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2019-03-07pack: Add '--save-provenance'.Ludovic Courtès
* guix/scripts/pack.scm (show-help, %options): Add '--save-provenance'. (guix-pack)[manifest-from-args]: Honor it. * doc/guix.texi (Invoking guix pack): Document it.
2019-03-07describe: Add 'package-provenance'.Ludovic Courtès
* guix/scripts/package.scm (package-provenance): Move to... * guix/describe.scm (package-provenance): ... here.
2019-03-07database: Make 'register-items' transactional.Caleb Ristvedt
* guix/store/database.scm (SQLITE_BUSY, register-output-sql): New variables. (add-references): Don't try finalizing after each use, only after all the uses (otherwise a finalized statement would be used if #:cache? was #f). (call-with-transaction): New procedure. (register-items): Use call-with-transaction to prevent broken intermediate states from being visible. * .dir-locals.el (call-with-transaction): indent it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-03-06gnu: linux-libre: Update to 5.0.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-version): Update to 5.0. (%linux-libre-hash): Update hash. (%linux-libre-4.20-patches): Rename to ... (%linux-libre-5.0-patches): ... this. (linux-libre, linux-libre-arm-generic, linux-libre-arm-omap2plus): Use %linux-libre-5.0-patches instead of %linux-libre-4.20-patches. * gnu/packages/aux-files/linux-libre/4.20-arm.conf, gnu/packages/aux-files/linux-libre/4.20-arm64.conf, gnu/packages/aux-files/linux-libre/4.20-i686.conf, gnu/packages/aux-files/linux-libre/4.20-x86_64.conf: Delete files. * gnu/packages/aux-files/linux-libre/5.0-arm.conf, gnu/packages/aux-files/linux-libre/5.0-arm64.conf, gnu/packages/aux-files/linux-libre/5.0-i686.conf, gnu/packages/aux-files/linux-libre/5.0-x86_64.conf: New files. * Makefile.am (AUX_FILES): Adjust accordingly.
2019-03-06gnu: linux-libre@4.19: Update to 4.19.27.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-4.19-version): Update to 4.19.27. (%linux-libre-4.19-hash): Update hash.
2019-03-06gnu: linux-libre@4.14: Update to 4.14.105.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.105. (%linux-libre-4.14-hash): Update hash.
2019-03-06gnu: linux-libre@4.9: Update to 4.9.162.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.162.
2019-03-06nls: Add Swedish translation.Julien Lepiller
* po/guix/sv.po: New file. * po/guix/LINGUAS: Add 'sv'.
2019-03-06gnu: synthv1: Update to 0.9.5.Ricardo Wurmus
* gnu/packages/music.scm (synthv1): Update to 0.9.5.
2019-03-06gnu: drumkv1: Update to 0.9.5.Ricardo Wurmus
* gnu/packages/music.scm (drumkv1): Update to 0.9.5.
2019-03-06gnu: samplv1: Update to 0.9.5.Ricardo Wurmus
* gnu/packages/music.scm (samplv1): Update to 0.9.5.
2019-03-06gnu: padthv1: Update to 0.9.5.Ricardo Wurmus
* gnu/packages/music.scm (padthv1): Update to 0.9.5.
2019-03-06gnu: yoshimi: Update to 1.5.10.2.Ricardo Wurmus
* gnu/packages/music.scm (yoshimi): Update to 1.5.10.2.
2019-03-06gnu: electron-cash: Update to 3.3.6.Vagrant Cascadian
* gnu/packages/finance (electron-cash): Update to 3.3.6. Signed-off-by: Leo Famulari <leo@famulari.name>
2019-03-06gnu: electrum: Update to 3.3.4.Vagrant Cascadian
* gnu/packages/finance (electrum): Update to 3.3.4. Signed-off-by: Leo Famulari <leo@famulari.name>
2019-03-06gnu: diffoscope: Update to 113.Vagrant Cascadian
* gnu/packages/package-management (diffoscope): Update to 113. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-03-06gnu: Add multitime.Ricardo Wurmus
* gnu/packages/benchmark.scm (multitime): New variable.
2019-03-06gnu: r-org-mm-eg-db: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Move from here... * gnu/packages/bioconductor.scm (r-org-mm-eg-db): ...to here.
2019-03-06gnu: r-org-hs-eg-db: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Move from here... * gnu/packages/bioconductor.scm (r-org-hs-eg-db): ...to here.
2019-03-06gnu: r-org-dm-eg-db: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Move from here... * gnu/packages/bioconductor.scm (r-org-dm-eg-db): ...to here.
