-03 14:59:49 -05:00
Ludovic Courtès 53334dd6e9 Merge branch 'master' into core-updates 2016-01-03 14:53:03 +01:00
Ludovic Courtès 1575dcd134 gnu: grep: Skip timing-sensitive test. 
This avoids failures on loaded machines as seen
at <http://hydra.gnu.org/build/906900/log/raw>.

* gnu/packages/patches/grep-timing-sensitive-test.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/base.scm (grep): Use it.
 2016-01-03 14:50:29 +01:00
Ludovic Courtès dd1937d75d gnu: pkg-config: Update to 0.29. 
* gnu/packages/pkg-config.scm (%pkg-config): Update to 0.29.
 2016-01-03 14:44:22 +01:00
Eric Bavier 8d0801ab23 gnu: libgc: Enable C++ support. 
* gnu/packages/bdw-gc.scm (libgc-7.2, libgc)[arguments]: Add
  --enable-cplusplus to #:configure-flags.
 2016-01-02 16:06:11 -06:00
Eric Bavier 209778717a gnu: Add Asymptote. 
* gnu/packages/bdw-gc.scm (libgc-for-c++): New variable.
* gnu/packages/plotutils.scm (asymptote): New variable.
* gnu/packages/patches/asymptote-gsl2.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
 2016-01-02 16:04:55 -06:00
Erik Edrosa b989390889 gnu: Add python-markdown. 
* gnu/packages/python.scm (python-markdown, python2-markdown): New
variables.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-01-02 00:07:29 -05:00
宋文武 05d48c5243 gnu: love: Update to 0.10.0. 
* gnu/packages/game-development.scm (love): Update to 0.10.0.
 2016-01-02 10:31:53 +08:00
Ludovic Courtès 319007c507 gnu: guile-ssh: Update to 0.9.0. 
* gnu/packages/ssh.scm (guile-ssh): Update to 0.9.0.
 2016-01-01 22:59:20 +01:00
Ludovic Courtès f453f637d5 system: Allow the root file system to be named by UUID. 
* gnu/build/file-systems.scm (canonicalize-device-spec)[canonical-title]:
Use 'string->uuid' to check whether SPEC is a UUID.
When SPEC is a string and CANONICAL-TITLE is 'uuid, call 'string->uuid'.
* gnu/system.scm (operating-system-grub.cfg): Add 'root-device'
variable and use it for the "--root=" argument.
 2016-01-01 22:50:26 +01:00
Ludovic Courtès f8865db6a0 file-systems: Move 'string->uuid' to the build side. 
* gnu/system/file-systems.scm (%uuid-rx, string->uuid): Move to...
* gnu/build/file-systems.scm (%uuid-rx, string->uuid): ... here.  New
variables.
 2016-01-01 22:41:35 +01:00
Ludovic Courtès 29824d80ec system: Allow the root file system to have a UUID. 
This is a followup to ab64483.

