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* Merge branch 'master' into core-updatesMark H Weaver2017-03-19
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| * gnu: Add pdfgrep.rennes2017-03-19
| | | | | | | | | | | | * guix/gnu/packages/pdf.scm (pdfgrep): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
| * gnu: linux-libre: Update to 4.10.4.Mark H Weaver2017-03-19
| | | | | | | | | | * gnu/packages/linux.scm (%linux-libre-version): Update to 4.10.4. (%linux-libre-hash): Update hash.
| * gnu: linux-libre@4.9: Update to 4.9.16.Mark H Weaver2017-03-19
| | | | | | | | * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.16.
| * gnu: linux-libre@4.4: Update to 4.4.55.Mark H Weaver2017-03-19
| | | | | | | | * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.55.
| * services: Remove Tab character from source code whitespace.Danny Milosavljevic2017-03-19
| | | | | | | | | | * gnu/services/base.scm (file-system-shepherd-service): Remove Tab character from source code whitespace.
| * gnu: u-boot: Update to 2017.03.Danny Milosavljevic2017-03-19
| | | | | | | | * gnu/packages/bootloaders.scm (u-boot): Update to 2017.03.
| * gnu: icecat: Add selected fixes from upstream mozilla-esr45.Mark H Weaver2017-03-19
| | | | | | | | | | * gnu/packages/gnuzilla.scm (icecat)[source][patches]: Add selected fixes from the upstream mozilla-esr45 repository.
| * gnu: libevent@2.0: Add fix from upstream.Mark H Weaver2017-03-19
| | | | | | | | | | | | | | | | | | | | This fix was cherry-picked by Mozilla from upstream libevent-2.1 to its bundled copy of libevent-2.0.21 in mozilla-esr45. * gnu/packages/patches/libevent-2.0-evbuffer-add-use-last-with-datap.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/libevent.scm (libevent-2.0)[source][patches]: Add it.
| * services: file-system-shepherd-service: Make it find the fsck programs.Danny Milosavljevic2017-03-19
| | | | | | | | | | | | | | Fixes <https://bugs.gnu.org/25917>. * gnu/services/base.scm (file-system-shepherd-service): Use file-system-packages.
| * gnu: guile-commonmark: Default to Guile 2.2.Ludovic Courtès2017-03-19
| | | | | | | | | | | | | | | | * gnu/packages/guile.scm (guile-commonmark)[inputs]: Replace GUILE-2.0 with GUILE-2.2. (guile2.0-commonmark): New variable. (guile2.2-commonmark): Mark as deprecated. (haunt)[propagated-inputs]: Use GUILE-COMMONMARK.
| * gnu: guile-reader: Default to Guile 2.2.Ludovic Courtès2017-03-19
| | | | | | | | | | | | | | | | | | * gnu/packages/guile.scm (guile-reader)[inputs]: Change GUILE-2.0 to GUILE-2.2. (guile2.0-reader): New variable. (guile2.2-reader): Mark as deprecated. (haunt)[propagated-inputs]: Use GUILE-READER instead of GUILE2.2-READER.
| * gnu: haunt: Default to Guile 2.2.Ludovic Courtès2017-03-19
| | | | | | | | | | | | | | | | | | * gnu/packages/guile.scm (haunt)[inputs]: Replace GUILE-2.0 with GUILE-2.2. [propagated-inputs]: Replace GUILE-READER and GUILE-COMMONMARK with their 2.2 variant. (guile2.0-haunt): New variable. (guile2.2-haunt): Mark as deprecated.
| * gnu: Add 'package-for-guile-2.0'.Ludovic Courtès2017-03-19
| | | | | | | | | | | | | | * gnu/packages/guile.scm (guile-2.2-package-name): Rename to... (guile-variant-package-name): ... this. Change to return a lambda. (package-for-guile-2.2): Adjust accordingly. (package-for-guile-2.0): New procedure.
| * gnu: Rename "guile-next" to "guile".Ludovic Courtès2017-03-19
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/guile.scm (guile-next): Rename to... (guile-2.2): ... this. Update users. [name]: Change to "guile". [synopsis]: Remove. [properties]: Remove 'upstream-name', 'ftp-server', and 'ftp-directory'. * gnu/packages/bioinformatics.scm (rcas-web): Update accordingly. * gnu/packages/tls.scm (gnutls/guile-2.2): Likewise. * tests/guix-build.sh: Use 'guile@2.2' instead of 'guile-next'. * doc/guix.texi (Package Transformation Options): Update examples that referred to "guile-next".
| * gnu: Add GNU Mach.Manolis Ragkousis2017-03-19
| | | | | | | | | | | | | | * gnu/packages/hurd.scm (gnumach): New variable. Co-authored-by: Rene Saavedra <rennes@openmailbox.org> Co-authored-by: Ludovic Courtès <ludo@gnu.org>
| * gnu: niftilib: Simplify build phases.Ricardo Wurmus2017-03-19
| | | | | | | | | | * gnu/packages/image.scm (niftilib)[arguments]: Use make-flags instead of replacing "configure" phase; simplify "install" phase.
