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* gnu: snakemake: Update to 3.11.2.Ricardo Wurmus2017-03-17
| | | | * gnu/packages/python.scm (snakemake): Update to 3.11.2.
* gnu: r-minimal: Fix remaining reproducibility problems.Ricardo Wurmus2017-03-17
| | | | | | | Fixes <https://bugs.gnu.org/25598>. * gnu/packages/statistics.scm (r-minimal)[arguments]: Add remaining reproducibility fixes to "build-reproducibly" phase.
* gnu: r: Rename to r-minimal.Ricardo Wurmus2017-03-17
| | | | | | | | | | | | | | | | * 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".
* gnu: Add r-with-recommended-packages.Ricardo Wurmus2017-03-17
| | | | * gnu/packages/statistics.scm (r-with-recommended-packages): New variable.
* gnu: r: Do not build recommended packages.Ricardo Wurmus2017-03-17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
* gnu: r-survival: Move to set of recommended R packages.Ricardo Wurmus2017-03-17
| | | | | * gnu/packages/statistics.scm (r-survival): Move up to set of recommended R packages.
* gnu: Add r-spatial.Ricardo Wurmus2017-03-17
| | | | * gnu/packages/statistics.scm (r-spatial): New variable.
* gnu: r-rpart: Move to the set of recommended packages.Ricardo Wurmus2017-03-17
| | | | | * gnu/packages/statistics.scm (r-rpart): Move up to the set of recommended packages.
* gnu: r-nnet: Move to set of recommended R packages.Ricardo Wurmus2017-03-17
| | | | | | * 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.
* gnu: r-mgcv: Move to set of recommended R packages.Ricardo Wurmus2017-03-17
| | | | | * gnu/packages/statistics.scm (r-mgcv): Move up to set of recommended R packages.
* gnu: Add r-nlme.Ricardo Wurmus2017-03-17
| | | | * gnu/packages/statistics.scm (r-nlme): New variable.
* gnu: r-matrix: Move to set of recommended R packages.Ricardo Wurmus2017-03-17
| | | | | * gnu/packages/statistics.scm (r-matrix): Move to set of recommended R packages.
* gnu: r-lattice: Move to other recommended R packages.Ricardo Wurmus2017-03-17
| | | | | * gnu/packages/statistics.scm (r-lattice): Move to the set of recommended R packages.
* gnu: Add r-kernsmooth.Ricardo Wurmus2017-03-17
| | | | * gnu/packages/statistics.scm (r-kernsmooth): New variable.
* gnu: Add r-foreign.Ricardo Wurmus2017-03-17
| | | | * gnu/packages/statistics.scm (r-foreign): New variable.
* gnu: Add r-codetools.Ricardo Wurmus2017-03-17
| | | | * gnu/packages/statistics.scm (r-codetools): New variable.
* gnu: Add r-cluster.Ricardo Wurmus2017-03-17
| | | | * gnu/packages/statistics.scm (r-cluster): New variable.
* gnu: Add r-class.Ricardo Wurmus2017-03-17
| | | | * gnu/packages/statistics.scm (r-class): New variable.
* gnu: Add r-mass.Ricardo Wurmus2017-03-17
| | | | * gnu/packages/statistics.scm (r-mass): New variable.
* gnu: Add r-boot.Ricardo Wurmus2017-03-17
| | | | * gnu/packages/statistics.scm (r-boot): New variable.
* gnu: youtube-dl: Update to 2017.03.16.Tobias Geerinckx-Rice2017-03-17
| | | | * gnu/packages/video.scm (youtube-dl): Update to 2017.03.16.
* gnu: asciidoc: Use local docbook-xml package.Kei Kebreau2017-03-16
| | | | | * gnu/packages/documentation.scm (asciidoc)[inputs]: Add docbook-xml. [arguments]: Add 'make-local-docbook-xml' phase.
* gnu: Add knot.Tobias Geerinckx-Rice2017-03-17
| | | | * gnu/packages/dns.scm (knot): New variable.
* gnu: Add liburcu.Tobias Geerinckx-Rice2017-03-17
| | | | * gnu/packages/datastructures.scm (liburcu): New variable.