* gnu/system.scm (mapped-device-user): Check whether the title of FS is
'device before calling 'string=?'.
* gnu/system/vm.scm (virtualized-operating-system)[user-file-systems]:
Likewise.
 2016-01-01 22:34:13 +01:00
Ludovic Courtès e80d2555f5 gnu: findutils: Update to 4.6.0. 
* gnu/packages/patches/findutils-absolute-paths.patch: Remove.
* gnu/packages/patches/findutils-test-xargs.patch: New file.
* gnu-system.am (dist_patch_DATA): Adjust accordingly.
* gnu/packages/base.scm (findutils): Update to 4.6.0.  Remove
'findutils-absolute-paths.patch' and add 'findutils-test-xargs.patch'.
 2016-01-01 01:05:06 +01:00
Fabian Harfert 45147b0caa gnu: Add xaos. 
* gnu/packages/maths.scm (xaos): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2015-12-31 11:29:43 +03:00
Leo Famulari 658212ebf7 gnu: Move cursynth to (gnu packages music). 
* gnu/packages/cursynth.scm: Remove.
* gnu/packages/music.scm (cursynth): New variable, from cursynth.scm.
* gnu-system.am (GNU_SYSTEM_MODULES): Remove cursynth.scm.
 2015-12-30 21:26:05 -05:00
Leo Famulari 2ef8bbc3ae gnu: libcue: Update source URL. 
* gnu/packages/cdrom.scm (libcue)[source]: Update URL.
 2015-12-30 19:59:58 -05:00
Efraim Flashner 34da7af4c1 gnu: python-mox3: Update to 0.13.0. 
* gnu/packages/openstack.scm (python-mox3): Update to 0.13.0.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 13fcc6df37 gnu: python-fixtures: Update to 1.4.0. 
* gnu/packages/python.scm (python-fixtures): Update to 1.4.0.
 2015-12-30 23:16:09 +02:00
Efraim Flashner af1ab77312 gnu: python-pyld: Update to 0.6.8. 
* gnu/packages/python.scm (python-pyld): Update to 0.6.8.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 1780424035 gnu: python-virtualenv: Update to 13.1.2. 
* gnu/packages/python.scm (python-virtualenv): Update to 13.1.2.
[arguments]: Custom test command.
[inputs]: Remove python-nose, add python-pytest.
 2015-12-30 23:16:09 +02:00
Efraim Flashner ec89a25cad gnu: python-oslosphinx: Update to 4.2.0. 
* gnu/packages/openstack.scm (python-oslosphinx): Update to 4.2.0.
 2015-12-30 23:16:09 +02:00
Efraim Flashner f66bb273de gnu: python-oslo.serialization: Update to 2.2.0. 
* gnu/packages/openstack.scm (python-oslo.serialization): Update to 2.2.0.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 4768988887 gnu: python-os-testr: Update to 0.5.0. 
* gnu/packages/openstack.scm (python-os-testr): Update to 0.5.0.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 45f4c28d80 gnu: python-stevedore: Update to 1.10.0. 
* gnu/packages/openstack.scm (python-stevedore): Update to 1.10.0.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 622d21bba9 gnu: python-tempest-lib: Update to 0.12.0. 
* gnu/packages/openstack.scm (python-tempest-lib): Update to 0.12.0.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 690e8c6637 gnu: python-passlib: Update to 1.6.5. 
* gnu/packages/python.scm (python-passlib): Update to 1.6.5.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 03fd001cef gnu: python-libarchive-c: Update to 2.2. 
* gnu/packages/python.scm (python-libarchive-c): Update to 2.2.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 99b00dc796 gnu: python-tlsh: Update to 3.4.4. 
* gnu/packages/python.scm (python-tlsh): Update to 3.4.4.
 2015-12-30 23:16:09 +02:00
Efraim Flashner b8834c219e gnu: python-webob: Update to 1.5.1. 
* gnu/packages/python.scm (python-webob): Update to 1.5.1.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 1b99553317 gnu: python-flake8: Update to 2.5.1. 
* gnu/packages/python.scm (python-flake8): Update to 2.5.1.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 2abc397225 gnu: python-pyflakes: Update to 1.0.0. 
* gnu/packages/python.scm (python-pyflakes): Update to 1.0.0.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 3655ee76a6 gnu: python-pyzmq: Update to 15.1.0. 
* gnu/packages/python.scm (python-pyzmq): Update to 15.1.0.
 2015-12-30 23:16:09 +02:00
Efraim Flashner f56777be0a gnu: python-psutil: Update to 3.3.0. 
* gnu/packages/python.scm (python-psutil): Update to 3.3.0.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 38eb6919e1 gnu: python-pycparser: Update to 2.14. 
* gnu/packages/python.scm (python-pycparser): Update to 2.14.
 2015-12-30 23:16:09 +02:00
Efraim Flashner d9aa097b96 gnu: python-pyrfc3339: Update to 1.0. 
* gnu/packages/python.scm (python-pyrfc3339): Update to 1.0.
 2015-12-30 23:16:09 +02:00
Efraim Flashner f7cb984133 gnu: python-nose: Update to 1.3.7. 
* gnu/packages/python.scm (python-nose): Update to 1.3.7.
 2015-12-30 23:16:09 +02:00
Efraim Flashner ec3bcbc7e4 gnu: python-rpy2: Update to 2.7.6. 
* gnu/packages/python.scm (python-rpy2): Update to 2.7.6.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 11f97c27bc gnu: pelican: Update to 3.6.3. 
* gnu/packages/python.scm (pelican): Update to 3.6.3.
 2015-12-30 23:16:09 +02:00
Efraim Flashner e98149b3a4 gnu: python-jinja2: Update to 2.8. 
* gnu/packages/python.scm (python-jinja2): Update to 2.8.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 8925d4f345 gnu: python-unidecode: Update to 0.04.18. 
* gnu/packages/python.scm (python-unidecode): Update to 0.04.18.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 7fb9ff4dea gnu: python-blinker: Update to 1.4. 
* gnu/packages/python.scm (python-blinker): Update to 1.4.
 2015-12-30 23:16:09 +02:00
Efraim Flashner c2a9c1c0bc gnu: python-dateutil: Update to 2.4.2. 
* gnu/packages/python.scm (python-dateutil): Update to 2.4.2.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 2c3d13fe1b gnu: isync: Update to 1.2.1. 
* gnu/packages/mail.scm (isync): Update to 1.2.1.
 2015-12-30 23:16:09 +02:00
Efraim Flashner aadf46253a gnu: getmail: Update to 4.48.0. 
* gnu/packages/mail.scm (getmail): Update to 4.48.0.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 866fade9e5 gnu: notmuch: Update to 0.21. 
* gnu/packages/mail.scm (notmuch): Update to 0.21.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 70e9d258c4 gnu: youtube-dl: Update to 2015.12.29. 
* gnu/packages/video.scm (youtube-dl): Update to 2015.12.29.
 2015-12-30 23:16:09 +02:00
Efraim Flashner 31e98ca63f gnu: offlineimap: Update to 6.6.1. 
* gnu/packages/mail.scm (offlineimap): Update to 6.6.1.
 2015-12-30 23:16:09 +02:00
Ricardo Wurmus 3d5fd24090 gnu: Add Fritzing. 
* gnu/packages/engineering.scm (fritzing): New variable.
 2015-12-30 20:41:33 +01:00
Ludovic Courtès 0084aaf3d4 gnu: Add lcov. 
* gnu/packages/code.scm (lcov): New variable.
 2015-12-30 19:14:04 +01:00
Alex Vong 0c1910ed03 gnu: ladspa: Update URLs. 
* gnu/packages/audio.scm (ladspa): Update source and home page url.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2015-12-30 18:18:38 +01:00
Andreas Enge f95dad899b gnu: texlive: Patch texmfcnf.lua. 
* gnu/packages/texlive.scm (texlive): Patch texmfcnf.lua to point to the
  absolute texlive-texmf tree.
 2015-12-30 11:24:26 +01:00
Mark H Weaver 826244f01a gnu: fuse: Fix source URI. 
This is a followup to commit b7e7d1b9d3.

