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* 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.
* doc: Make "Application Setup" slightly more visible.Ludovic Courtès2017-03-18
| | | | | | | Suggested by Arne Babenhauserheide. * doc/guix.texi (Binary Installation): Make the "Application Setup" reference an 8th item in the list.
* http-client: Avoid name clash with 'open-connection-for-uri' in 2.2.0.Ludovic Courtès2017-03-18
| | | | | | | | | * guix/build/download.scm (open-connection-for-uri): Add note about same-named binding in Guile 2.2.0. * guix/http-client.scm: Use 'guix:open-connection-for-uri' for the procedure coming from (guix build download). * guix/scripts/lint.scm: Likewise. * guix/scripts/substitute.scm: Likewise.
* build: Require Guile >= 2.0.9.Ludovic Courtès2017-03-18
| | | | | | | | | | | | | | | | * configure.ac: Bump requirement to 2.0.9. * doc/guix.texi (Requirements): Adjust accordingly. * README (Requirements): Likewise. * build-aux/download.scm: Remove workaround for <http://bugs.gnu.org/13095>. * guix/build/download.scm: Likewise. (http-fetch)[post-2.0.7?]: Remove. Remove conditional code for not POST-2.0.7?. * guix/http-client.scm: Remove workaround for <http://bugs.gnu.org/13095>. (http-fetch)[post-2.0.7?]: Remove. Remove conditional code for not POST-2.0.7?. * guix/serialization.scm (read-latin1-string): Remove mention of 2.0.9. * tests/nar.scm: Use (ice-9 control). (let/ec): Remove.
* pack: Add '--target'.Ludovic Courtès2017-03-18
| | | | | | | | | | | | * guix/scripts/pack.scm (self-contained-tarball): Add #:target. (docker-image): Add #:target. [build]: Pass it to 'build-docker-image'. (%options, show-help): Add '--target'. (guix-pack): Pass TARGET to 'profile-derivation' and to 'build-image'. * guix/docker.scm (build-docker-image): Add #:system parameter and honor it. * doc/guix.texi (Invoking guix pack): Document '--target'. (Additional Build Options): Refer to the Autoconf manual instead of the obsolete 'configure.info' for cross-compilation.
* profiles: Packages in a profile can be cross-compiled.Ludovic Courtès2017-03-17
| | | | | | * guix/profiles.scm (profile-derivation): Add #:target parameter; pass it to 'gexp->derivation'. * tests/profiles.scm ("profile-derivation, cross-compilation"): New test.
* pack: Move absolute file name to <compressor>.Ludovic Courtès2017-03-17
| | | | | | | | | | * guix/scripts/pack.scm (<compressor>)[package]: Remove. [command]: Document as being a gexp with an absolute file name. (%compressors): Adjust accordingly. (self-contained-tarball): Simplify PATH expression. Move 'string-join' for the compressor command on the build side. (docker-image): Simplify PATH expression. * tests/pack.scm (%gzip-compressor): Adjust accordingly.
* 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.
* build/cargo-build-system: Make cargo-build-system install working packages.Danny Milosavljevic2017-03-17
| | | | | | | | | | * 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.Danny Milosavljevic2017-03-17
| | | | | * guix/build-system/cargo.scm (cargo-build): Add cargo-build-flags, remove configure-flags.
* 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.
* 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.
* doc: Really document 'guix pack --format'.Ludovic Courtès2017-03-17
| | | | * doc/guix.texi (Invoking guix pack): Properly document --format.
* gnu: youtube-dl: Update to 2017.03.16.Tobias Geerinckx-Rice2017-03-17
| | | | * gnu/packages/video.scm (youtube-dl): Update to 2017.03.16.
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