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8008 commits

Author SHA1 Message Date
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
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
Ricardo Wurmus
96101b6718
gnu: r-zlibbioc: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.18.0.
 2016-05-16 20:59:50 +02:00
Ricardo Wurmus
a0fe3aeecf
gnu: r-motifrg: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.16.0.
 2016-05-16 20:59:38 +02:00
Ricardo Wurmus
1f5786a918
gnu: r-seqlogo: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.38.0.
 2016-05-16 20:59:27 +02:00
Ricardo Wurmus
8adc3b628d
gnu: r-genomation: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.0.
 2016-05-16 20:59:14 +02:00
Ricardo Wurmus
7555817c2b
gnu: r-seqpattern: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.4.0.
 2016-05-16 20:59:04 +02:00
Ricardo Wurmus
d1bff89d26
gnu: r-impute: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.46.0.
 2016-05-16 20:58:49 +02:00
Ricardo Wurmus
5190ed1751
gnu: r-bsgenome: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.0.
 2016-05-16 20:58:35 +02:00
Ricardo Wurmus
e48e88c217
gnu: r-topgo: Update to 2.24.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.24.0.
[propagated-inputs]: Add r-matrixstats.
 2016-05-16 20:58:24 +02:00
Ricardo Wurmus
0c56023557
gnu: r-graph: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.50.0.
 2016-05-16 20:58:08 +02:00
Ricardo Wurmus
c12b0a5a30
gnu: r-genomicfeatures: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.0.
 2016-05-16 20:57:55 +02:00
Ricardo Wurmus
d23fbf1eb9
gnu: r-rtracklayer: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.0.
 2016-05-16 20:57:43 +02:00
Ricardo Wurmus
3cd551ea7b
gnu: r-genomicalignments: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.0.
 2016-05-16 20:57:30 +02:00
Ricardo Wurmus
d848ed7cf2
gnu: r-summarizedexperiment: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.0.
 2016-05-16 20:57:21 +02:00
Ricardo Wurmus
b4c5a0db22
gnu: r-rsamtools: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.24.0.
 2016-05-16 20:57:10 +02:00
Ricardo Wurmus
2477d9773a
gnu: r-biostrings: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.0.
 2016-05-16 20:56:58 +02:00
Ricardo Wurmus
6a2a0de1ab
gnu: r-biocparallel: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.0.
 2016-05-16 20:56:39 +02:00
Ricardo Wurmus
63cea37234
gnu: r-biomart: Update to 2.28.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.28.0.
 2016-05-16 20:56:29 +02:00
Ricardo Wurmus
c4a4e17938
gnu: r-annotationdbi: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.0.
 2016-05-16 20:56:19 +02:00
Ricardo Wurmus
4466a02c9f
gnu: r-biobase: Update to 2.32.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.32.0.
 2016-05-16 20:56:09 +02:00
Ricardo Wurmus
828980cad6
gnu: r-genomicranges: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.0.
 2016-05-16 20:55:58 +02:00
Ricardo Wurmus
e782ca3e97
gnu: r-xvector: Update to 0.12.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.0.
 2016-05-16 20:55:46 +02:00
Ricardo Wurmus
052ee32b24
gnu: r-variantannotation: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to
  1.18.0.
 2016-05-16 20:55:32 +02:00
Ricardo Wurmus
d1ab3d8fa5
gnu: r-genomeinfodb: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.0.
 2016-05-16 20:55:20 +02:00
Ricardo Wurmus
952ff8c862
gnu: r-iranges: Update to 2.6.0. 
* gnu/packages/bioinformatics (r-iranges): Update to 2.6.0.
 2016-05-16 20:55:11 +02:00
Ricardo Wurmus
3654a61146
gnu: r-s4vectors: Update to 0.10.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.0.
 2016-05-16 20:54:59 +02:00
Ricardo Wurmus
a936bf59ea
gnu: r-dnacopy: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.46.0.