* gnu/packages/linux.scm (fuse)[source]: Fix source URI.
 2015-12-29 22:25:02 -05:00
Ben Woodcroft 19f4554c94 gnu: Add fraggenescan. 
* gnu/packages/bioinformatics.scm (fraggenescan): New variable.
 2015-12-29 20:14:03 -05:00
Leo Famulari 6819a8ddd6 gnu: Add shntool. 
* gnu/packages/audio.scm (shntool): New variable.
 2015-12-29 19:55:21 -05:00
Leo Famulari 6da16993eb gnu: Add cuetools. 
* gnu/packages/audio.scm (cuetools): New variable.
 2015-12-29 19:55:21 -05:00
Efraim Flashner 11afbbc651 gnu: enlightenment: Update to 0.20.2. 
* gnu/packages/enlightenment.scm (enlightenment): Update to 0.20.2.
 2015-12-29 22:52:20 +02:00
Leo Famulari 6959a13271 gnu: sshfs-fuse: Update source URL. 
* gnu/packages/linux.scm (sshfs-fuse)[source]: Update URL.
 2015-12-29 14:20:55 -05:00
Leo Famulari b7e7d1b9d3 gnu: fuse: Update to 2.9.4. 
* gnu/packages/patches/fuse-CVE-2015-3202.patch: Delete file.
* gnu-system.am (dist_patch_DATA): Remove it.
* gnu/packages/linux.scm (fuse): Update to 2.9.4.
  [source]: Remove patch.
 2015-12-29 14:20:55 -05:00
Efraim Flashner c7d0bf0071 gnu: youtube-dl: Update to 2015.12.23. 
* gnu/packages/video.scm (youtube-dl): Update to 2015.12.23.
 2015-12-29 09:33:10 +02:00
Ricardo Wurmus 6da2e99e2e gnu: tuxguitar: Set missing GCJFLAGS. 
* gnu/packages/music.scm (tuxguitar)[arguments]: Set compiler flags
  "-fsource=1.4" and "-fPIC".
 2015-12-29 07:52:19 +01:00
Ricardo Wurmus 5f1c949866 gnu: tuxguitar: Use "modify-phases" syntax. 
* gnu/packages/music.scm (tuxguitar)[arguments]: Use "modify-phases"
  syntax.
 2015-12-29 07:52:19 +01:00
Leo Famulari c1ff0f2fed gnu: irssi: Update source URL. 
* gnu/packages/irssi.scm (irssi)[source]: Update URL.
 2015-12-27 17:39:03 -05:00
Efraim Flashner 85d42329b3 gnu: elementary: Update to 1.16.1. 
* gnu/packages/enlightenment.scm (elementary): Update to 1.16.1.
 2015-12-27 15:33:20 +02:00
Efraim Flashner c1a064c96e gnu: efl: Update to 1.16.1. 
* gnu/packages/enlightenment.scm (efl): Update to 1.16.1.
 2015-12-27 14:44:29 +02:00
Efraim Flashner e21338bec5 gnu: python-decorator: Update to 4.0.6. 
* gnu/packages/python.scm (python-decorator): Update to 4.0.6.
 2015-12-26 23:10:53 +02:00
Efraim Flashner 2a2d098195 gnu: python-exif-read: Update to 2.1.2. 
* gnu/packages/python.scm (python-exif-read): Update to 2.1.2.
 2015-12-26 23:10:53 +02:00
Efraim Flashner 82a3c582a3 gnu: python-coverage: Update to 4.0.3. 
* gnu/packages/python.scm (python-coverage): Update to 4.0.3.
 2015-12-26 23:10:53 +02:00
Efraim Flashner 9f44228512 gnu: python-pygments: Update to 2.0.2. 
* gnu/packages/python.scm (python-pygments): Update to 2.0.2.
 2015-12-26 23:10:53 +02:00
Efraim Flashner 2d3a437c79 gnu: python-cffi: Update to 1.4.2. 
* gnu/packages/python.scm (python-cffi): Update to 1.4.2.
 2015-12-26 23:10:53 +02:00
Efraim Flashner 71c8a804b9 gnu: python-py: Update to 1.4.31. 
* gnu/packages/python.scm (python-py): Update to 1.4.31.
 2015-12-26 23:10:53 +02:00
Leo Famulari b8ae816b0e gnu: tinyproxy: Update source URL. 
* gnu/packages/web.scm (tinyproxy)[source]: Update URL.
 2015-12-26 11:47:42 -05:00
Leo Famulari 4beb9f3a3b gnu: zsh: Add alternate source URL. 
* gnu/packages/zsh.scm (zsh)[source]: Add alternate URL.
 2015-12-26 11:26:57 -05:00
Leo Famulari 7b10135386 gnu: znc: Update to 1.6.2. 
* gnu/packages/messaging.scm (znc): Update to 1.6.2.
 2015-12-26 11:24:55 -05:00
Leo Famulari eb2371bcdd gnu: znc: Update source URL. 
* gnu/packages/messaging.scm (znc)[source]: Update URL.
 2015-12-26 11:24:55 -05:00
Mark H Weaver ce755b609d gnu: libpng: Update to 1.5.26 [fixes CVE-2015-8472 and CVE-2015-8540]. 
* gnu/packages/image.scm (libpng): Update to 1.5.26.
 2015-12-26 11:01:01 -05:00
Efraim Flashner fe08b6e1eb gnu: gdk-pixbuf: Update to 2.32.3. (fixes CVE-2015-4491) 
* gnu/packages/gtk.scm (gdk-pixbuf): Update to 2.32.3.
 2015-12-26 11:01:01 -05:00
Efraim Flashner 4d6b8da717 gnu: cups-filters: Update to 1.4.0. (fixes CVE-2015-8560) 
* gnu/packages/cups.scm (cups-filters): Update to 1.4.0.
 2015-12-26 11:01:01 -05:00
Leo Famulari 75bae747cc gnu: xlockmore: Update to 5.46. 
* gnu/packages/xdisorg.scm (xlockmore): Update to 5.46.
 2015-12-26 02:22:20 -05:00
Leo Famulari 20c043587a gnu: xlockmore: Add alternate URL. 
* gnu/packages/xdisorg.scm (xlockmore)[source]: Add alternate URL.
 2015-12-26 02:17:46 -05:00
Leo Famulari d642053386 gnu: wmctrl: Update source URL. 
* gnu/packages/xdisorg.scm (wmctrl)[source]: Update URL.
 2015-12-26 01:55:14 -05:00
Leo Famulari 3759bfad32 gnu: colordiff: Update to 1.0.16. 
* gnu/packages/patchutils.scm (colordiff): Update to 1.0.16.
 2015-12-26 00:10:32 -05:00
Leo Famulari 8d479d27ca gnu: colordiff: Update source URL. 
* gnu/packages/patchutils.scm (colordiff)[source]: Update URL.
 2015-12-26 00:10:09 -05:00
Leo Famulari 97a79b19d1 gnu: opus-tools: Update source URL. 
* gnu/packages/xiph.sch (opus-tools)[source]: Update URL.
 2015-12-26 00:00:21 -05:00
Leo Famulari 5b0bcecdd1 gnu: moreutils: Update to 0.57. 
* gnu/packages/moreutils.scm (moreutils): Update to 0.57.
 2015-12-25 23:59:26 -05:00
Leo Famulari d4ec43392b gnu: lynx: Update source URL. 
* gnu/packages/lynx.scm (lynx)[source]: Update URL.
 2015-12-25 23:58:33 -05:00
Leo Famulari 4150ac88bc gnu: libsodium: Add alternate URL. 
* gnu/packages/crypto.scm (libsodium)[source]: Add alternate URL.
 2015-12-25 23:56:15 -05:00
Leo Famulari 8fa16f63e7 gnu: libev: Update source URL. 
