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Author SHA1 Message Date
Tobias Geerinckx-Rice
0d3ddd490b
gnu: btrfs-progs: Update to 4.10.1. 
* gnu/packages/linux.scm (btrfs-progs): Update to 4.10.1.
 2017-03-17 20:39:58 +01:00
Danny Milosavljevic
893bc3f402
gnu: cargo: Use upstream cargo. 
* gnu/packages/rust.scm (cargo): Use upstream cargo.
 2017-03-17 16:48:08 +01:00
Danny Milosavljevic
b0dcb529af
gnu: rust: Update to 1.15.0. 
* gnu/packages/rust.scm (%rust-bootstrap-binaries-version): Update to 1.14.0.
(%rust-bootstrap-binaries): Update to 1.14.0.
(rustc): Update to 1.15.0.
[arguments]: Pass "--disable-rustbuild" to configure.
 2017-03-17 16:48:06 +01:00
Kei Kebreau
8f98581613
gnu: libpng-apng: Remove unnecessary call to libtool. 
* gnu/packages/image.scm (libpng-apng)[phases]: Remove it.
 2017-03-17 11:36:27 -04:00
ng0
114a325e8f
gnu: Add libpng-apng. 
* gnu/packages/image.scm (libpng-apng): New variable.

Co-authored-by: Kei Kebreau <kei@openmailbox.org>
 2017-03-17 11:25:15 -04:00
Ben Woodcroft
0a3063d640
gnu: Add ocaml-mcl. 
* gnu/packages/machine-learning.scm (ocaml-mcl): New variable.
 2017-03-17 21:43:27 +10:00
Ben Woodcroft
ba1be533ad
gnu: Add ocaml-gsl. 
* gnu/packages/maths.scm (ocaml-gsl): New variable.
 2017-03-17 21:43:25 +10:00
Ben Woodcroft
91df9eaefa
gnu: Add ocaml-csv. 
* gnu/packages/ocaml.scm (ocaml-csv): New variable.
 2017-03-17 21:43:13 +10:00
Ben Woodcroft
0c4dbdc23e
gnu: Add ocaml-sqlite3. 
* gnu/packages/ocaml.scm (ocaml-sqlite3): New variable.
 2017-03-17 21:19:23 +10:00
Ricardo Wurmus
ef71ed8ffa
gnu: snakemake: Update to 3.11.2. 
* gnu/packages/python.scm (snakemake): Update to 3.11.2.
 2017-03-17 10:14:03 +01:00
Ricardo Wurmus
60c9190e21
gnu: r-minimal: Fix remaining reproducibility problems. 
Fixes <https://bugs.gnu.org/25598>.

* gnu/packages/statistics.scm (r-minimal)[arguments]: Add remaining
reproducibility fixes to "build-reproducibly" phase.
 2017-03-17 10:14:02 +01:00
Ricardo Wurmus
2d7c4ae3ee
gnu: r: Rename to r-minimal. 
* gnu/packages/statistics.scm (r): Rename to...
(r-minimal): ...this new variable.
(r-with-recommended-packages): Rename to...
(r): ...this.
* guix/build-system/r.scm (default-r): Reference r-minimal.
* gnu/packages/emacs.scm (emacs-ess)[inputs],
gnu/packages/machine-learning.scm (shogun)[inputs],
gnu/packages/python.scm (python-rpy2)[inputs],
gnu/packages/bioinformatics.scm (ribotaper)[inputs],
(couger)[propagated-inputs],
(roary)[inputs],
(rsem)[inputs],
(rcas-web)[inputs]: Change "r" to "r-minimal".
 2017-03-17 10:14:02 +01:00
Ricardo Wurmus
f1fe5283c9
gnu: Add r-with-recommended-packages. 
* gnu/packages/statistics.scm (r-with-recommended-packages): New variable.
 2017-03-17 10:14:02 +01:00
Ricardo Wurmus
aeb64f3cb2
gnu: r: Do not build recommended packages. 
* gnu/packages/statistics.scm (r)[arguments]: Rename phase
"build-recommended-packages-reproducibly" to "build-reproducibly"; add
configure flag "--without-recommended-packages".
* guix/import/cran.scm (default-r-packages): Remove recommended packages.
* gnu/packages/python.scm (python-rpy2)[inputs]: Add r-survival.
* gnu/packages/bioinformatics.scm (r-ape)[propagated-inputs]: Add r-lattice
and r-nlme.
(r-vegan)[propagated-inputs]: Add r-mass.
(r-genefilter)[propagated-inputs]: Add r-survival.
(r-grohmm)[propagated-inputs]: Add r-mass.
