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Author SHA1 Message Date
Ricardo Wurmus
4cd07e487e
gnu: r-genomeinfodb: Update to 1.10.3. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.3.
[propagated-inputs]: Add "r-rcurl".
 2017-04-06 14:39:11 +02:00
Ricardo Wurmus
acbeb2d56b
gnu: r-xvector: Update to 0.14.1. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.1.
 2017-04-06 14:39:11 +02:00
Ricardo Wurmus
da250f733a
gnu: r-bioccheck: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.10.1.
[propagated-inputs]: Remove "r-knitr" and "r-devtools".
 2017-04-06 14:39:11 +02:00
Ricardo Wurmus
d51f05f769
gnu: r-tidyr: Update to 0.6.1. 
* gnu/packages/statistics.scm (r-tidyr): Update to 0.6.1.
[propagated-inputs]: Add "r-tibble".
 2017-04-06 14:39:10 +02:00
Ricardo Wurmus
1db293757b
gnu: r-roxygen2: Update to 6.0.1. 
* gnu/packages/statistics.scm (r-roxygen2): Update to 6.0.1.
[propagated-inputs]: Add "r-commonmark", "r-desc", "r-r6", and "r-xml2".
 2017-04-06 14:39:10 +02:00
Ricardo Wurmus
bf6dcf59eb
gnu: Add r-commonmark. 
* gnu/packages/statistics.scm (r-commonmark): New variable.
 2017-04-06 14:39:10 +02:00
Ricardo Wurmus
1cbb07a8e4
gnu: Add r-desc. 
* gnu/packages/statistics.scm (r-desc): New variable.
 2017-04-06 14:39:10 +02:00
Ricardo Wurmus
67deeea41b
gnu: r-readr: Update to 1.1.0. 
* gnu/packages/statistics.scm (r-readr): Update to 1.1.0.
[propagated-inputs]: Remove "r-curl".
 2017-04-06 14:39:09 +02:00
Ricardo Wurmus
33eb555e6f
gnu: r-tibble: Update to 1.3.0. 
* gnu/packages/statistics.scm (r-tibble): Update to 1.3.0.
[propagated-inputs]: Remove "r-assertthat".
 2017-04-06 14:39:09 +02:00
Ricardo Wurmus
aad7808526
gnu: r-jsonlite: Update to 1.3. 
* gnu/packages/web.scm (r-jsonlite): Update to 1.3.
 2017-04-06 14:39:09 +02:00
Ricardo Wurmus
538bce2472
gnu: ldc-bootstrap: Delete failing test. 
* gnu/packages/ldc.scm (ldc-bootstrap)[arguments]: Delete failing test in
build phase.
 2017-04-06 14:34:12 +02:00
Ludovic Courtès
cb5be6df91
gnu: guile-aspell: Switch to Guile 2.2. 
* gnu/packages/guile.scm (guile-aspell)[inputs]: Replace GUILE-2.0 with
GUILE-2.2.
 2017-04-06 10:45:55 +02:00
Ludovic Courtès
7295087eb1
gnu: guile-aspell: Remove hard-coded "site/2.0" from $(guilesitedir). 
* gnu/packages/guile.scm (guile-aspell)[arguments]: Remove
  #:configure-flags.  Add 'set-guilesitedir' phase.
 2017-04-06 10:42:51 +02:00
Ludovic Courtès
234ea3d653
gnu: guile-aspell: Update to 0.4. 
* gnu/packages/guile.scm (guile-aspell): Update to 0.4.
[arguments] <#:phases>: Adjust 'set-libaspell-file-name' to new source
tree layout.
 2017-04-06 10:37:52 +02:00
Chris Marusich
5ea69d9a56
system: Support the --root option in 'guix system'. 
Fixes <https://bugs.gnu.org/26271>.

* guix/scripts/system.scm (perform-action): Add #:gc-root parameter and
honor it.
(show-help): Document the --root option.
(%options): Add 'root'.
(process-action): Pass 'root' option to perform-action as #:gc-root.
* doc/guix.texi (Invoking guix system): Document '--root'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-04-06 10:24:32 +02:00
Chris Marusich
a09b45da6f
build: Add and export procedure 'register-root*'. 
* guix/scripts/build.scm (register-root*): Add and export it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-04-06 10:11:26 +02:00
Ludovic Courtès
50f4ea18c4
environment: Deal with single-entry search paths. 
This is a followup to fcd75bdbfa.