* gnu/packages/libevent.scm (libev)[source]: Update URL.
 2015-12-25 23:51:08 -05:00
Leo Famulari 8f26f23926 gnu: hevea: Update URL. 
* gnu/packages/ocaml.scm (hevea)[source]: Update URL.
 2015-12-25 23:46:55 -05:00
Leo Famulari 513f8ab4f3 gnu: exim: Update to 4.86. 
* gnu/packages/mail.scm (exim): Update to 4.86.
 2015-12-25 23:42:17 -05:00
Leo Famulari fc6fdc05cb gnu: exim: Add alternate URL. 
* gnu/packages/mail.scm (exim)[source]: Add alternate URL.
 2015-12-25 23:42:17 -05:00
Leo Famulari e1921a384c gnu: eudev: Update home-page URL. 
* gnu/packages/linux.scm (eudev)[home-page]: Add up-to-date URL.
 2015-12-25 23:40:32 -05:00
Ricardo Wurmus 9625029401 gnu: Add Bristol. 
* gnu/packages/music.scm (bristol): New variable.
 2015-12-24 19:39:17 +01:00
Ricardo Wurmus 398abcf81a gnu: lilypond: Update to 2.19.33. 
* gnu/packages/music.scm (lilypond): Update to 2.19.33.
 2015-12-24 10:10:40 +01:00
Ricardo Wurmus 409be57b09 gnu: lilypond: Build info pages with images. 
* gnu/packages/music.scm (lilypond)[arguments]: Set "conf" and "out" to
  "www"; rename phase "hardcode-path-to-gs" to "fix-path-references";
  fix reference to "/bin/sh"; add phase "install-info".
 2015-12-24 10:10:40 +01:00
Ricardo Wurmus c493679f9a gnu: Add Yoshimi. 
* gnu/packages/music.scm (yoshimi): New variable.
 2015-12-24 10:10:40 +01:00
Ricardo Wurmus 6a91494898 gnu: Add XML::Compile::WSDL11. 
* gnu/packages/xml.scm (perl-xml-compile-wsdl11): New variable.
 2015-12-24 10:10:40 +01:00
Ricardo Wurmus baeab9b8b9 gnu: Add XML::Compile::SOAP. 
* gnu/packages/xml.scm (perl-xml-compile-soap): New variable.
 2015-12-24 10:10:40 +01:00
Ricardo Wurmus c1d41b5df3 gnu: Add XML::Compile::Cache. 
* gnu/packages/xml.scm (perl-xml-compile-cache): New variable.
 2015-12-24 10:10:40 +01:00
Ricardo Wurmus f7c4dc2f55 gnu: Add XML::LibXML::Simple. 
* gnu/packages/xml.scm (perl-xml-libxml-simple): New variable.
 2015-12-24 10:10:40 +01:00
Ricardo Wurmus 8aad646637 gnu: Add File::Slurp::Tiny. 
* gnu/packages/perl.scm (perl-file-slurp-tiny): New variable.
 2015-12-24 10:10:40 +01:00
Ricardo Wurmus a05996e000 gnu: Add HTML::Template. 
* gnu/packages/web.scm (perl-html-template): New variable.
 2015-12-24 10:10:40 +01:00
Ricardo Wurmus b494a5f1bd gnu: Add XML::Compile. 
* gnu/packages/xml.scm (perl-xml-compile): New variable.
 2015-12-24 10:10:40 +01:00
Ricardo Wurmus 649e1676bc gnu: Add XML::Compile::Tester. 
* gnu/packages/xml.scm (perl-xml-compile-tester): New variable.
 2015-12-24 10:10:40 +01:00
Ricardo Wurmus dd686c0838 gnu: Add Log::Report. 
* gnu/packages/perl.scm (perl-log-report): New variable.
 2015-12-24 10:10:39 +01:00
Ricardo Wurmus fc2448bf89 gnu: Add Log::Report::Optional. 
* gnu/packages/perl.scm (perl-log-report-optional): New variable.
 2015-12-24 10:10:39 +01:00
Ricardo Wurmus c47b85de0c gnu: Add String::Print. 
* gnu/packages/perl.scm (perl-string-print): New variable.
 2015-12-24 10:10:39 +01:00
Ricardo Wurmus e92468d803 gnu: Add Unicode::LineBreak. 
* gnu/packages/perl.scm (perl-unicode-linebreak): New variable.
 2015-12-24 10:10:39 +01:00
Ricardo Wurmus 55932aeee1 gnu: Add MIME::Charset. 
* gnu/packages/perl.scm (perl-mime-charset): New variable.
 2015-12-24 10:10:39 +01:00
Leo Famulari 8f1640ed8f gnu: gusb: Update home-page. 
* gnu/packages/gnome.scm (gusb)[home-page]: Update home-page.
 2015-12-24 02:16:57 -05:00
Mark H Weaver 097190417f gnu: icecat: Update to 38.5.0-gnu1. 
* gnu/packages/patches/icecat-CVE-2015-7201-pt1.patch,
  gnu/packages/patches/icecat-CVE-2015-7201-pt2.patch,
  gnu/packages/patches/icecat-CVE-2015-7201-pt3.patch,
  gnu/packages/patches/icecat-CVE-2015-7205.patch,
  gnu/packages/patches/icecat-CVE-2015-7210.patch,
  gnu/packages/patches/icecat-CVE-2015-7212.patch,
  gnu/packages/patches/icecat-CVE-2015-7213-pt1.patch,
  gnu/packages/patches/icecat-CVE-2015-7213-pt2.patch,
  gnu/packages/patches/icecat-CVE-2015-7214.patch,
  gnu/packages/patches/icecat-CVE-2015-7222-pt1.patch,
  gnu/packages/patches/icecat-CVE-2015-7222-pt2.patch,
  gnu/packages/patches/icecat-CVE-2015-7222-pt3.patch,
  gnu/packages/patches/icecat-freetype-2.6.patch: Delete files.
* gnu-system.am (dist_patch_DATA): Remove them.
* gnu/packages/gnuzilla.scm (icecat): Update to 38.5.0-gnu1.
  [source]: Remove patches.
 2015-12-23 18:19:59 -05:00
Mark H Weaver bba5de0e43 gnu: nss: Update to 3.20.2. 
* gnu/packages/gnuzilla.scm (nss): Update to 3.20.2.
 2015-12-23 18:19:59 -05:00
Ben Woodcroft 1b9d4e2e20 gnu: ruby-nokogiri: Upgrade to 1.6.7.1. 
* gnu/packages/ruby.scm (ruby-nokogiri): Upgrade to 1.6.7.1.
 2015-12-23 14:02:10 -05:00
Ben Woodcroft d000fc92b1 gnu: Add ruby-mini-portile-2. 
* gnu/packages/ruby.scm (ruby-mini-portile-2): New variable.
 2015-12-23 14:02:06 -05:00
Ricardo Wurmus 4de7aede50 gnu: icedtea7: Update to 2.6.3. 
* gnu/packages/java.scm (icedtea7): Update to 2.6.3.
 2015-12-23 14:57:58 +01:00
Ricardo Wurmus e7173df87a gnu: icedtea6: Update to 1.13.9. 
* gnu/packages/java.scm (icedtea6): Update to 1.13.9.
 2015-12-23 14:57:58 +01:00
Ludovic Courtès 05f1e95638 gnu: guile-2.0: Add "lib/guile/2.0/ccache" to the search path. 
* gnu/packages/guile.scm (guile-2.0)[native-search-paths]: Add
"lib/guile/2.0/ccache" to GUILE_LOAD_COMPILED_PATH.
 2015-12-22 22:29:34 +01:00
Ludovic Courtès 64cb064c0c gnu: python-wrapper: Append "-wrapper" to the underlying package name. 
Reported by Federico Beffa <beffa@ieee.org>.

