Commit Graph

8745 Commits

Author SHA1 Message Date
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
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