* guix/scripts/environment.scm (create-environment): Check whether
SEPARATOR is #f.
 2017-04-05 22:50:21 +02:00
Ludovic Courtès
31f1f593fb
doc: Add "Documentation" section. 
* doc/guix.texi (Documentation): New node.
 2017-04-05 22:45:42 +02:00
Maxim Cournoyer
a0b87ef8ec
profiles: Generate database file for man pages. 
The mandb database file (index.db) is used by the "apropos" (whatis) or
"man -k" commands.  This change introduces a profile hook to generate
such database file.

* guix/profiles.scm (manual-database): New procedure.
(%default-profile-hooks): Add it.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2017-04-05 22:45:41 +02:00
Ludovic Courtès
1618006d0b
build-system/python: 'package-with-explicit-python' uses 'package-mapping'. 
* guix/build-system/python.scm (package-with-explicit-python)
[package-variant, cut?]: New procedures.
[transform]: Remove 'mlambdaq' form and input tuple handling.
Use 'package-mapping'.
 2017-04-05 22:45:41 +02:00
Ludovic Courtès
f37f2b83fa
packages: Add 'package-mapping' and base 'package-input-rewriting' on it. 
* guix/packages.scm (package-mapping): New procedure.
(package-input-rewriting): Rewrite in terms of 'package-mapping'.
* tests/packages.scm ("package-mapping"): New test.
* doc/guix.texi (Defining Packages): Document it.
 2017-04-05 22:45:41 +02:00
Ludovic Courtès
79f912c710
Revert "gnu: openexr: Add IlmBase include sub-directory to 'OpenEXR.pc'." 
This reverts commit 01fe019166,
which was unneeded because IlmBase is already listed as 'Requires'
in 'OpenEXR.pc'.
 2017-04-05 22:45:41 +02:00
Tobias Geerinckx-Rice
b28187cd0c
Revert "gnu: bc: Update to 1.07." 
This reverts commit dfee7daedb.  It causes
the linux-libre@4.9 build to hang (command-line usage works fine).
 2017-04-05 21:23:41 +02:00
Kei Kebreau
cd381c317b
gnu: Move audacity to audio.scm. 
* gnu/packages/audacity.scm: Remove file and move audacity...
* gnu/packages/audio.scm: ...here.
* gnu/local.mk: Remove reference to removed file.
 2017-04-05 15:08:14 -04:00
Ricardo Wurmus
5ae63362ae
import cran: Distinguish Bioconductor data packages. 
* guix/import/cran.scm (bioconductor-package?): Exclude Bioconductor
data packages.
(bioconductor-data-package?): New procedure.
 2017-04-05 18:38:51 +02:00
Ricardo Wurmus
1108a920bd
gnu: sra-tools: Fix glibc naming conflict. 
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Add build phase
"patch-away-glibc-conflict" to fix a definition conflict with glibc 2.25.
 2017-04-05 18:06:51 +02:00
Ricardo Wurmus
beebe43176
gnu: sra-tools: Use "modify-phases" syntax. 
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use "modify-phases"
syntax.
 2017-04-05 18:06:51 +02:00
Ben Woodcroft
fc5b12879f
gnu: diamond: Update to 0.8.37. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.37.
 2017-04-05 22:49:01 +10:00
Leo Famulari
b23c1a71be
download: Update the GnuPG mirror list. 
* guix/download.scm (%mirrors) <gnupg>: Use HTTP for TU Wien mirror.
 2017-04-05 07:07:35 -04:00
Thomas Danckaert
52b2d666ca
gnu: kdevelop: Update to 5.1.0. 
* gnu/packages/kde.scm (kdevelop, kdevplatform): Update to 5.1.0.
 2017-04-05 12:12:34 +02:00
Tobias Geerinckx-Rice
dfee7daedb
gnu: bc: Update to 1.07. 
* gnu/packages/algebra.scm (bc): Update to 1.07.
[native-inputs]: Add ed and texinfo.
[arguments]: Use default ‘configure’ phase.
 2017-04-05 03:31:58 +02:00
Tobias Geerinckx-Rice
f0bacad682
gnu: bc: Actually use readline. 
* gnu/packages/algebra.scm (bc)[arguments]: Add ‘--with-readline’
to #:configure-flags.
 2017-04-05 03:31:58 +02:00
Tobias Geerinckx-Rice
5894b60491
gnu: algebra: Re-order imports. 
* gnu/packages/algebra.scm: Order imports alphabetically.