(r-bioccheck)[propagated-inputs]: Add r-codetools.
(r-summarizedexperiment)[propagated-inputs]: Add r-matrix.
(r-topgo)[propagated-inputs]: Add r-lattice.
(r-sva)[propagated-inputs]: Add r-mgcv.
(r-raremetals2)[propagated-inputs]: Add r-mass.
(r-vsn)[propagated-inputs]: Add r-lattice.
(r-pcamethods)[propagated-inputs]: Add r-mass.
* gnu/packages/bioinformatics.scm (r-ggplot2)[propagated-inputs]: Add r-mass.
(r-locfit)[propagated-inputs]: Add r-lattice.
(r-coda)[propagated-inputs]: Add r-lattice.
(r-irlba)[propagated-inputs]: Add r-matrix.
(r-glmnet)[propagated-inputs]: Add r-matrix.
(r-e1071)[propagated-inputs]: Add r-class.
(r-spams)[propagated-inputs]: Add r-lattice and r-matrix.
(r-hmisc)[propagated-inputs]: Add r-cluster, r-foreign, r-lattice, r-nnet, and
r-rpart.
(r-zoo)[propagated-inputs]: Add r-lattice.
(r-mixtools)[propagated-inputs]: Add r-boot and r-mass.
(r-flexmix)[propagated-inputs]: Add r-lattice and r-nnet.
(r-prabclus)[propagated-inputs]: Add r-mass.
(r-fpc)[propagated-inputs]: Add r-class, r-cluster, and r-mass.
(r-rcppeigen)[propagated-inputs]: Add r-matrix.
(r-matrixmodels)[propagated-inputs]: Add r-matrix.
(r-lme4)[propagated-inputs]: Add r-mass and r-nlme.
(r-pbkrtest)[propagated-inputs]: Add r-mass and r-matrix.
(r-car)[propagated-inputs]: Add r-mass, r-mgcv, and r-nnet.
(r-tclust)[propagated-inputs]: Add r-cluster.
 2017-03-17 10:14:02 +01:00
Ricardo Wurmus
6eaa9bfba6
gnu: r-survival: Move to set of recommended R packages. 
* gnu/packages/statistics.scm (r-survival): Move up to set of recommended R
packages.
 2017-03-17 10:14:02 +01:00
Ricardo Wurmus
4b005c7a75
gnu: Add r-spatial. 
* gnu/packages/statistics.scm (r-spatial): New variable.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus
567b154fb0
gnu: r-rpart: Move to the set of recommended packages. 
* gnu/packages/statistics.scm (r-rpart): Move up to the set of recommended
packages.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus
a5a343656b
gnu: r-nnet: Move to set of recommended R packages. 
* gnu/packages/machine-learning.scm (r-nnet): Move from here...
* gnu/packages/statistics.scm (r-nnet): ...to here because the other
recommended R packages are here.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus
ac8d738b97
gnu: r-mgcv: Move to set of recommended R packages. 
* gnu/packages/statistics.scm (r-mgcv): Move up to set of recommended R
packages.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus
248f65269a
gnu: Add r-nlme. 
* gnu/packages/statistics.scm (r-nlme): New variable.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus
69e14f9ec7
gnu: r-matrix: Move to set of recommended R packages. 
* gnu/packages/statistics.scm (r-matrix): Move to set of recommended R
packages.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus
060c12868b
gnu: r-lattice: Move to other recommended R packages. 
* gnu/packages/statistics.scm (r-lattice): Move to the set of recommended R
packages.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus
e88bad6ddb
gnu: Add r-kernsmooth. 
* gnu/packages/statistics.scm (r-kernsmooth): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus
69fddd2d6e
gnu: Add r-foreign. 
* gnu/packages/statistics.scm (r-foreign): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus
c1999c5910
gnu: Add r-codetools. 
* gnu/packages/statistics.scm (r-codetools): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus
a27bfb8484
gnu: Add r-cluster. 
* gnu/packages/statistics.scm (r-cluster): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus
7489258751
gnu: Add r-class. 
* gnu/packages/statistics.scm (r-class): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus
c7e80a7e0d
gnu: Add r-mass. 
* gnu/packages/statistics.scm (r-mass): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus
8f0069170c
gnu: Add r-boot. 
* gnu/packages/statistics.scm (r-boot): New variable.
 2017-03-17 10:14:00 +01:00
Tobias Geerinckx-Rice
54d556bdd7
gnu: youtube-dl: Update to 2017.03.16. 
* gnu/packages/video.scm (youtube-dl): Update to 2017.03.16.