* gnu/packages/python.scm (wrap-python3): Change the default value of
'name' to include the name of PYTHON.  This disambiguates between
'python-minimal-wrapper' and 'python-wrapper'.
 2015-12-22 22:24:41 +01:00
Efraim Flashner a9257a873f gnu: libmicrohttpd: Update to 0.9.48. 
* gnu/packages/gnunet.scm (libmicrohttpd): Update to 0.9.48.
 2015-12-22 22:50:58 +02:00
Efraim Flashner 0877ef4342 gnu: parallel: Update to 20151222. 
* gnu/packages/parallel.scm (parallel): Update to 20151222.
 2015-12-22 22:47:44 +02:00
Efraim Flashner 419fa59b17 gnu: sipwitch: Update to 1.9.15. 
* gnu/packages/telephony.scm (sipwitch): Update to 1.9.15.
 2015-12-22 22:45:41 +02:00
Efraim Flashner 99e6f9c828 gnu: ucommon: Update to 7.0.0. 
* gnu/packages/telephony.scm (ucommon): Update to 7.0.0.
[inputs]: Add gnutls.
 2015-12-22 22:39:48 +02:00
Mark H Weaver e54465ff85 gnu: isc-dhcp: Disable parallel build. 
* gnu/packages/admin.scm (isc-dhcp)[arguments]: Disable parallel build.
 2015-12-22 10:45:13 -05:00
Mark H Weaver 6548b1e122 gnu: isc-dhcp: Update to 4.3.3; update bundled bind to 9.9.8-P2. 
Fixes CVE-2015-8000 and CVE-2015-8461.