 2017-04-05 03:31:58 +02:00
Ludovic Courtès
01fe019166
gnu: openexr: Add IlmBase include sub-directory to 'OpenEXR.pc'. 
* gnu/packages/graphics.scm (openexr)[arguments]: Add
'set-ilmbase-directory-in-pc-file' phase.
 2017-04-05 00:53:03 +02:00
Ludovic Courtès
f84011d04a
services: cuirass: Wait for networking. 
* gnu/services/cuirass.scm (cuirass-shepherd-service): Add 'networking'
to 'requirements'.
 2017-04-05 00:53:03 +02:00
Chris Marusich
1c6b2d3f98
build: Export register-root procedure. 
* guix/scripts/build.scm: Export register-root procedure.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-04-05 00:53:03 +02:00
Clément Lassieur
8db947169f
gnu: icecat: Use bundled ICU to avoid crashes. 
* gnu/packages/gnuzilla.scm (icecat)[arguments] <#:configure-flags>:
Temporarily comment out "--with-system-icu".
 2017-04-04 20:18:38 +02:00
Clément Lassieur
cca906754d
gnu: icecat: Re-enable parallel build. 
* gnu/packages/gnuzilla.scm (icecat)[arguments]: Re-enable parallel build.
 2017-04-04 20:18:38 +02:00
Marius Bakke
33b2520175
gnu: python-django: Specify CPE name. 
* gnu/packages/django.scm (python-django, python2-django)[properties]: Add
"cpe-name".
 2017-04-04 18:30:52 +02:00
Marius Bakke
dcc9b6abc7
gnu: python-django: Update to 1.10.7 [fixes CVE-2017-7233 and CVE-2017-7234]. 
* gnu/packages/django.scm (python-django, python2-django): Update to 1.10.7.
 2017-04-04 18:01:32 +02:00
Marius Bakke
4dc12417d2
gnu: gnupg: Update to 2.1.20. 
* gnu/packages/gnupg.scm (gnupg): Update to 2.1.20.
[source]: Remove patch.
* gnu/packages/patches/gnupg-2.1-fix-Y2038-test-failure.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-04-04 17:46:28 +02:00
Marius Bakke
a3dea99107
gnu: python2-cython: Fix build on 32-bit platforms. 
* gnu/packages/python.scm (python-cython, python2-cython)[source]: Add patch.
* gnu/packages/patches/python-cython-fix-tests-32bit.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2017-04-04 17:46:28 +02:00
Mark Meyer
6beaa5a02a
gnu: moc: Add Ogg Vorbis support. 
* gnu/packages/music.scm (moc)[inputs]: Add libogg and libvorbis.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2017-04-04 15:16:25 +02:00
Mark Meyer
0d78e37746
gnu: Add qjackctl. 
* gnu/packages/audio.scm (qjackctl): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-04-04 14:30:00 +02:00
Ludovic Courtès
b7506f74df
gnu: glog: Fix name demangling for GCC 5. 
* gnu/packages/patches/glog-gcc-5-demangling.patch: New file.
* gnu/packages/logging.scm (glog)[sources]: Add it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2017-04-04 14:30:00 +02:00
Leo Famulari
6c17422eac
utils: Fix handling of shell arguments for xz compression. 
Fixes test failures related to xz compression in tests/utils.scm.

This is a followup to commit 63102406f2.

* guix/utils.scm (decompressed-port, compressed-port, compressed-output-port):
Split each shell argument into its own list element.
 2017-04-03 23:23:39 -04:00
Tobias Geerinckx-Rice
f49ced6827
gnu: youtube-dl: Update to 2017.04.03. 
* gnu/packages/video.scm (youtube-dl): Update to 2017.04.03.
 2017-04-04 00:17:58 +02:00
Tobias Geerinckx-Rice
f751b7596d
gnu: perl-email-simple: Update to 2.213. 
* gnu/packages/mail.scm (perl-email-simple): Update to 2.213.
 2017-04-04 00:17:58 +02:00
Tobias Geerinckx-Rice
e26f2c67d6
gnu: perl-email-mime: Update to 1.940. 
* gnu/packages/mail.scm (perl-email-mime): Update to 1.940.
 2017-04-04 00:17:57 +02:00
Tobias Geerinckx-Rice
153ea992e8
gnu: perl-lingua-en-tagger: Update to 0.28. 
* gnu/packages/language.scm (perl-lingua-en-tagger): Update to 0.28.
 2017-04-04 00:17:29 +02:00