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22882 Commits

Author SHA1 Message Date
Danny Milosavljevic dd4b7476ec
gnu: Add grub-hybrid. 
* gnu/packages/bootloaders.scm (grub-hybrid): New variable.
 2017-08-03 16:35:34 +02:00
Ben Woodcroft 75e6639f36
gnu: htseq: Use PyPI URI. 
This is a follow-up to 92971d68ac.

* gnu/packages/bioinformatics.scm (htseq)[source]: Use 'pypi-uri'.
 2017-08-03 21:08:13 +10:00
Ben Woodcroft 92971d68ac
gnu: htseq: Update to 0.9.1. 
* gnu/packages/bioinformatics.scm (htseq): Update to 0.9.1.
[arguments]: Use python-3 by removing field.
[native-inputs]: Add 'python-cython'.
[propagated-inputs]: Use python3 numpy package.
[inputs]: Use python3 pysam package.  Add 'python-matplotlib'.
(python2-htseq): New variable.
(clipper)[inputs]: Use it.
 2017-08-03 21:02:30 +10:00
Efraim Flashner a8ead6f91b
gnu: vc: Limit to x86_64 and i686. 
* gnu/packages/maths.scm (vc)[supported-systems]: New field.
 2017-08-03 13:34:18 +03:00
Manolis Ragkousis 5638d71502
gnu: openscenegraph: Add 'Release' configure flag. 
* gnu/packages/graphics.scm (openscenegraph)[arguments]: Add "-DCMAKE_BUILD_TYPE=Release".
 2017-08-03 10:35:31 +03:00
Eric Bavier 68a29ab8d0
gnu: Add LeoCAD. 
* gnu/packages/lego.scm (leocad): New variable.
 2017-08-03 00:33:02 -05:00
Tobias Geerinckx-Rice 5d8312f1c6
gnu: youtube-dl: Update to 2017.07.30.1. 
* gnu/packages/video.scm (youtube-dl): Update to 2017.07.30.1.
 2017-08-03 05:31:24 +02:00
Tobias Geerinckx-Rice 6862c72373
gnu: tor: Update to 0.3.0.10. 
* gnu/packages/tor.scm (tor): Update to 0.3.0.10.
 2017-08-03 01:56:22 +02:00
Ludovic Courtès 49962b15a1
activation: Make sure /etc exists. 
Fixes <http://bugs.gnu.org/27146>.
Reported by ng0 <ng0@pragmatique.xyz>.

* gnu/build/activation.scm (activate-etc): Add call to 'mkdir-p'.
 2017-08-03 00:35:59 +02:00
Ludovic Courtès ec5495ba3f
doc: 'patches' field of <origin> can list file-like objects. 
Fixes <http://bugs.gnu.org/27165>.
Reported by sirgazil <sirgazil@zoho.com>.

* doc/guix.texi (origin Reference): 'patches' can contain file-like
objects.
 2017-08-03 00:35:59 +02:00
Efraim Flashner edd08fb7ac
gnu: glibc@2.22: Fix security issues. 
Fixes CVE-2015-{5180,7547}, CVE-2016-{3075,3706,4429}.

* gnu/packages/base.scm (glibc@2.22)[source]: Add patches.
* gnu/packages/patches/glibc-CVE-2015-7547.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2017-08-02 21:51:35 +03:00
Efraim Flashner a0ae64a334
gnu: glibc@2.23: Fix CVE-2015-5180, CVE-2016-{3075,3706,4429}. 
* gnu/packages/base.scm (glibc@2.23)[source]: Add patches.
* gnu/packages/patches/glibc-CVE-2016-3075.patch,
gnu/packages/patches/glibc-CVE-2016-3706.patch,
gnu/packages/patches/glibc-CVE-2016-4429.patch: New files.
* gnu/local.mk (dist_patch_DATA): Register them.
 2017-08-02 21:51:33 +03:00
Efraim Flashner 575e5e4e51
gnu: glibc@2.24: Fix CVE-2015-5180. 
* gnu/packages/base.scm (glibc@2.24)[source]: Add patch.
* gnu/packages/patches/glibc-CVE-2015-5180.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2017-08-02 21:51:31 +03:00
Leo Famulari 2c5cf84430
gnu: python2-conda: Fix build by building with enum34. 
* gnu/packages/package-management.scm (python2-conda): Use 'python2-variant'.
[native-inputs]: Add python2-enum34.
 2017-08-02 14:39:33 -04:00
Manolis Ragkousis 9ef5940ce4
gnu: calibre: Add python2-msgpack as an input. 
* gnu/packages/ebook.scm (calibre)[inputs]: Add python2-msgpack.
 2017-08-02 20:20:12 +03:00
Efraim Flashner 721d7a6912
gnu: gcc@4.7: Don't built on aarch64. 
* gnu/packages/gcc.scm (gcc@4.7, gcc@4.8, gcc@4.9)[supported-systems]:
New field.
 2017-08-02 19:14:26 +03:00
Leo Famulari 696f1d0fb1
gnu: libpng-apng: Be sure to apply the APNG patch. 
* gnu/packages/image.scm (libpng-apng)[arguments]: Check the return status of
the patching procedures.
 2017-08-02 11:17:57 -04:00
ng0 e0958c2df8
gnu: libpng-apng: Update to 1.6.28. 
Fixes <https://bugs.gnu.org/27556>.

