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2017-03-30Merge branch 'master' into core-updatesMarius Bakke
Most conflicts are from 6fd52309b8f52c9bb59fccffac53e029ce94b698.
2017-03-30gnu: Use HTTPS for almost all gnu.org HOME-PAGEs.Tobias Geerinckx-Rice
All HTTP gnu.org (and supported subdomain) HOME-PAGEs changed to HTTPS.
2017-03-22Merge remote-tracking branch 'origin/master' into core-updatesEfraim Flashner
2017-03-20gnu: Add r-cairo.Ricardo Wurmus
* gnu/packages/statistics.scm (r-cairo): New variable.
2017-03-19Merge branch 'master' into core-updatesMark H Weaver
2017-03-17gnu: r-minimal: Fix remaining reproducibility problems.Ricardo Wurmus
Fixes <https://bugs.gnu.org/25598>. * gnu/packages/statistics.scm (r-minimal)[arguments]: Add remaining reproducibility fixes to "build-reproducibly" phase.
2017-03-17gnu: r: Rename to r-minimal.Ricardo Wurmus
* 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".
2017-03-17gnu: Add r-with-recommended-packages.Ricardo Wurmus
* gnu/packages/statistics.scm (r-with-recommended-packages): New variable.
2017-03-17gnu: r: Do not build recommended packages.Ricardo Wurmus
* 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.
2017-03-17gnu: r-survival: Move to set of recommended R packages.Ricardo Wurmus
* gnu/packages/statistics.scm (r-survival): Move up to set of recommended R packages.
2017-03-17gnu: Add r-spatial.Ricardo Wurmus
* gnu/packages/statistics.scm (r-spatial): New variable.
2017-03-17gnu: r-rpart: Move to the set of recommended packages.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rpart): Move up to the set of recommended packages.
2017-03-17gnu: r-nnet: Move to set of recommended R packages.Ricardo Wurmus
* 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.
2017-03-17gnu: r-mgcv: Move to set of recommended R packages.Ricardo Wurmus
* gnu/packages/statistics.scm (r-mgcv): Move up to set of recommended R packages.
2017-03-17gnu: Add r-nlme.Ricardo Wurmus
* gnu/packages/statistics.scm (r-nlme): New variable.
2017-03-17gnu: r-matrix: Move to set of recommended R packages.Ricardo Wurmus
* gnu/packages/statistics.scm (r-matrix): Move to set of recommended R packages.
2017-03-17gnu: r-lattice: Move to other recommended R packages.Ricardo Wurmus
* gnu/packages/statistics.scm (r-lattice): Move to the set of recommended R packages.
2017-03-17gnu: Add r-kernsmooth.Ricardo Wurmus
* gnu/packages/statistics.scm (r-kernsmooth): New variable.
2017-03-17gnu: Add r-foreign.Ricardo Wurmus
* gnu/packages/statistics.scm (r-foreign): New variable.
2017-03-17gnu: Add r-codetools.Ricardo Wurmus
* gnu/packages/statistics.scm (r-codetools): New variable.
2017-03-17gnu: Add r-cluster.Ricardo Wurmus
* gnu/packages/statistics.scm (r-cluster): New variable.
2017-03-17gnu: Add r-class.Ricardo Wurmus
* gnu/packages/statistics.scm (r-class): New variable.
2017-03-17gnu: Add r-mass.Ricardo Wurmus
* gnu/packages/statistics.scm (r-mass): New variable.
2017-03-17gnu: Add r-boot.Ricardo Wurmus
* gnu/packages/statistics.scm (r-boot): New variable.
2017-03-13Merge remote-tracking branch 'origin/master' into core-updatesEfraim Flashner
2017-03-13gnu: r-hexbin: Update to 1.27.1-1.pjotrp
The package tarball was updated in place, resulting in a change in the hash value. We decided to bump the version to 1.27.1-1 instead of keeping the version at upstream's 1.27.1. * gnu/packages/statistics.scm (r-hexbin): Update to 1.27.1-1.
2017-03-12gnu: Add a tzdata variant for testing purposes.Leo Famulari
* gnu/packages/base.scm (tzdata-2017a): New variable. * gnu/packages/glib.scm (glib)[inputs]: Remove tzdata. [native-inputs]: Add tzdata-2017a. [arguments]: Add tzdata-2017a to #:disallowed-references. * gnu/packages/statistics.scm (r)[inputs]: Remove tzdata. [native-inputs]: Add tzdata-2017a. [arguments]: Add tzdata-2017a to #:disallowed-references.
2017-03-12gnu: Add r-tsne.Raoul Jean Pierre Bonnal
* gnu/packages/bioinformatics.scm (r-tsne): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-12gnu: Add r-ranger.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-ranger): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-12gnu: Add r-tclust.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-tclust): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-12gnu: Add r-sn.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-sn): New variable. Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-12gnu: Add r-numderiv.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-numderiv): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-12gnu: Add r-mnormt.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-mnormt): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-12gnu: Add r-rcppprogress.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-rcppprogress): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-12gnu: Add r-caret.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-caret): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-12gnu: Add r-car.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-car): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-12gnu: Add r-pbkrtest.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-pbkrtest): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-12gnu: Add r-lme4.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-lme4): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-12gnu: Add r-nloptr.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-nloptr): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-12gnu: Add r-quantreg.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-quantreg): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-12gnu: Add r-matrixmodels.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-matrixmodels): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-12gnu: Add r-modelmetrics.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-modelmetrics): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-12gnu: Add r-rcppeigen.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-rcppeigen): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-12gnu: Add r-minqa.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-minqa): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-11gnu: Add r-fnn.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-fnn): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-11gnu: Add r-pbapply.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-pbapply): New variable. Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-11gnu: Add r-vgam.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-vgam): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-11gnu: Add r-fpc.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-fpc): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-11gnu: Add r-trimcluster.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-trimcluster): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-11gnu: Add r-robustbase.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-robustbase): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
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