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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'.
2017-03-16memoization: Micro-optimize code produced by 'define-cache-procedure'.Ludovic Courtès
* guix/memoization.scm (%nothing): Remove. (define-cache-procedure): Make '%nothing' a local variable, with a literal list.
2017-03-16services: connman: Rework service.Mathieu Othacehe
* gnu/services/networking.scm (connman-service): Remove. (<connman-configuration>): New record specifying the package to be used (connman) and whether vpn plugin shall be disabled (disable-vpn?). (connman-configuration): New exported variable. (connman-configuration?): New exported variable. (connman-service-type): Export it. * doc/guix.texi (Networking Services): Adjust accordingly. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-03-16gexp: Add '=>' syntax to import computed modules.Ludovic Courtès
* guix/gexp.scm (imported-files)[file-pair]: Add case for pairs where the cdr is not a string. (imported-modules): Support '=>' syntax in MODULES. * tests/gexp.scm ("imported-files with file-like objects") ("gexp->derivation & with-imported-module & computed module"): New tests. * doc/guix.texi (G-Expressions): Document '=>' syntax for 'with-imported-modules'.
2017-03-16utils: Move base16 procedures to (guix base16).Ludovic Courtès
* guix/utils.scm (bytevector->base16-string, base16-string->bytevector): Move to... * guix/base16.scm: ... here. New file. * tests/utils.scm ("bytevector->base16-string->bytevector"): Move to... * tests/base16.scm: ... here. New file. * Makefile.am (MODULES): Add guix/base16.scm. (SCM_TESTS): Add tests/base16.scm. * build-aux/download.scm, guix/derivations.scm, guix/docker.scm, guix/import/snix.scm, guix/pk-crypto.scm, guix/scripts/authenticate.scm, guix/scripts/download.scm, guix/scripts/hash.scm, guix/store.scm, tests/hash.scm, tests/pk-crypto.scm: Adjust imports accordingly.
2017-03-16gnu: password-store: Fix compatibility with GnuPG 2.1.19.Clément Lassieur
* gnu/packages/patches/password-store-gnupg-compat.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/password-utils.scm (password-store)[source]: Use it. Signed-off-by: Clément Lassieur <clement@lassieur.org>
2017-03-16gnu: Add r-seurat.Raoul Jean Pierre Bonnal
* gnu/packages/bioinformatics.scm (r-seurat): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2017-03-16gnu: sra-tools: Update to 2.8.2-1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.8.2-1. [arguments]: Add DEFAULT_CRT and DEFAULT_KFG to make flags.
2017-03-16gnu: ncbi-vdb: Install configuration files.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase "install-configuration-files".
2017-03-16gnu: ncbi-vdb: Override search path for java-ngs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Patch "package.prl" to ensure that java-ngs is found by the configure script; remove configure flag "--with-ngs-java-prefix".
2017-03-16gnu: ncbi-vdb: Use modify-phases syntax.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases syntax.
2017-03-16gnu: ncbi-vdb: Update to 2.8.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2.
2017-03-16gnu: ngs-sdk: Update to 1.3.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0.
2017-03-16gnu: Add pzstd.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (pzstd): New variable.
2017-03-16gnu: Add zstd.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (zstd): New variable.
2017-03-16gnu: python-publicsuffix2: Update to 2.20160818.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-publicsuffix2): Update to 2.20160818.
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