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2017-03-17gnu: btrfs-progs: Update to 4.10.1.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (btrfs-progs): Update to 4.10.1.
2017-03-17build/cargo-build-system: Make cargo-build-system install working packages.Danny Milosavljevic
* 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.
2017-03-17build-system/cargo (cargo-build): Add cargo-build-flags, remove configure-flags.Danny Milosavljevic
* guix/build-system/cargo.scm (cargo-build): Add cargo-build-flags, remove configure-flags.
2017-03-17gnu: cargo: Use upstream cargo.Danny Milosavljevic
* gnu/packages/rust.scm (cargo): Use upstream cargo.
2017-03-17gnu: rust: Update to 1.15.0.Danny Milosavljevic
* 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.
2017-03-17gnu: libpng-apng: Remove unnecessary call to libtool.Kei Kebreau
* gnu/packages/image.scm (libpng-apng)[phases]: Remove it.
2017-03-17gnu: Add libpng-apng.ng0
* gnu/packages/image.scm (libpng-apng): New variable. Co-authored-by: Kei Kebreau <kei@openmailbox.org>
2017-03-17gnu: Add ocaml-mcl.Ben Woodcroft
* gnu/packages/machine-learning.scm (ocaml-mcl): New variable.
2017-03-17gnu: Add ocaml-gsl.Ben Woodcroft
* gnu/packages/maths.scm (ocaml-gsl): New variable.
2017-03-17gnu: Add ocaml-csv.Ben Woodcroft
* gnu/packages/ocaml.scm (ocaml-csv): New variable.
2017-03-17gnu: Add ocaml-sqlite3.Ben Woodcroft
* gnu/packages/ocaml.scm (ocaml-sqlite3): New variable.
2017-03-17gnu: snakemake: Update to 3.11.2.Ricardo Wurmus
* gnu/packages/python.scm (snakemake): Update to 3.11.2.
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.
2017-03-17doc: Really document 'guix pack --format'.Ludovic Courtès
* doc/guix.texi (Invoking guix pack): Properly document --format.
2017-03-17gnu: youtube-dl: Update to 2017.03.16.Tobias Geerinckx-Rice
* gnu/packages/video.scm (youtube-dl): Update to 2017.03.16.
2017-03-16gnu: asciidoc: Use local docbook-xml package.Kei Kebreau
* gnu/packages/documentation.scm (asciidoc)[inputs]: Add docbook-xml. [arguments]: Add 'make-local-docbook-xml' phase.
2017-03-17gnu: Add knot.Tobias Geerinckx-Rice
* gnu/packages/dns.scm (knot): New variable.
2017-03-17gnu: Add liburcu.Tobias Geerinckx-Rice
* gnu/packages/datastructures.scm (liburcu): New variable.
2017-03-17gnu: dns: Fix typo and use @dfn in descriptions.Tobias Geerinckx-Rice
* gnu/packages/dns.scm (bind)[description]: Use @dfn to expand acronyms. (yadifa)[description]: Likewise, and fix a typo.
2017-03-16gnu: linux-libre: Update to 4.10.3.Leo Famulari
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.10.3. (%linux-libre-hash): Update hash.
2017-03-16gnu: linux-libre@4.4: Update to 4.4.54.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.54.
2017-03-16gnu: linux-libre@4.9: Update to 4.9.15.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.15.
2017-03-16gnu: qemu: Fix CVE-2017-{2620,2630}.Leo Famulari
* 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.
2017-03-16gnu: virglrenderer: Fix CVE-2017-6386.Leo Famulari
* 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.
2017-03-16doc: Reorganize categories.Ludovic Courtès
* doc/guix.texi: Move "guix build" to the "Software Development" category; add "guix pack".
2017-03-16doc: Mention 'guix pack' reproducibility.Ludovic Courtès
* doc/guix.texi (Invoking guix pack): Mention reproducibility.
2017-03-16pack: Allow for "-S /opt/foo=".Ludovic Courtès
Reported by Andy Wingo. * guix/scripts/pack.scm (%options): Use 'string-split' instead of 'string-tokenize'.
2017-03-16pack: Honor symlinks in the Docker back-end.Ludovic Courtès
* guix/docker.scm (symlink-source, topmost-component): New procedures. (build-docker-image): Add #:symlinks parameter and honor it. Remove hard-coded /bin symlink. * guix/scripts/pack.scm (docker-image): Pass #:symlinks to 'build-docker-image'.
2017-03-16docker: Build images in a reproducible fashion.Ludovic Courtès
* guix/docker.scm (%tar-determinism-options): New variable. (build-docker-image): Use it on the two 'tar' invocations.
2017-03-16pack: Use a fixed timestamp in Docker images.Ludovic Courtès
* guix/docker.scm (build-docker-image): Add #:creation-time parameter. Use SRFI-19 'date->string' instead of 'strftime' et al. * guix/scripts/pack.scm (docker-image)[build]: Pass #:creation-time to 'build-docker-image'.
2017-03-16pack: Add '--format' option and Docker output support.Ludovic Courtès
* guix/docker.scm: Remove dependency on (guix store) and (guix utils). Use (guix build store-copy). Load (json) lazily. (build-docker-image): Remove #:system. Add #:closure, #:compressor, and 'image' parameters. Use 'uname' to determine the architecture. Remove use of 'call-with-temporary-directory'. Use 'read-reference-graph' to compute ITEMS. Honor #:compressor. * guix/scripts/pack.scm (docker-image): New procedure. (%default-options): Add 'format'. (%formats): New variable. (%options, show-help): Add '--format'. (guix-pack): Honor '--format'. * guix/scripts/archive.scm: Remove '--format' option. This reverts commits 1545a012cb7cd78e25ed99ecee26df457be590e9, 01445711db6771cea6122859c3f717f130359f55, and 03476a23ff2d4175b7d3c808726178f764359bec. * doc/guix.texi (Invoking guix pack): Document '--format'. (Invoking guix archive): Remove documentation of '--format'.
2017-03-16pack: Honor command-line options related to the store.Ludovic Courtès
* guix/scripts/pack.scm (guix-pack): Call 'set-build-options-from-command-line'.
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