* gnu/packages/image.scm (libpng-apng): Update to 1.6.28.
Remove inherit of 'libpng'.
[version]: Use own version, remove 'package-version libpng'.
[source]: Don't inherit the source of libpng.
[arguments]: Update hash of libpng-apng source.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-08-02 11:10:31 -04:00
Thomas Danckaert 33485fa913
gnu: eyed3: Update to 0.8, build with python3. 
* gnu/packages/mp3.scm (eyed3): [source] Update to 0.8.
[arguments]: Disable tests; don't use python-2.
[propagated-inputs]: Add python-six and python-grako.
[native-inputs]: Remove.
 2017-08-02 14:08:33 +02:00
Thomas Danckaert a70b03d413
gnu: Add python-grako 
* gnu/packages/python.scm (python-grako): New variable.
 2017-08-02 14:08:33 +02:00
Thomas Danckaert 0abf526420
gnu: hdf4: Update to 4.12.13. 
* gnu/packages/maths.scm (hdf4): Update to 4.12.13.
 2017-08-02 14:08:24 +02:00
Tobias Geerinckx-Rice ced2d2b7ca
gnu: libvirt: Update to 3.6.0. 
* gnu/packages/virtualization.scm (libvirt): Update to 3.6.0.
 2017-08-02 07:15:21 +02:00
Tobias Geerinckx-Rice 2e508b6dc0
gnu: libvirt: Use HTTPS. 
* gnu/packages/virtualization.scm (libvirt)[source, home-page]: Use HTTPS.
 2017-08-02 07:15:21 +02:00
Roel Janssen 2f06dc0435
gnu: Add r-rlang. 
* gnu/packages/statistics.scm (r-rlang): New variable.
 2017-08-02 00:57:39 +02:00
Roel Janssen f1915a5dd0
gnu: r-deseq2: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.1.
 2017-08-02 00:33:23 +02:00
Roel Janssen fd215c2978
gnu: r-annotationforge: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.1.
 2017-08-02 00:33:07 +02:00
Roel Janssen bd4a0bab5f
gnu: r-category: Update to 2.42.1. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.42.1.
 2017-08-02 00:32:46 +02:00
Roel Janssen 0ff478344b
gnu: r-biocstyle: Update to 2.4.1. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.4.1.
 2017-08-02 00:32:31 +02:00
Roel Janssen 9c4348d8c4
gnu: r-dnacopy: Update to 1.50.1. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.50.1.
 2017-08-02 00:32:11 +02:00
Roel Janssen 3ec25eb2a8
gnu: r-iranges: Update to 2.10.2. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.2.
 2017-08-02 00:31:46 +02:00
Roel Janssen 6252dd0f15
gnu: r-genomeinfodb: Update to 1.12.2. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.12.2.
 2017-08-02 00:31:28 +02:00
Roel Janssen 48f5d283b2
gnu: r-variantannotation: Update to 1.22.3. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.3.
 2017-08-02 00:31:08 +02:00
Roel Janssen 1b4738e23c
gnu: r-limma: Update to 3.32.5. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.32.5.
 2017-08-02 00:30:49 +02:00
Roel Janssen 1898a7832f
gnu: r-biobase: Update to 2.36.2. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.36.2.
 2017-08-02 00:30:27 +02:00
Roel Janssen 62eb93a7d0
gnu: r-annotationdbi: Update to 1.38.2. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.38.2.
 2017-08-02 00:28:32 +02:00
Roel Janssen 0c6494a1db
gnu: r-biomart: Update to 2.32.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.32.1.
 2017-08-02 00:28:16 +02:00
Roel Janssen 1ff74d074e
gnu: r-biocparallel: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.10.1.
 2017-08-02 00:27:57 +02:00
Roel Janssen 5077bc3e2e
gnu: r-biostrings: Update to 2.44.2. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.44.2.
 2017-08-02 00:27:35 +02:00
Roel Janssen adf5d0a0bc
gnu: r-delayedarray: Update to 0.2.7. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.2.7.
 2017-08-02 00:27:16 +02:00
Roel Janssen f41150f13d
gnu: r-summarizedexperiment: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.6.3.
 2017-08-02 00:26:55 +02:00
Roel Janssen 26760c80cd
gnu: r-genomicalignments: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.1.
 2017-08-02 00:26:33 +02:00
Roel Janssen 15afa9bf8f
gnu: r-rtracklayer: Update to 1.36.4. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.36.4.
 2017-08-02 00:26:00 +02:00
Roel Janssen 8cfaa9ab4e
gnu: r-genomicfeatures: Update to 1.28.4. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.28.4.
 2017-08-02 00:25:26 +02:00
Roel Janssen 9eb2714625
gnu: r-copywriter: Update to 2.8.1. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.1.
 2017-08-02 00:25:00 +02:00
Roel Janssen bfa0d1e773
gnu: r-sva: Update to 3.24.4. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.4.
 2017-08-02 00:24:27 +02:00
Roel Janssen 8060a61798
gnu: r-rsqlite: Update to 2.0. 
* gnu/packages/statistics.scm (r-rsqlite): Update to 2.0.
 2017-08-02 00:23:16 +02:00
Roel Janssen 796237a9a4
gnu: Add r-blob. 
* gnu/packages/statistics.scm (r-blob): New variable.
 2017-08-02 00:22:33 +02:00
Roel Janssen aa184803f8
gnu: Add r-pkgconfig. 
* gnu/packages/statistics.scm (r-pkgconfig): New variable.
 2017-08-02 00:21:40 +02:00
Ludovic Courtès c53fc48144
pull: Honor '--no-grafts'. 
* guix/scripts/pull.scm (guix-pull): Parameterize %GRAFT? as a function
of OPTS.
 2017-08-02 00:04:00 +02:00
Ludovic Courtès 3085b50200
pull: Use the commit ID as the version string. 
* guix/scripts/pull.scm (build-from-source): Add #:commit parameter.
Pass it to BUILD.
(build-and-install): Add #:commit and pass it to 'build-from-source'.
(guix-pull): Pass #:commit to 'build-and-install'.
 2017-08-02 00:04:00 +02:00