 2016-05-16 20:54:37 +02:00
Ricardo Wurmus
dbfeba5209
gnu: r-biocgenerics: Update to 0.18.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.18.0.
 2016-05-16 20:53:48 +02:00
Leo Famulari
af3ac1f5f7
gnu: imagemagick: Update to 6.9.4-1. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.4-1.
 2016-05-16 14:27:48 -04:00
Efraim Flashner
b6c2f7dafd
gnu: libgit2: Update to 0.24.1. 
* gnu/packages/version-control.scm (libgit2): Update to 0.24.1.
 2016-05-16 19:34:49 +03:00
Efraim Flashner
8a0ac5bd55
gnu: tmux: Update to 2.2. 
* gnu/packages/tmux.scm (tmux): Update to 2.2.
 2016-05-16 19:34:49 +03:00
Alex Griffin
d3699b311b gnu: Add ledger. 
* gnu/packages/finance.scm (ledger): New variable.

Co-authored-by: Alex Kost <alezost@gmail.com>
 2016-05-16 18:01:18 +03:00
Alex Griffin
f17a544756 gnu: Add utfcpp. 
* gnu/packages/textutils.scm (utfcpp): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-05-16 18:01:18 +03:00
Nicolas Goaziou
80ed14d38f gnu: asymptote: Install Emacs data. 
* gnu/packages/plotutils.scm (asymptote)[arguments]: Add a phase to
  install Emacs-Lisp files in an appropriate place.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-05-16 18:01:18 +03:00
Alex Kost
47c96a577d gnu: mu: Update to 0.9.16. 
* gnu/packages/mail.scm (%mu-gtester-patch): Remove.
(mu): Update to 0.9.16.
[source]: Remove 'patches'.
 2016-05-16 18:01:18 +03:00
Alex Kost
704f219668 gnu: mu: Install emacs autoloads. 
* gnu/packages/mail.scm (mu)[arguments]: Add 'install-emacs-autoloads'
  phase.  Use appropriate modules and imported-modules.
 2016-05-16 18:01:18 +03:00
Alex Kost
789bda83d2 gnu: mu: Install emacs files in a proper place. 
* gnu/packages/mail.scm (mu)[arguments]: Add 'patch-configure.ac' phase
  to avoid adding "mu4e" sub-directory to 'lispdir' variable.
 2016-05-16 18:01:18 +03:00
Alex Kost
99404fff9f gnu: mu: Use 'modify-phases'. 
* gnu/packages/mail.scm (mu): Use 'modify-phases'.
 2016-05-16 18:01:18 +03:00
Efraim Flashner
7d0c3c8d01
gnu: python-pandas: Update to 0.18.1. 
* gnu/packages/python.scm (python-pandas): Update to 0.18.1.
[native-inputs]: Remove python-setuptools.
[properties]: Define python2-pandas.
(python2-pandas)[native-inputs]: Add python2-setuptools.
* gnu/packages/patches/python-pandas-fix-tslib-test-failure.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2016-05-16 17:39:42 +03:00
Ricardo Wurmus
8226c2717c gnu:: java-swt: Use ant-build-system. 
* gnu/packages/java.scm (java-swt): Use ant-build-system.
[native-inputs]: Remove JDK.
 2016-05-16 16:17:18 +02:00
Ricardo Wurmus
81b98756a3 gnu: Add SBC. 
* gnu/packages/linux.scm (sbc): New variable.
 2016-05-16 16:16:21 +02:00
Ricardo Wurmus
002528bca5 gnu: rapicorn: Fix tests. 
* gnu/packages/graphics.scm (rapicorn)[arguments]: Add build phases
"fix-tests" and "pre-check".  Generalize "replace-/bin/ls" phase to
"replace-fhs-paths".
[propagated-inputs]: Add python2-enum34.
[native-inputs]: Add xorg-server.
 2016-05-16 16:16:15 +02:00