* gnu/packages/admin.scm (isc-dhcp): Update to 4.3.3.
  [inputs]: Add 'bind-source-tarball'.
  [arguments]: Use modify-phases.  Add 'replace-bundled-bind' phase.
  In 'post-configure' phase, avoid hard-coding version numbers of
  bundled bind.
 2015-12-21 19:47:27 -05:00
Mark H Weaver f9a5b18897 gnu: bind-utils: Update to 9.10.3-P2. 
* gnu/packages/dns.scm (bind-utils): Update to 9.10.3-P2.
  [source]: Use HTTP URI instead of FTP.
 2015-12-21 19:47:26 -05:00
Ludovic Courtès ab64483f64 file-systems: The 'device' field can be a UUID (bytevector). 
Previously a wrong-type-arg error would be raised when a file system
with a UUID (bytevector) field was encountered.

* gnu/system.scm (other-file-system-services)[device-mappings]: Check
whether FS's device is a string.
 2015-12-22 00:29:43 +01:00
Ludovic Courtès be21979d85 file-systems: Add a 'mount?' field. 
Fixes <http://bugs.gnu.org/22176>.
Reported by Florian Paul Schmidt <mista.tapas@gmx.net>.

* gnu/system/file-systems.scm (<file-system>)[mount?]: New field.
(file-system->spec): Adjust accordingly.
* gnu/services/base.scm (file-system-dmd-service): Return the empty list
when FILE-SYSTEM has 'mount?' set to false.
(user-processes-service): Select the subset of FILE-SYSTEMS that matches
'file-system-mount?'.
* doc/guix.texi (File Systems): Document it.
 2015-12-22 00:29:21 +01:00
Ludovic Courtès e43e84ba7a services: Add 'fstab-service-type'. 
* gnu/services/base.scm (file-system->fstab-entry)
(file-systems->fstab): New procedures.
(fstab-service-type): New variable.
* gnu/services/base.scm (file-system-dmd-service): New procedure, taken
from...
(file-system-service-type): ... here.
* gnu/system.scm (essential-services): Add FSTAB-SERVICE-TYPE instance.
 2015-12-22 00:04:36 +01:00
Ricardo Wurmus 8e92cfb101 gnu: Add vmpk. 
* gnu/packages/music.scm (vmpk): New variable.
 2015-12-21 22:09:47 +01:00
Ricardo Wurmus bf76d7802c gnu: Add drumstick. 
* gnu/packages/music.scm (drumstick): New variable.
 2015-12-21 22:09:47 +01:00
Leo Famulari ef9006451f gnu: letsencrypt and acme: Update to 0.1.1. 
These packages should be updated together.

