gnu: libx264: Update to 20170316-2245.

* gnu/packages/video.scm (libx264): Update to 20170316-2245.

gnu: libwebp: Update to 0.6.0.

* gnu/packages/image.scm (libwebp): Update to 0.6.0.
[source]: Remove patch.
* gnu/packages/patches/libwebp-CVE-2016-9085.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

gnu: ninja: Update to 1.7.2.

* gnu/packages/ninja.scm (ninja): Update to 1.7.2.
[source]: Remove patch.
* gnu/packages/patches/ninja-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

gnu: btrfs-progs: Use @dfn in description.

* gnu/packages/linux.scm (btrfs-progs)[description]: Use @dfn.

gnu: btrfs-progs: Update to 4.10.1.

* gnu/packages/linux.scm (btrfs-progs): Update to 4.10.1.

build/cargo-build-system: Make cargo-build-system install working packages.

* guix/build/cargo-build-system.scm (configure): Remove proprietary
dependencies. Add rust dependencies and configure Cargo to find them.
(build): Also build libraries, not just applications.
(file-sha256): New variable.
(generate-checksums): New variable. Export it.
(touch): New variable.
(install): Generate checksums so Cargo accepts the package.

build-system/cargo (cargo-build): Add cargo-build-flags, remove configure-flags.

* guix/build-system/cargo.scm (cargo-build): Add cargo-build-flags,
remove configure-flags.

gnu: cargo: Use upstream cargo.

* gnu/packages/rust.scm (cargo): Use upstream cargo.

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.

gnu: libpng-apng: Remove unnecessary call to libtool.

* gnu/packages/image.scm (libpng-apng)[phases]: Remove it.

gnu: Add libpng-apng.

* gnu/packages/image.scm (libpng-apng): New variable.

Co-authored-by: Kei Kebreau <kei@openmailbox.org>

gnu: Add ocaml-mcl.

* gnu/packages/machine-learning.scm (ocaml-mcl): New variable.

gnu: Add ocaml-gsl.

* gnu/packages/maths.scm (ocaml-gsl): New variable.

gnu: Add ocaml-csv.

* gnu/packages/ocaml.scm (ocaml-csv): New variable.

gnu: Add ocaml-sqlite3.

* gnu/packages/ocaml.scm (ocaml-sqlite3): New variable.

gnu: snakemake: Update to 3.11.2.

* gnu/packages/python.scm (snakemake): Update to 3.11.2.

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.

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".

gnu: Add r-with-recommended-packages.

* gnu/packages/statistics.scm (r-with-recommended-packages): New variable.

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.