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12546 Commits

Author SHA1 Message Date
Ricardo Wurmus 84e5368719
gnu: r-evaluate: Update to 0.9. 
* gnu/packages/statistics.scm (r-evaluate): Update to 0.9.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 9a0ccf43cc
gnu: r-bh: Update to 1.60.0-2. 
* gnu/packages/statistics.scm (r-bh): Update to 1.60.0-2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus a76b3f6914
gnu: r-dbi: Update to 0.4-1. 
* gnu/packages/statistics.scm (r-dbi): Update to 0.4-1.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus eb1a5b65c0
gnu: r-rcpp: Update to 0.12.5. 
* gnu/packages/statistics.scm (r-rcpp): Update to 0.12.5.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 8ede249e0a
gnu: r-genomicfeatures: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 192e1ea8d1
gnu: r-summarizedexperiment: Update to 1.2.2. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus d7420566a9
gnu: r-biocparallel: Update to 1.6.2. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 73af676feb
gnu: r-annotationdbi: Update to 1.34.2. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 679e670b36
gnu: r-variantannotation: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.1.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 186ed87337
gnu: r-genomeinfodb: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.1.
 2016-05-20 15:18:23 +02:00
Leo Famulari 0fc4a8afba
gnu: btrfs-progs: Update to 4.5.3. 
* gnu/packages/linux.scm (btrfs-progs): Update to 4.5.3.
 2016-05-19 21:04:22 -04:00
Jelle Licht 0e40755d35
gnu: jemalloc: Update to 4.2.0. 
* gnu/packages/jemalloc.scm (jemalloc): Update to 4.2.0.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2016-05-19 20:43:13 +03:00
Leo Famulari 119b83989d
gnu: expat: Fix CVE-2016-0718. Improve fix for CVE-2015-1283. 
* gnu/packages/patches/expat-CVE-2015-1283-refix.patch,
gnu/packages/patches/expat-CVE-2016-0718.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/xml.scm (expat)[replacement]: New field.
(expat/fixed): New variable.
[source]: Use new patches.
 2016-05-19 10:27:18 -04:00
Ludovic Courtès 9684e30b9b
gnu: flann: Do not install .a files. 
* gnu/packages/maths.scm (flann)[arguments]: Add #:phases.
 2016-05-19 14:51:21 +02:00
Hartmut Goebel 458480235b
gnu: python: Add 'python' variables for different major/minor versions. 
* gnu/packages/python.scm (python-2): Rename variable to...
  (python-2.7): ...this.
  (python-2): Refer to "python-2.7".
  (python): Rename variable to...
  (python-3.4): ...this.
  (python-3): Refer to "python-3.4".
  (python): Refer to "python-3".

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-05-19 14:51:21 +02:00
Ludovic Courtès 39b3033731
gnu: flann: Strip .mex file. 
* gnu/packages/maths.scm (flann)[arguments]: Add #:strip-directories.
 2016-05-19 14:51:21 +02:00
Ben Woodcroft 0947698c42 gnu: Add r-biased-urn. 
* gnu/packages/statistics.scm (r-biased-urn): New variable.
 2016-05-19 22:13:43 +10:00
Efraim Flashner 44c5f0258d
gnu: giflib: Use 'modify-phases'. 
* gnu/packages/image.scm (giflib)[arguments]: Use 'modify-phases'.
 2016-05-19 13:06:49 +03:00
Efraim Flashner 3fdb2a84be
gnu: giflib: Update to 5.1.4 [fixes CVE-2015-7555, CVE-2016-3977]. 
* gnu/packages/image.scm (giflib): Update to 5.1.4.
 2016-05-19 13:01:55 +03:00
humanitiesNerd 5c447e280e
gnu: Add emacs-smartparens. 
*  gnu/packages/emacs.scm (emacs-smartparens): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-05-19 11:45:15 +03:00
Kei Kebreau 21f05134fc
Update name for Kei Kebreau. 
* .mailmap: Add Kei Kebreau.