* gnu/packages/tls.scm (letsencrypt): Update to 0.1.1.
[source]: Use pypi-uri.
* gnu/packages/tls.scm (acme): Update to 0.1.1.
[source]: Use pypi-uri.
 2015-12-21 14:35:58 -05:00
Efraim Flashner 704989660f gnu: ffmpeg: Update to 2.8.4. 
* gnu/packages/video.scm (ffmpeg): Update to 2.8.4.
 2015-12-21 21:30:46 +02:00
Leo Famulari d12717cba0 doc: Be more explicit in example of file-systems configuration. 
* gnu/system/examples/bare-bones.tmpl (file-systems): Change device
label.
* gnu/system/examples/desktop.tmpl (file-systems): Likewise.
 2015-12-21 13:12:07 -05:00
Leo Famulari f0150f8724 gnu: grub: Add fix for CVE-2015-8730. 
* gnu/packages/patches/grub-CVE-2015-8370.patch: New file.
* gnu-system.am (dist_patch_DATA): Register patch.
* gnu/packages/grub.scm: Apply patch.
 2015-12-21 12:33:55 -05:00
Ricardo Wurmus e2cd1d0fb9 gnu: Add GenomicRanges. 
* gnu/packages/bioinformatics.scm (r-genomicranges): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus 0e7d5560de gnu: Add XVector. 
* gnu/packages/bioinformatics.scm (r-xvector): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus bf7764b74f gnu: Add GenomeInfoDb. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus 78addcb0eb gnu: Add IRanges. 
* gnu/packages/bioinformatics.scm (r-iranges): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus 7485129e4f gnu: Add S4Vectors. 
* gnu/packages/bioinformatics.scm (r-s4vectors): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus d29b25c490 gnu: Add BiocGenerics. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus 9fba89e829 gnu: Add r-acsnminer. 
* gnu/packages/bioinformatics.scm (r-acsnminer): New variable.
 2015-12-21 17:21:26 +01:00
Ricardo Wurmus 9e47f30b08 gnu: Add r-gridextra. 
* gnu/packages/statistics.scm (r-gridextra): New variable.
 2015-12-21 17:21:26 +01:00
Ricardo Wurmus b73751c8ff gnu: Add r-gtable. 
* gnu/packages/statistics.scm (r-gtable): New variable.
 2015-12-21 17:21:26 +01:00
Ricardo Wurmus 77bdb276e9 gnu: Add r-rmarkdown. 
* gnu/packages/statistics.scm (r-rmarkdown): New variable.
* gnu/packages/haskell.scm: Do not select libxml2 from the xml module to
  prevent circular package module imports.
 2015-12-21 17:13:44 +01:00
Ricardo Wurmus 4c1f2705b5 gnu: Add r-catools. 
* gnu/packages/statistics.scm (r-catools): New variable.
 2015-12-21 17:13:44 +01:00
Ricardo Wurmus bb6d2dadf7 gnu: Add r-bitops. 
* gnu/packages/statistics.scm (r-bitops): New variable.
 2015-12-21 17:13:44 +01:00
Ricardo Wurmus 8406138b72 gnu: Add AdaptiveSparsity. 
* gnu/packages/machine-learning.scm (r-adaptivesparsity): New variable.
 2015-12-21 16:05:38 +01:00
Ricardo Wurmus e22d4ca4c4 gnu: Add r-rcpparmadillo. 
* gnu/packages/maths.scm (armadillo-for-rcpparmadillo): New variable.
* gnu/packages/statistics.scm (r-rcpparmadillo): New variable.
 2015-12-21 16:05:37 +01:00
Ricardo Wurmus b15e47f9e6 gnu: Add armadillo. 
* gnu/packages/maths.scm (armadillo): New variable.
 2015-12-21 15:47:40 +01:00
Ricardo Wurmus 086e498bcf gnu: Add libgit2. 
* gnu/packages/version-control.scm (libgit2): New variable.
 2015-12-21 15:22:14 +01:00
Ben Woodcroft 02f35bb5a7 gnu: mafft: Update to 7.267. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.267.
[arguments]: Don't include mafft-homologs manpage.
[inputs]: Add gawk and grep.
[propagated-inputs]: Add coreutils.
 2015-12-21 15:16:01 +01:00
Mathieu Lirzin 1ef3f91a70 gnu: rxvt-unicode: Install the terminal capability data. 
This provides the necessary terminal capability data, which are required
by ncurses-based applications.

* gnu/packages/xdisorg.scm (rxvt-unicode)[native-inputs]: Add ncurses.
[arguments]: Set the destination of the terminfo files.
[native-search-path]: New field.  Make them automatically available to
the user.
 2015-12-21 13:35:34 +01:00
Efraim Flashner 72d8b5baf4 gnu: msmtp: Update to 1.6.3. 
* gnu/packages/mail.scm (msmtp): Update to 1.6.3.
[inputs]: Add libsecret.
 2015-12-21 09:36:15 +02:00
Efraim Flashner ec92806ae5 gnu: claws-mail: Update to 3.13.1. 
* gnu/packages/mail.scm (claws-mail): Update to 3.13.1.
 2015-12-21 09:17:47 +02:00
Efraim Flashner 56918e26cf gnu: python-cython: Update to 0.23.4. 
* gnu/packages/python.scm (python-cython): Update to 0.23.4.
 2015-12-21 06:55:13 +02:00
David Thompson e99711af22 gnu: ruby: Update to 2.2.4. 
This version fixes CVE-2015-7551.

* gnu/packages/ruby.scm (ruby): Update to 2.2.4.
 2015-12-20 22:40:53 -05:00
Ludovic Courtès 724a7d9c74 packages: Remove now redundant graph procedures. 
These procedures are now redundant with those in (guix graph) and are no
longer used since commit a51cbecb.

* gnu/packages.scm (vhash-refq, package-dependencies)
(package-direct-dependents, package-transitive-dependents)
(package-covering-dependents): Remove.
 2015-12-20 22:34:22 +01:00
Efraim Flashner 54b7f63a72 gnu: offlineimap: Update to 6.6.0. 
* gnu/packages/mail.scm (offlineimap): Update to 6.6.0.
 2015-12-20 21:39:18 +02:00
Efraim Flashner b5d47a5a53 gnu: gnupg: Update to 1.4.20. 
* gnu/packages/gnupg.scm (gnupg-1): Update to 1.4.20.
 2015-12-20 20:07:31 +02:00
宋文武 a4df575631 gnu: Add gnome-shell. 
* gnu/packages/gnome.scm (gnome-shell): New variable.
 2015-12-20 18:59:22 +08:00
宋文武 b645146f00 gnu: Add gnome-control-center. 
* gnu/packages/gnome.scm (gnome-control-center): New variable.
 2015-12-20 18:59:22 +08:00
宋文武 b96c42605b gnu: Add gnome-bluetooth. 
* gnu/packages/gnome.scm (gnome-bluetooth): New variable.
 2015-12-20 18:59:22 +08:00
宋文武 8e1dd04f45 gnu: Add libgtop. 
* gnu/packages/gnome.scm (libgtop): New variable.
 2015-12-20 18:59:21 +08:00
宋文武 e682327976 gnu: Add colord-gtk. 
* gnu/packages/freedesktop.scm (colord-gtk): New variable.
 2015-12-20 18:59:21 +08:00
宋文武 6976e7d2ff gnu: Add telepathy-logger. 
* gnu/packages/freedesktop.scm (telepathy-logger): New variable.
 2015-12-20 18:59:21 +08:00
Efraim Flashner ff80b96378 gnu: tilda: Update to 1.3.1. 
* gnu/packages/terminals.scm (tilda): Update to 1.3.1.
 2015-12-20 09:40:56 +02:00
Ludovic Courtès 604d20a251 gnu: Add tlsdate. 
* gnu/packages/ntp.scm (tlsdate): New variable.
 2015-12-19 23:16:18 +01:00
宋文武 04dc6c9992 gnu: mpv: Update to 0.14.0. 
* gnu/packages/video.scm (mpv): Update to 0.14.0.
 2015-12-19 12:21:59 +08:00
宋文武 599fd84227 gnu: mpv: Fix build by using pkg-config for smbclient. 
This is a followup to commit 710964d.