2019-03-06gnu: r-org-ce-eg-db: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Move from here... * gnu/packages/bioconductor.scm (r-org-ce-eg-db): ...to here.
2019-03-06gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): Move from here... * gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): ...to here.
2019-03-06gnu: r-bsgenome-dmelanogaster-ucsc-dm3: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-dmelanogaster-ucsc-dm3): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3): ...to here.
2019-03-06gnu: r-bsgenome-celegans-ucsc-ce10: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce10): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce10): ...to here.
2019-03-06gnu: r-bsgenome-celegans-ucsc-ce6: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce6): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce6): ...to here.
2019-03-06gnu: r-bsgenome-mmusculus-ucsc-mm10: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm10): ...to here.
2019-03-06gnu: r-bsgenome-mmusculus-ucsc-mm9: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm9): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9): ...to here.
2019-03-06gnu: r-bsgenome-hsapiens-ucsc-hg19: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19): ...to here.
2019-03-06gnu: r-bsgenome-hsapiens-1000genomes-hs37d5: Move to (gnu packages ↵Ricardo Wurmus
bioconductor). * gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-1000genomes-hs37d5): ...to here.
2019-03-06gnu: r-txdb-hsapiens-ucsc-hg19-knowngene: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): Move from here... * gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): ...to here.
2019-03-06gnu: r-geneplotter: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-geneplotter): Move from here... * gnu/packages/bioconductor.scm (r-geneplotter): ...to here.
2019-03-06gnu: Add guile-stis-parser.Ricardo Wurmus
* gnu/packages/guile-xyz.scm (guile-stis-parser): New variable.
2019-03-06gnu: r-copynumber: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-copynumber): Move from here... * gnu/packages/bioconductor.scm (r-copynumber): ...to here.
2019-03-06gnu: Update copyright headers.Ricardo Wurmus
This is a follow-up to commit 1fe9a36173335b559c695357bc8d884f1d4b144a. * gnu/packages/bioconductor.scm: Update copyright header to account for moved package.
2019-03-06gnu: font-gnu-unifont: Update to 12.0.01.Efraim Flashner
* gnu/packages/fonts.scm (font-gnu-unifont): Update to 12.0.01.
2019-03-06gnu: cabextract: Don't use NAME in source URI.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (cabextract)[source]: Hard-code NAME.
2019-03-06gnu: cabextract: Update to 1.9.1.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (cabextract): Update to 1.9.1.
2019-03-06gnu: lcov: Update to 1.14.Tobias Geerinckx-Rice
* gnu/packages/code.scm (lcov): Update to 1.14.
2019-03-06gnu: python-mako: Update home page.Marius Bakke
* gnu/packages/python-xyz.scm (python-mako)[home-page]: Use HTTPS.
2019-03-06gnu: fuseiso: Fix typo.Marius Bakke
* gnu/packages/linux.scm (fuseiso)[synopsis]: s/imsages/images.
2019-03-06gnu: valgrind: Add download mirror.Marius Bakke
* gnu/packages/valgrind.scm (valgrind)[source](uri): Add mirror.
2019-03-06gnu: bismark: Update to 0.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bismark): Update to 0.20.1. [source]: Remove obsolete snippet. [arguments]: Add build phase "replace-plotly.js" and add requried modules; adjust "install" phase. [inputs]: Add perl-carp and perl-getopt-long. [native-inputs]: Add plotly.js and uglify-js.
2019-03-06gnu: Add fuseiso.Pierre Neidhardt
* gnu/packages/linux.scm (fuseiso): New variable.
2019-03-06gnu: Add r-scde.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scde): New variable.
2019-03-06gnu: Add bowtie1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bowtie1): New variable.
2019-03-06gnu: octave, octave-cli: Update to 5.1.0.Kei Kebreau
* gnu/packages/maths.scm (octave, octave-cli): Update to 5.1.0.
2019-03-06gnu: crawl, crawl-tiles: Update to 0.23.1.Kei Kebreau
* gnu/packages/games.scm (crawl, crawl-tiles): Update to 0.23.1. [native-inputs]: Add python and python-pyyaml. [arguments]: Add 'patch-python' phase, modify the 'check' phase and move the 'check' phase back after the 'build' phase.
2019-03-06gnu: perl-czplib: Fix installation directory.Ricardo Wurmus
* gnu/packages/perl.scm (perl-czplib)[arguments]: Fix installation directory.
2019-03-06gnu: Add guile-studio.Ricardo Wurmus
* gnu/packages/guile-xyz.scm (guile-studio): New variable.
2019-03-06gnu: Add genrich.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (genrich): New variable.
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