* gnu/local.mk: Replace "Kei Yamashita" with "Kei Kebreau".
* gnu/packages/calendar.scm: Likewise.
* gnu/packages/dillo.scm: Likewise.
* gnu/packages/fltk.scm: Likewise.
* gnu/packages/game-development.scm: Likewise.
* gnu/packages/games.scm: Likewise.
* gnu/packages/gnome.scm: Likewise.
* gnu/packages/gtk.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/xfce.scm: Likewise.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-05-19 11:42:03 +03:00
Kei Yamashita b7b27a8f28
gnu: octave: Update to 4.0.2. 
* gnu/packages/maths.scm (octave): Update to 4.0.2.
[inputs]: Added cyrus-sasl, openssl.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2016-05-19 04:32:23 +03:00
Ludovic Courtès 91231156ce
gnu: Add ntfs-3g. 
* gnu/packages/linux.scm (ntfs-3g): New variable.
 2016-05-18 23:41:03 +02:00
Kei Yamashita 64851f4a23
gnu: wmbattery: Fix UPower-related memory leak. 
* gnu/packages/gnustep.scm (wmbattery)[source](snippet): New field.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-05-18 23:41:03 +02:00
Efraim Flashner 65e46ca0ed
gnu: qtkeychain: Update to 0.6.2. 
* gnu/packages/qt.scm (qtkeychain): Update to 0.6.2.
 2016-05-18 18:06:47 +03:00
Ben Woodcroft bd9fe0f03b gnu: Add krona-tools. 
* gnu/packages/web.scm (krona-tools): New variable.
 2016-05-18 22:21:52 +10:00
Manolis Ragkousis 0affdfb805 gnu: hurd-headers: Update to 0.8. 
* gnu/packages/hurd.scm (hurd-headers): Update to version 0.8.
 2016-05-18 15:17:52 +03:00
Manolis Ragkousis eb3be3a791 gnu: mig: Update to 1.7. 
* gnu/packages/hurd.scm (mig): Update to version 1.7.
 2016-05-18 15:17:44 +03:00
Manolis Ragkousis 614f39271e gnu: gnumach-headers: Update to 1.7. 
* gnu/packages/hurd.scm (gnumach-headers): Update to version 1.7.
 2016-05-18 15:17:38 +03:00
Ben Woodcroft 7c544991dc gnu: diamond: Do not specify target architecture. 
* gnu/packages/bioinformatics.scm (diamond)[arguments]: Do not
specify target architecture.
 2016-05-18 21:25:06 +10:00
Ricardo Wurmus e62ffce538 gnu: Add Piranha. 
* gnu/packages/bioinformatics.scm (piranha): New variable.
 2016-05-18 11:59:34 +02:00
Efraim Flashner dbd40ac19d
gnu: python2-pandas: Fix native-inputs. 
* gnu/packages/python.scm (python2-pandas)[native-inputs]: Use python2-
versions of python-panda's native-inputs, not of inputs.
 2016-05-18 10:52:41 +03:00
Leo Famulari f1876bfc7a
gnu: Add signify. 
* gnu/packages/crypto.scm (signify): New variable.
 2016-05-17 17:52:59 -04:00
Leo Famulari ad42be8388
gnu: libndp: Update to 1.6 [fixes CVE-2016-3698]. 
* gnu/packages/networking.scm (libndp): Update to 1.6.
 2016-05-17 14:31:09 -04:00
humanitiesNerd 9576cc72dc gnu: Add emacs-zenburn-theme. 
* gnu/packages/emacs.scm (emacs-zenburn-theme): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-05-17 21:06:36 +03:00
Leo Famulari fb2b0f5c87
gnu: gd: Fix-CVE-2016-3074. 
* gnu/packages/patches/gd-CVE-2016-3074.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd)[source]: Use it.
 2016-05-17 13:18:15 -04:00
Ludovic Courtès bbb5d8aeea
gnu: gd: Specify 'cpe-name'. 
