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2018-06-02gnu: r-xvector: Update to 0.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.20.0.
2018-06-02gnu: r-limma: Update to 3.36.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.1.
2018-06-02gnu: r-variantannotation: Update to 1.26.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.0.
2018-06-02gnu: r-edger: Update to 3.22.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.2.
2018-06-02gnu: r-genomeinfodb: Update to 1.16.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.16.0.
2018-06-02gnu: r-iranges: Update to 2.14.10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.10.
2018-06-02gnu: r-s4vectors: Update to 0.18.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.2.
2018-06-02gnu: r-dnacopy: Update to 1.54.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.54.0.
2018-06-02gnu: r-bioccheck: Update to 1.16.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.16.0.
2018-06-02gnu: r-biocstyle: Update to 2.8.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.8.2.
2018-06-02gnu: r-biocviews: Update to 1.48.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.0.
2018-06-02gnu: r-biocinstaller: Update to 1.30.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.30.0.
2018-06-02gnu: r-biocgenerics: Update to 0.26.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.26.0.
2018-06-02gnu: r-grohmm: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.14.0.
2018-06-02gnu: r-systempiper: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.14.0.
2018-06-02gnu: r-shortread: Update to 1.38.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.38.0.
2018-06-02gnu: r-gostats: Update to 2.46.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.46.0.
2018-06-02gnu: r-category: Update to 2.46.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-category): Update to 2.46.0.
2018-06-02gnu: r-gseabase: Update to 1.42.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.42.0.
2018-06-02gnu: r-rbgl: Update to 1.56.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.56.0.
2018-06-02gnu: r-annotationforge: Update to 1.22.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.0.
2018-06-02gnu: r-dexseq: Update to 1.26.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.26.0.
2018-06-02gnu: r-deseq2: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.20.0.
2018-06-02gnu: r-genefilter: Update to 1.62.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.62.0.
2018-06-02gnu: r-geneplotter: Update to 1.58.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.58.0.
2018-06-02gnu: r-copynumber: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-copynumber): Update to 1.20.0.
2018-06-02gnu: r-annotate: Update to 1.58.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.58.0.
2018-06-02gnu: r-qdnaseq: Update to 1.16.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.16.0. [propagated-inputs]: Add r-biocparallel.
2018-06-02gnu: r-cghcall: Update to 2.42.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-cghcall): Update to 2.42.0.
2018-06-02gnu: r-cghbase: Update to 1.40.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-cghbase): Update to 1.40.0.
2018-06-02gnu: r-marray: Update to 1.58.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-marray): Update to 1.58.0. [propagated-inputs]: Remove r-biobase.
2018-06-02gnu: r-chippeakanno: Update to 3.14.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.0. [propagated-inputs]: Add r-biostrings, r-delayedarray, r-genomicranges, r-iranges, and r-s4vectors.
2018-06-02gnu: r-ripseeker: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ripseeker): Update to 1.20.0.
2018-06-02gnu: r-diffbind: Update to 2.8.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-diffbind): Update to 2.8.0. [propagated-inputs]: Add r-genomicranges, r-ggplot2, and r-summarizedexperiment.
2018-06-02gnu: r-regioner: Update to 1.12.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.12.0. [propagated-inputs]: Add r-s4vectors.
2018-06-02gnu: r-hpar: Update to 1.22.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-hpar): Update to 1.22.2.
2018-06-02gnu: r-minimal: Update to 3.5.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-with-tests): New variable derived from r-minimal; update to 3.5.0. [arguments]: Build recommended packages. (r-minimal): Inherit from r-with-tests. [arguments]: Disable recommended packages and tests.
2018-06-02gnu: emacs-elfeed: Update to 3.0.0.Clément Lassieur
* gnu/packages/emacs.scm (emacs-elfeed): Update to 3.0.0.
2018-06-02self: Include gnu/build/* in the result.Ludovic Courtès
Previously, modules like gnu/build/cross-toolchain.scm or gnu/build/svg.scm were missing from the result. * guix/self.scm (compiled-guix)[*system-modules*]: Add gnu/build/* to #:extra-files. (imported-files)[same-target?]: New procedure. [build]: Call 'delete-duplicates' on FILES.
2018-06-02self: 'compiled-files' builds the given list of files.Ludovic Courtès
* guix/self.scm (compiled-files): Add 'module-files' parameter. [build]: 'process-directory' now honors MODULE-FILES instead of building any '.scm' file it sees. (scheme-node): Adjust accordingly.
2018-06-02self: Improve backtraces for 'imported-files'.Ludovic Courtès
* guix/self.scm (imported-files): Pass #:env-vars.
2018-06-01gnu: icecat: Add more fixes from upstream esr52.Mark H Weaver
* gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from the upstream mozilla-esr52 repository.
2018-06-01self: Show backtraces on more columns.Ludovic Courtès
* guix/self.scm (compiled-modules): Add "COLUMNS" to #:env-vars.
2018-06-01self: Add dependency on guile-gdbm-ffi.Ludovic Courtès
Fixes a regression introduced in 331ac4cc239727992329207ba428b3f26cae91d9 whereby "guile-gdbm-ffi" would now be mandatory. * guix/self.scm (specification->package): Add "guile-gdbm-ffi" and "guile2.0-gdbm-ffi". (compiled-guix)[guile-gdbm-ffi]: New variables. [dependencies]: Add it.
2018-06-01gnu: qtbase: Fix build on older kernels.Ricardo Wurmus
* gnu/packages/qt.scm (qtbase)[arguments]: Add configure flags "-no-feature-getentropy" and "-no-feature-renameat2".
2018-06-01Add (guix store deduplication).Caleb Ristvedt
* guix/store/database.scm (register-path): Add #:deduplicate? and call 'deduplicate' when it's true. (counting-wrapper-port, nar-sha256): Move to... * guix/store/deduplication.scm: ... here. New file. * tests/store-deduplication.scm: New file. * Makefile.am (STORE_MODULES): Add deduplication.scm. (SCM_TESTS) [HAVE_GUILE_SQLITE3]: Add store-deduplication.scm. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2018-06-01database: 'register-path' resets timestamps.Ludovic Courtès
* guix/store/database.scm (reset-timestamps): New procedure. (register-path): Use it.
2018-06-01Add (gnu store database).Caleb Ristvedt
* guix/config.scm.in (%store-database-directory): New variable. * guix/store/database.scm: New file. * tests/store-database.scm: New file. * Makefile.am (STORE_MODULES): New variable. (MODULES, MODULES_NOT_COMPILED): Adjust accordingly. (SCM_TESTS) [HAVE_GUILE_SQLITE3]: Add tests/store-database.scm. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2018-06-01build: Check for Guile-SQLite3.Ludovic Courtès
* m4/guix.m4 (GUIX_CHECK_GUILE_SQLITE3): New macro. * configure.ac: Use it and define 'HAVE_GUILE_SQLITE3'. * guix/self.scm (specification->package): Add "guile-sqlite3". (compiled-guix)[guile-sqlite3]: New variable. [dependencies]: Add it.
2018-06-01vm: Use 'with-extensions'.Ludovic Courtès
* gnu/system/vm.scm (system-docker-image)[build]: Use 'with-extensions'. Remove 'add-to-load-path' calls.
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