| * gnu: apl: Update to 1.7.Efraim Flashner2017-03-18
| | | | | | | | | | * gnu/packages/apl.scm (apl): Update to 1.7. [home-page]: Use https.
| * gnu: guile-8sync: Update to 0.4.2.Christopher Allan Webber2017-03-18
| | | | | | | | * gnu/packages/guile.scm (guile-8sync): Update to 0.4.2.
| * gnu: guix: Don't ignore user's GUILE_LOAD_COMPILED_PATH.Taylan Ulrich Bayırlı/Kammer2017-03-18
| | | | | | | | | | | | * gnu/packages/package-management.scm (guix-0.12.0): Guile skips invalid .go files since 2.0.12 so we don't need to override GUILE_LOAD_COMPILED_PATH to prevent problems anymore.
| * gnu: wine: Update to 2.4.Danny Milosavljevic2017-03-18
| | | | | | | | * gnu/packages/wine.scm (wine): Update to 2.4.
| * gnu: Add niftilib.John Darrington2017-03-18
| | | | | | | | * gnu/packages/image.scm (niftilib): New variable.
| * bug#26152: [PATCH] gnu: limnoria: Update to 20170110.ng02017-03-18
| | | | | | | | | | | | * gnu/packages/irc.scm (limnoria): Update to 20170110. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
| * file-systems: Factorize file-system-packages.Danny Milosavljevic2017-03-18
| | | | | | | | | | | | * gnu/system/linux-initrd.scm (base-initrd): Move helper-packages body to ... * gnu/system/file-systems.scm (file-system-packages): ... here. New variable. Also export it.
| * gnu: rustc: Fix process test.Danny Milosavljevic2017-03-18
| | | | | | | | | | * gnu/packages/rust.scm (rustc)[arguments]: Rename 'patch-lockfile-test to 'patch-tests. Add another substitution.
| * gnu: Add maxflow.John Darrington2017-03-18
| | | | | | | | * gnu/packages/maths.scm (maxflow): New variable.
| * gnu: Add itpp.John Darrington2017-03-18
| | | | | | | | * gnu/packages/maths.scm (itpp): New variable.
| * gnu: emacs-slime: Update to 2.19.Tobias Geerinckx-Rice2017-03-18
| | | | | | | | * gnu/packages/emacs.scm (emacs-slime): Update to 2.19.
| * gnu: ocaml-qtest: Update to 2.5.Ben Woodcroft2017-03-18
| | | | | | | | * gnu/packages/ocaml.scm (ocaml-qtest): Update to 2.5.
| * gnu: libbluray: Update to 1.0.0.Marius Bakke2017-03-17
| | | | | | | | * gnu/packages/video.scm (libbluray): Update to 1.0.0.
| * gnu: libx264: Update to 20170316-2245.Marius Bakke2017-03-17
| | | | | | | | * gnu/packages/video.scm (libx264): Update to 20170316-2245.
| * gnu: libwebp: Update to 0.6.0.Marius Bakke2017-03-17
| | | | | | | | | | | | | | * 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.Marius Bakke2017-03-17
| | | | | | | | | | | | | | * 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.Tobias Geerinckx-Rice2017-03-17
| | | | | | | | * gnu/packages/linux.scm (btrfs-progs)[description]: Use @dfn.
| * gnu: btrfs-progs: Update to 4.10.1.Tobias Geerinckx-Rice2017-03-17
| | | | | | | | * gnu/packages/linux.scm (btrfs-progs): Update to 4.10.1.
| * gnu: cargo: Use upstream cargo.Danny Milosavljevic2017-03-17
| | | | | | | | * gnu/packages/rust.scm (cargo): Use upstream cargo.
| * gnu: rust: Update to 1.15.0.Danny Milosavljevic2017-03-17
| | | | | | | | | | | | | | * 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.Kei Kebreau2017-03-17
| | | | | | | | * gnu/packages/image.scm (libpng-apng)[phases]: Remove it.
| * gnu: Add libpng-apng.ng02017-03-17
| | | | | | | | | | | | * gnu/packages/image.scm (libpng-apng): New variable. Co-authored-by: Kei Kebreau <kei@openmailbox.org>
| * gnu: Add ocaml-mcl.Ben Woodcroft2017-03-17
| | | | | | | | * gnu/packages/machine-learning.scm (ocaml-mcl): New variable.
| * gnu: Add ocaml-gsl.Ben Woodcroft2017-03-17
| | | | | | | | * gnu/packages/maths.scm (ocaml-gsl): New variable.
| * gnu: Add ocaml-csv.Ben Woodcroft2017-03-17
| | | | | | | | * gnu/packages/ocaml.scm (ocaml-csv): New variable.
| * gnu: Add ocaml-sqlite3.Ben Woodcroft2017-03-17
| | | | | | | | * gnu/packages/ocaml.scm (ocaml-sqlite3): New variable.
| * 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.
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