* gnu: dns: Fix typo and use @dfn in descriptions.Tobias Geerinckx-Rice2017-03-17
| | | | | * gnu/packages/dns.scm (bind)[description]: Use @dfn to expand acronyms. (yadifa)[description]: Likewise, and fix a typo.
* gnu: linux-libre: Update to 4.10.3.Leo Famulari2017-03-16
| | | | | * gnu/packages/linux.scm (%linux-libre-version): Update to 4.10.3. (%linux-libre-hash): Update hash.
* gnu: linux-libre@4.4: Update to 4.4.54.Leo Famulari2017-03-16
| | | | * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.54.
* gnu: linux-libre@4.9: Update to 4.9.15.Leo Famulari2017-03-16
| | | | * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.15.
* gnu: qemu: Fix CVE-2017-{2620,2630}.Leo Famulari2017-03-16
| | | | | | | * 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.
* gnu: virglrenderer: Fix CVE-2017-6386.Leo Famulari2017-03-16
| | | | | | * 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.
* gnu: password-store: Fix compatibility with GnuPG 2.1.19.Clément Lassieur2017-03-16
| | | | | | | | * 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>
* gnu: Add r-seurat.Raoul Jean Pierre Bonnal2017-03-16
| | | | | | * gnu/packages/bioinformatics.scm (r-seurat): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: sra-tools: Update to 2.8.2-1.Ricardo Wurmus2017-03-16
| | | | | * gnu/packages/bioinformatics.scm (sra-tools): Update to 2.8.2-1. [arguments]: Add DEFAULT_CRT and DEFAULT_KFG to make flags.
* gnu: ncbi-vdb: Install configuration files.Ricardo Wurmus2017-03-16
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase "install-configuration-files".
* gnu: ncbi-vdb: Override search path for java-ngs.Ricardo Wurmus2017-03-16
| | | | | | * 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".
* gnu: ncbi-vdb: Use modify-phases syntax.Ricardo Wurmus2017-03-16
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases syntax.
* gnu: ncbi-vdb: Update to 2.8.2.Ricardo Wurmus2017-03-16
| | | | * gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2.
* gnu: ngs-sdk: Update to 1.3.0.Ricardo Wurmus2017-03-16
| | | | * gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0.
* gnu: Add pzstd.Tobias Geerinckx-Rice2017-03-16
| | | | * gnu/packages/compression.scm (pzstd): New variable.
* gnu: Add zstd.Tobias Geerinckx-Rice2017-03-16
| | | | * gnu/packages/compression.scm (zstd): New variable.
* gnu: python-publicsuffix2: Update to 2.20160818.Tobias Geerinckx-Rice2017-03-16
| | | | * gnu/packages/python.scm (python-publicsuffix2): Update to 2.20160818.
* gnu: awscli: Update to 1.11.63.Tobias Geerinckx-Rice2017-03-16
| | | | * gnu/packages/python.scm (awscli): Update to 1.11.63.
* gnu: python-botocore: Update to 1.5.26.Tobias Geerinckx-Rice2017-03-16
| | | | * gnu/packages/python.scm (python-botocore): Update to 1.5.26.
* gnu: python-ptyprocess: Update to 0.5.1.Tobias Geerinckx-Rice2017-03-16
| | | | * gnu/packages/python.scm (python-ptyprocess): Update to 0.5.1.
* gnu: Add prboom-plus.Kei Kebreau2017-03-15
| | | | * gnu/packages/games.scm (prboom-plus): New variable.
* gnu: Add tftp-hpa.Gábor Boskovits2017-03-15
| | | | | | * gnu/packages/networking.scm (tftp-hpa): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: guile-next: Update to 2.2.0.Andy Wingo2017-03-15
| | | | * gnu/packages/guile.scm (guile-next): Update to 2.2.0.
* gnu: profanity: Make the source URL version-agnostic.Leo Famulari2017-03-15
| | | | | * gnu/packages/messaging.scm (profanity)[source]: Use (version) in the source URL.
* gnu: units: Update to 2.14.Tobias Geerinckx-Rice2017-03-15
| | | | * gnu/packages/maths.scm (units): Update to 2.14.
* gnu: no-more-secrets: Update to 0.3.2.Tobias Geerinckx-Rice2017-03-15
| | | | * gnu/packages/games.scm (no-more-secrets): Update to 0.3.2.
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