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2017-03-17gnu: Add r-spatial.•••* gnu/packages/statistics.scm (r-spatial): New variable. Ricardo Wurmus
2017-03-17gnu: r-rpart: Move to the set of recommended packages.•••* gnu/packages/statistics.scm (r-rpart): Move up to the set of recommended packages. Ricardo Wurmus
2017-03-17gnu: r-nnet: Move to set of recommended R packages.•••* 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. Ricardo Wurmus
2017-03-17gnu: r-mgcv: Move to set of recommended R packages.•••* gnu/packages/statistics.scm (r-mgcv): Move up to set of recommended R packages. Ricardo Wurmus
2017-03-17gnu: Add r-nlme.•••* gnu/packages/statistics.scm (r-nlme): New variable. Ricardo Wurmus
2017-03-17gnu: r-matrix: Move to set of recommended R packages.•••* gnu/packages/statistics.scm (r-matrix): Move to set of recommended R packages. Ricardo Wurmus
2017-03-17gnu: r-lattice: Move to other recommended R packages.•••* gnu/packages/statistics.scm (r-lattice): Move to the set of recommended R packages. Ricardo Wurmus
2017-03-17gnu: Add r-kernsmooth.•••* gnu/packages/statistics.scm (r-kernsmooth): New variable. Ricardo Wurmus
2017-03-17gnu: Add r-foreign.•••* gnu/packages/statistics.scm (r-foreign): New variable. Ricardo Wurmus
2017-03-17gnu: Add r-codetools.•••* gnu/packages/statistics.scm (r-codetools): New variable. Ricardo Wurmus
2017-03-17gnu: Add r-cluster.•••* gnu/packages/statistics.scm (r-cluster): New variable. Ricardo Wurmus
2017-03-17gnu: Add r-class.•••* gnu/packages/statistics.scm (r-class): New variable. Ricardo Wurmus
2017-03-17gnu: Add r-mass.•••* gnu/packages/statistics.scm (r-mass): New variable. Ricardo Wurmus
2017-03-17gnu: Add r-boot.•••* gnu/packages/statistics.scm (r-boot): New variable. Ricardo Wurmus
2017-03-17doc: Really document 'guix pack --format'.•••* doc/guix.texi (Invoking guix pack): Properly document --format. Ludovic Courtès
2017-03-17gnu: youtube-dl: Update to 2017.03.16.•••* gnu/packages/video.scm (youtube-dl): Update to 2017.03.16. Tobias Geerinckx-Rice
2017-03-16gnu: asciidoc: Use local docbook-xml package.•••* gnu/packages/documentation.scm (asciidoc)[inputs]: Add docbook-xml. [arguments]: Add 'make-local-docbook-xml' phase. Kei Kebreau
2017-03-17gnu: Add knot.•••* gnu/packages/dns.scm (knot): New variable. Tobias Geerinckx-Rice
2017-03-17gnu: Add liburcu.•••* gnu/packages/datastructures.scm (liburcu): New variable. Tobias Geerinckx-Rice
2017-03-17gnu: dns: Fix typo and use @dfn in descriptions.•••* gnu/packages/dns.scm (bind)[description]: Use @dfn to expand acronyms. (yadifa)[description]: Likewise, and fix a typo. Tobias Geerinckx-Rice
2017-03-16gnu: linux-libre: Update to 4.10.3.•••* gnu/packages/linux.scm (%linux-libre-version): Update to 4.10.3. (%linux-libre-hash): Update hash. Leo Famulari
2017-03-16gnu: linux-libre@4.4: Update to 4.4.54.•••* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.54. Leo Famulari
2017-03-16gnu: linux-libre@4.9: Update to 4.9.15.•••* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.15. Leo Famulari
2017-03-16gnu: qemu: Fix CVE-2017-{2620,2630}.•••* 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. Leo Famulari
2017-03-16gnu: virglrenderer: Fix CVE-2017-6386.•••* 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. Leo Famulari
2017-03-16doc: Reorganize categories.•••* doc/guix.texi: Move "guix build" to the "Software Development" category; add "guix pack". Ludovic Courtès
2017-03-16doc: Mention 'guix pack' reproducibility.•••* doc/guix.texi (Invoking guix pack): Mention reproducibility. Ludovic Courtès
2017-03-16pack: Allow for "-S /opt/foo=".•••Reported by Andy Wingo. * guix/scripts/pack.scm (%options): Use 'string-split' instead of 'string-tokenize'. Ludovic Courtès
2017-03-16pack: Honor symlinks in the Docker back-end.•••* 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'. Ludovic Courtès
2017-03-16docker: Build images in a reproducible fashion.•••* guix/docker.scm (%tar-determinism-options): New variable. (build-docker-image): Use it on the two 'tar' invocations. Ludovic Courtès
2017-03-16pack: Use a fixed timestamp in Docker images.•••* 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'. Ludovic Courtès
2017-03-16pack: Add '--format' option and Docker output support.•••* 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'. Ludovic Courtès
2017-03-16pack: Honor command-line options related to the store.•••* guix/scripts/pack.scm (guix-pack): Call 'set-build-options-from-command-line'. Ludovic Courtès
2017-03-16memoization: Micro-optimize code produced by 'define-cache-procedure'.•••* guix/memoization.scm (%nothing): Remove. (define-cache-procedure): Make '%nothing' a local variable, with a literal list. Ludovic Courtès
2017-03-16services: connman: Rework service.•••* 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> Mathieu Othacehe
2017-03-16gexp: Add '=>' syntax to import computed modules.•••* 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'. Ludovic Courtès
2017-03-16utils: Move base16 procedures to (guix base16).•••* 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. Ludovic Courtès
2017-03-16gnu: password-store: Fix compatibility with GnuPG 2.1.19.•••* 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> Clément Lassieur
2017-03-16gnu: Add r-seurat.•••* gnu/packages/bioinformatics.scm (r-seurat): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Raoul Jean Pierre Bonnal
2017-03-16gnu: sra-tools: Update to 2.8.2-1.•••* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.8.2-1. [arguments]: Add DEFAULT_CRT and DEFAULT_KFG to make flags. Ricardo Wurmus
2017-03-16gnu: ncbi-vdb: Install configuration files.•••* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase "install-configuration-files". Ricardo Wurmus
2017-03-16gnu: ncbi-vdb: Override search path for java-ngs.•••* 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". Ricardo Wurmus
2017-03-16gnu: ncbi-vdb: Use modify-phases syntax.•••* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases syntax. Ricardo Wurmus
2017-03-16gnu: ncbi-vdb: Update to 2.8.2.•••* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2. Ricardo Wurmus
2017-03-16gnu: ngs-sdk: Update to 1.3.0.•••* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0. Ricardo Wurmus
2017-03-16gnu: Add pzstd.•••* gnu/packages/compression.scm (pzstd): New variable. Tobias Geerinckx-Rice
2017-03-16gnu: Add zstd.•••* gnu/packages/compression.scm (zstd): New variable. Tobias Geerinckx-Rice
2017-03-16gnu: python-publicsuffix2: Update to 2.20160818.•••* gnu/packages/python.scm (python-publicsuffix2): Update to 2.20160818. Tobias Geerinckx-Rice
2017-03-16gnu: awscli: Update to 1.11.63.•••* gnu/packages/python.scm (awscli): Update to 1.11.63. Tobias Geerinckx-Rice
2017-03-16gnu: python-botocore: Update to 1.5.26.•••* gnu/packages/python.scm (python-botocore): Update to 1.5.26. Tobias Geerinckx-Rice
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