 2017-03-17 03:11:35 +01:00
Kei Kebreau
3078821d13
gnu: asciidoc: Use local docbook-xml package. 
* gnu/packages/documentation.scm (asciidoc)[inputs]: Add docbook-xml.
[arguments]: Add 'make-local-docbook-xml' phase.
 2017-03-16 21:35:50 -04:00
Tobias Geerinckx-Rice
f9cdf1c15b
gnu: Add knot. 
* gnu/packages/dns.scm (knot): New variable.
 2017-03-17 02:32:01 +01:00
Tobias Geerinckx-Rice
754667f0eb
gnu: Add liburcu. 
* gnu/packages/datastructures.scm (liburcu): New variable.
 2017-03-17 02:32:00 +01:00
Tobias Geerinckx-Rice
366efcb2fb
gnu: dns: Fix typo and use @dfn in descriptions. 
* gnu/packages/dns.scm (bind)[description]: Use @dfn to expand acronyms.
(yadifa)[description]: Likewise, and fix a typo.
 2017-03-17 02:32:00 +01:00
Leo Famulari
2ec5ba859f
gnu: linux-libre: Update to 4.10.3. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.10.3.
(%linux-libre-hash): Update hash.
 2017-03-16 19:40:40 -04:00
Leo Famulari
2044306f05
gnu: linux-libre@4.4: Update to 4.4.54. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.54.
 2017-03-16 19:40:39 -04:00
Leo Famulari
bcc5b74173
gnu: linux-libre@4.9: Update to 4.9.15. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.15.
 2017-03-16 19:40:39 -04:00
Leo Famulari
49ac6dbb0a
gnu: qemu: Fix CVE-2017-{2620,2630}. 
* gnu/packages/patches/qemu-CVE-2017-2620.patch,
gnu/packages/patches/qemu-CVE-2017-2630.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/qemu.scm (qemu)[source]: Use them.
 2017-03-16 19:40:08 -04:00
Leo Famulari
1e5b8beeff
gnu: virglrenderer: Fix CVE-2017-6386. 
* gnu/packages/patches/virglrenderer-CVE-2017-6386.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/spice.scm (virglrenderer)[source]: Use it.
 2017-03-16 19:39:55 -04:00
Clément Lassieur
2c715a9223
gnu: password-store: Fix compatibility with GnuPG 2.1.19. 
* gnu/packages/patches/password-store-gnupg-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/password-utils.scm (password-store)[source]: Use it.

Signed-off-by: Clément Lassieur <clement@lassieur.org>
 2017-03-16 19:58:43 +01:00
Raoul Jean Pierre Bonnal
2441c28414
gnu: Add r-seurat. 
* gnu/packages/bioinformatics.scm (r-seurat): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2017-03-16 14:54:58 +01:00
Ricardo Wurmus
79849358f8
gnu: sra-tools: Update to 2.8.2-1. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.8.2-1.
[arguments]: Add DEFAULT_CRT and DEFAULT_KFG to make flags.
 2017-03-16 13:40:36 +01:00
Ricardo Wurmus
d5e1716239
gnu: ncbi-vdb: Install configuration files. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase
"install-configuration-files".
 2017-03-16 13:39:53 +01:00
Ricardo Wurmus
558e23074e
gnu: ncbi-vdb: Override search path for java-ngs. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Patch "package.prl"
to ensure that java-ngs is found by the configure script; remove configure
flag "--with-ngs-java-prefix".
 2017-03-16 13:38:39 +01:00
Ricardo Wurmus
701111989e
gnu: ncbi-vdb: Use modify-phases syntax. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases
syntax.
 2017-03-16 10:20:56 +01:00
Ricardo Wurmus
5021f54787
gnu: ncbi-vdb: Update to 2.8.2. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2.
 2017-03-16 10:19:25 +01:00
Ricardo Wurmus
6c4ccf3228
gnu: ngs-sdk: Update to 1.3.0. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0.
 2017-03-16 10:18:48 +01:00
Tobias Geerinckx-Rice
0f03c53168
gnu: Add pzstd. 
* gnu/packages/compression.scm (pzstd): New variable.
 2017-03-16 05:44:02 +01:00
Tobias Geerinckx-Rice
f6ac3101ff
gnu: Add zstd. 
* gnu/packages/compression.scm (zstd): New variable.
 2017-03-16 05:44:02 +01:00
Tobias Geerinckx-Rice
9186216268
gnu: python-publicsuffix2: Update to 2.20160818. 
* gnu/packages/python.scm (python-publicsuffix2): Update to 2.20160818.
 2017-03-16 05:44:02 +01:00