* gnu/packages/gd.scm (gd)[properties]: New field.
 2016-05-17 18:15:59 +02:00
Ludovic Courtès 99effc8faa
lint: Honor 'cpe-name' and 'cpe-version' package properties. 
* guix/scripts/lint.scm (package-name->cpe-name): Remove.
(package-vulnerabilities): Honor 'cpe-name' and 'cpe-version'
properties.
* gnu/packages/grub.scm (grub)[properties]: New field.
* gnu/packages/gnuzilla.scm (icecat)[properties]: Add 'cpe-name' and
'cpe-version'.
* doc/guix.texi (Invoking guix lint): Mention 'cpe-name'.
 2016-05-17 18:15:53 +02:00
Federico Beffa 1c29f3ef84 gnu: emacs-constants: Remove old patch. 
* gnu/packages/patches/emacs-constants-lisp-like.patch: Remove it.
* gnu/local.mk (dist_patch_DATA): Remove entry for above patch.
 2016-05-17 14:17:38 +02:00
Ludovic Courtès aa8fff0ceb
store: Clarify 'query-path-hash' docstring. 
* guix/store.scm (query-path-hash): Clarify docstring.
 2016-05-17 14:02:48 +02:00
Ludovic Courtès 149590380a
import: Gracefully report import failures. 
Previously, something like 'guix import gnu which' would spit out a
backtrace if, say, the 'which' tarball could not be authenticated.

* guix/upstream.scm (download-tarball): Mention failure modes in
docstring.
* guix/import/gnu.scm (gnu-package->sexp): Return #f when
'download-tarball' returns #f.
* guix/scripts/import.scm (guix-import): Call 'leave' when IMPORTER does
not return a (package ...) sexp.
 2016-05-17 14:02:48 +02:00
Ludovic Courtès 787afdd0f1
import: Exit with non-zero when an unknown importer is asked. 
* guix/scripts/import.scm (guix-import): Use 'leave' instead of 'format'
when IMPORTER is unknown.
 2016-05-17 14:02:48 +02:00
Federico Beffa f99f3f24ef gnu: emacs-constants: Update to 2.6. 
* gnu/packages/emacs.scm (emacs-constants): Change to versioned repository and
  update to 2.6.
 2016-05-17 14:01:20 +02:00
Ben Woodcroft 849485f5a0 gnu: sortmerna: Update to 2.1b. 
* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1b.
[inputs]: New field.
 2016-05-17 21:45:49 +10:00
Ben Woodcroft daaeed765a gnu: vsearch: Update to 1.11.1. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 1.11.1.
 2016-05-17 21:36:46 +10:00
Ben Woodcroft 122395f9fc gnu: diamond: Update to 0.8.1. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.1.
[source]: Remove 'snippet'.
[build-system]: Use cmake-build-system.
[arguments]: Remove modifications to phases.
[native-inputs]: Remove field.
[inputs]: Remove 'boost'.
 2016-05-17 21:07:00 +10:00
Ludovic Courtès a9e41d2faf
gnu: emacs-constants: Factorize home-page in source URL. 
* gnu/packages/emacs.scm (emacs-constants): Move 'home-page' above.  Use
it in 'uri'.
 2016-05-17 09:41:40 +02:00
Ludovic Courtès 4f04243405
gnu: 'uncompressed-file-fetch' no longer depends on gzip. 
* gnu/packages/emacs.scm (uncompressed-file-fetch): Remove dependency on
GZIP.
 2016-05-17 09:41:40 +02:00
Efraim Flashner cb307c0833
gnu: cflow: Update to 1.5. 
* gnu/packages/code.scm (cflow): Update to 1.5.
 2016-05-17 09:04:38 +03:00
Christopher Allan Webber 11e4c1fd10 gnu: Add geiser-next. 
Also, I previously committed to this repository in 2015; add self to copyright
headers for that year too.

* gnu/packages/emacs.scm (geiser-next): New variable.
 2016-05-16 14:48:57 -05:00