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Author SHA1 Message Date
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
Ben Woodcroft 869cda545d import: gem: Beautify description field. 
* guix/import/gem.scm (gem->guix-package): Use 'beautify-description'.
 2016-01-14 19:44:40 +10:00
Ben Woodcroft 2028a2c960 import: cran: Move beautify-description to utils module. 
* guix/import/cran.scm (beautify-description): Move from here...
* guix/import/utils.scm: ... to here.
 2016-01-14 19:44:36 +10:00
Alex Kost 6b3a1ce8d7 emacs: Fix heading face in "Package Info". 
Reported by Ludovic Courtès <ludo@gnu.org> on #guix.
This fixes a regression introduced in commit 7171d824.

'insert-text-button' procedure does not allow to override a button face,
so a specialized button type should be used instead.

* emacs/guix-ui-package.el (guix-package-heading): New button type.
  (guix-package-info-insert-heading): Use it.
 2016-01-14 01:12:24 +03:00
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
Ludovic Courtès 7a2eed3aac hydra: Add missing phase and inputs for 'make dist' job. 
* build-aux/hydra/guix.scm (tarball-package): Inherit from 'guix-devel'
rather than 'guix'.  Pass #:phases to 'dist-package'.
 2016-01-13 17:43:21 +01:00
Ludovic Courtès b8a35309f8 build-system/gnu: 'dist-package' can be passed the phases. 
* guix/build-system/gnu.scm (dist-package): Add #:phases parameter and
honor it.
 2016-01-13 17:43:21 +01:00
Ludovic Courtès 8c9ef2c3a2 monad-repl: Close connection when leaving the monad REPL. 
* guix/monad-repl.scm (store-monad-language): Add 'store' parameter and
use it.  Remove call to 'open-connection'.
(enter-store-monad): Use 'with-store' and pass the store to
'store-monad-language.
 2016-01-13 17:43:21 +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
Alex Kost 6d268e5281 emacs: Move loading packages to "guix-emacs.el". 
* emacs/guix-init.el: Move the code for auto-loading Emacs packages to...
  (guix-package-enable-at-startup): Move to...
* emacs/guix-emacs.el (guix-package-enable-at-startup): ... here.
 2016-01-13 17:56:14 +03:00
Alex Kost e4e2154644 emacs: Make "guix-emacs.el" independent. 
"guix-emacs.el" may be used just for "instructing" Emacs where to find
Emacs packages installed with Guix, so it should have as few
dependencies as possible.

See <http://lists.gnu.org/archive/html/guix-devel/2016-01/msg00022.html>.

* emacs/guix-emacs.el: Require 'guix-profiles' optionally.
  (guix-emacs-load-autoloads): Use 'guix-profile-prompt' only if it is
  available.
 2016-01-13 17:56:14 +03:00
Alex Kost 08207339aa emacs: Complete --file in 'guix build' popup. 
* emacs/guix-command.el (guix-command-improve-build-argument): Use
  'guix-read-file-name' to complete --file option.
 2016-01-13 17:55:47 +03:00
Alex Kost 883fc5ed42 emacs: Add missing shell completions. 
* emacs/guix-pcomplete.el (guix-pcomplete-complete-option-arg): Complete
  file name for '--install-from-file' option of 'guix package' command,
  and for '--file' and '--with-source' options of 'guix build' command.
 2016-01-13 17:55:47 +03:00
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 93ce8a8e00 build: Use 127 as the Linux hash-bang limit. 
Reported by taylanbayirli@gmail.com (Taylan Ulrich Bayırlı/Kammer).

* m4/guix.m4 (LINUX_HASH_BANG_LIMIT): Set to 127.
 2016-01-13 11:13:34 +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
Leo Famulari 0917e80ea8 doc: Fix typo in "Build Systems". 
* doc/guix.texi (Build Systems): Remove extra 's'.
 2016-01-12 17:55:59 -05:00
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
Ludovic Courtès bb25130764 build: 'make check' errors out if file name limits would be hit. 
* Makefile.am (SCM_TESTS, SH_TESTS, TESTS, AM_TESTS_ENVIRONMENT)
(SCM_LOG_COMPILER, SH_LOG_COMPILER, AM_SCM_LOG_FLAGS)
(AM_SH_LOG_FLAGS): Move within 'if CAN_RUN_TESTS'.
(check-local) [!CAN_RUN_TESTS]: New target.
* daemon.am (AM_TESTS_ENVIRONMENT, TESTS): Ditto.
* m4/guix.m4 (GUIX_CHECK_FILE_NAME_LIMITS): Add parameter and set it.
 2016-01-12 17:47:36 +01:00
Ludovic Courtès 27ab3cee75 build: Warn against long hash bang lines for tests. 
* m4/guix.m4 (GUIX_TEST_HASH_BANG_LENGTH): New macro.
(GUIX_CHECK_FILE_NAME_LIMITS): Use it.  Warn against long hash bang
lines in tests.
 2016-01-12 17:47:36 +01:00
Ludovic Courtès d33fa0c714 doc: Show bootstrapping at the package level. 
* doc/images/bootstrap-packages.dot: New file.
* doc.am (DOT_FILES): Add it.
* doc/guix.texi (Bootstrapping): Show 'guix graph' commands.  Includes
'images/bootstrap-packages' and comment it.
 2016-01-12 17:47:36 +01:00
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
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
Taylan Ulrich Bayırlı/Kammer ce9a304251 build: Fix out-of-tree building of documentation. 
* doc.am (.dot.png, .dot.pdf, .dot.eps): Put the generated files into
  $(srcdir).
 2016-01-10 22:30:29 +01:00
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
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 17ad0a2714 build-system/python: 'pypi-uri' takes an optional file name extension. 
Suggested by swedebugia <swedebugia@riseup.net>.

* guix/build-system/python.scm (pypi-uri): Add 'extension' parameter and
use it.
 2016-01-08 19:06:26 +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