* gnu/packages/video.scm (mpv)[arguments]: Remove 'patch-wscript' phase.
 2015-12-19 12:15:59 +08:00
Ludovic Courtès 7db0799dc9 gnu: agg: Update URLs. 
* gnu/packages/graphics.scm (agg)[source, home-page]: Add up-to-date
URLs.
 2015-12-19 00:42:10 +01:00
Ludovic Courtès 3ac732715d gnu: Use #:prefix when importing (guix licenses). 
This works around a problem with #:hide, whereby Guile would report
'zlib', 'openssl', and/or 'expat as colliding bindings at run time
despite the #:hide.

* gnu/packages/linux.scm: Use #:prefix license for (guix licenses).
* gnu/packages/haskell.scm: Likewise.
 2015-12-19 00:34:00 +01:00
Ludovic Courtès 793bcc1933 gnu: Do not #:select from (gnu packages …) modules. 
This is to avoid <http://bugs.gnu.org/15540>.

* gnu/packages/bittorrent.scm: Do not #:select from (gnu packages
compression).
* gnu/packages/dictionaries.scm: Likewise.
* gnu/packages/disk.scm: Likewise.
* gnu/packages/gimp.scm: Likewise.
* gnu/packages/haskell.scm: Likewise.
 2015-12-19 00:22:42 +01:00
Ludovic Courtès 53088d0045 gnu: commencement: Build Bison deterministically. 
Before that entries in liby.a would contain the build time.

* gnu/packages/commencement.scm (bison-boot1): Add #:make-flags.
 2015-12-19 00:02:37 +01:00
Ludovic Courtès f1e0c85ad2 gnu: commencement: Build the final Bash with "bison-boot1". 
This removes a round of Bison + Flex + M4 + Perl rebuild.

* gnu/packages/commencement.scm (bash-final): Add 'native-inputs'
field pointing to BISON-BOOT1.
 2015-12-18 23:57:11 +01:00
Ludovic Courtès 32243bfb57 gnu: commencement: Avoid redundant Perl rebuild. 
This removes a redundant (yet different) "perl-boot0" node from the
early derivation graph.

* gnu/packages/commencement.scm (bison-boot1): Move 'native-inputs'
field to the final package.  Previously PERL-BOOT0 got rebuilt with
%BOOT0-INPUTS, leading to a different derivation.
(static-bash-for-glibc): Likewise.
 2015-12-18 23:53:00 +01:00
Ludovic Courtès 09964b4fc6 gnu: commencement: Add "-boot0" to early packages. 
* gnu/packages/commencement.scm (diffutils-boot0)[name]: New field.
* gnu/packages/commencement.scm (findutils-boot0, file-boot0,
perl-boot0): Change 'name' field to include "-boot0".
 2015-12-18 22:19:07 +01:00
Ludovic Courtès 009b53fd1c gnu: gcc: Prefer language-specific variables over 'CPATH'. 
Suggested by Andy Wingo <wingo@igalia.com>.
Fixes <http://bugs.gnu.org/22186>.

* gnu/packages/gcc.scm (gcc-4.7)[native-search-paths]: Remove 'CPATH';
add 'C_INCLUDE_PATH' and 'CPLUS_INCLUDE_PATH' instead.
* gnu/packages/gcc.scm (custom-gcc): Add 'search-paths' parameter and
honor it.
(%generic-search-paths): New variable.
(gfortran-4.8, gfortran-4.9, gfortran, gfortran-5, gccgo-4.8): Pass
%GENERIC-SEARCH-PATHS to 'custom-gcc'.
(gcj)[native-search-paths]: New field.
(gcc-objc-4.8, gcc-objc++-4.8): Use 'OBJC_INCLUDE_PATH' and
'OBJCPLUS_INCLUDE_PATH', respectively.
 2015-12-18 21:38:49 +01:00
Ludovic Courtès 8309c3899a gnu: commencement: Use GMP 6.0.0a for bootstrapping. 
* gnu/packages/multiprecision.scm (gmp-6.0): New variable.
* gnu/packages/commencement.scm (gcc-boot0, gcc-final): Use it.
* gnu/packages/patches/gmp-arm-asm-nothumb.patch: New file, reinstated
from before e414a7d.
* gnu-system.am (dist_patch_DATA): Add it.
 2015-12-18 18:38:22 +01:00
Ludovic Courtès bf46f74160 gnu: key-mon: Remove unnecessary propagated inputs. 
* gnu/packages/key-mon.scm (key-mon)[propagated-inputs]: Rename to...
[inputs]: ... this.  Propagated was unnecessary since the 'key-mon'
program is wrapped.
 2015-12-18 11:04:22 +01:00
Ludovic Courtès 594e7b479a gnu: python2-pygtk: Add "doc" output. 
* gnu/packages/gtk.scm (python2-pygtk)[outputs]: New field.
[arguments]: Add 'set-gtk-doc-directory' phase.
 2015-12-18 11:04:22 +01:00