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2017-11-07gnu: r-variantannotation: Update to 1.24.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.0.
2017-11-07gnu: r-genomeinfodb: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.14.0.
2017-11-07gnu: r-iranges: Update to 2.12.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.12.0.
2017-11-07gnu: r-s4vectors: Update to 0.16.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.16.0.
2017-11-07gnu: r-biocstyle: Update to 2.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.0.
2017-11-07gnu: r-biocinstaller: Update to 1.28.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.28.0.
2017-11-07gnu: r-biocgenerics: Update to 0.24.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.24.0.
2017-11-07gnu: r-grohmm: Update to 1.12.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.12.0.
2017-11-07gnu: r-shortread: Update to 1.36.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.0.
2017-11-07gnu: r-systempiper: Update to 1.12.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.12.0.
2017-11-07gnu: r-gseabase: Update to 1.40.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.0.
2017-11-07gnu: r-sva: Update to 3.26.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.26.0.
2017-11-07gnu: r-methylkit: Update to 1.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.4.0.
2017-11-07gnu: r-copywriter: Update to 2.10.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.10.0.
2017-11-07gnu: r-annotationfilter: Update to 1.2.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.2.0.
2017-11-07gnu: r-rhdf5: Update to 2.22.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.22.0.
2017-11-07gnu: r-tximport: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.6.0.
2017-11-07gnu: r-bamsignals: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.10.0.
2017-11-07gnu: r-zlibbioc: Update to 1.24.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.24.0.
2017-11-07gnu: r-rhtslib: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.10.0.
2017-11-07gnu: r-rbgl: Update to 1.54.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.54.0.
2017-11-07gnu: r-annotationforge: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.20.0.
2017-11-07gnu: r-dexseq: Update to 1.24.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.0.
2017-11-07gnu: r-deseq2: Update to 1.18.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.0.
2017-11-07gnu: r-genefilter: Update to 1.60.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.60.0.
2017-11-07gnu: r-geneplotter: Update to 1.56.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.56.0.
2017-11-07gnu: r-annotate: Update to 1.56.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.0.
2017-11-07gnu: r-dnacopy: Update to 1.52.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.52.0.
2017-11-07gnu: r-biocviews: Update to 1.46.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.46.0. [propagated-inputs]: Remove r-knitr.
2017-11-07gnu: r-bioccheck: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.14.0. [native-inputs]: Remove which. [propagated-inputs]: Add r-stringdist.
2017-11-07gnu: Add r-stringdist.Ricardo Wurmus
* gnu/packages/cran.scm (r-stringdist): New variable.
2017-11-07gnu: r-rgraphviz: Update to 2.22.0.Ricardo Wurmus
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.22.0.
2017-11-07guix: Add archive support for bioconductor-uri.Ricardo Wurmus
* guix/build-system/r.scm (bioconductor-uri): Also return the archive URL. * guix/import/cran.scm (latest-bioconductor-release, fetch-description): Adjust because bioconductor-uri now returns a list.
2017-11-07import: cran: Use Bioconductor 3.6 helpers.Ricardo Wurmus
* guix/import/cran.scm (bioconductor-mirror-url): Remove procedure. (fetch-description): Extract DESCRIPTION file from tarball for Bioconductor packages. (latest-bioconductor-release): Use latest-bioconductor-package-version.
2017-11-07import: cran: Add support for Bioconductor 3.6.Ricardo Wurmus
* guix/import/cran.scm (%bioconductor-version, %bioconductor-packages-list-url): New variables. (bioconductor-packages-list, latest-bioconductor-package-version): New procedures.
2017-11-07import: utils: Add string helpers.Ricardo Wurmus
* guix/import/utils.scm (read-lines, chunk-lines): New procedures.
2017-11-06build: Conditionally build json importer.Eric Bavier
* Makefile.am (MODULES): Add guix/scripts/import/json.scm when HAVE_GUILE_JSON.
2017-11-07gnu: guile-git: Update snapshot.Ludovic Courtès
* gnu/packages/guile.scm (guile-git): Update to commit 951a32c.
2017-11-07gnu: moka-icon-theme: Fix license.Brendan Tildesley
* gnu/packages/gnome.scm (moka-icon-theme): Add cc-by-sa4.0 to license field. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07gnu: moka-icon-theme: Add faba-icon-theme as propagated input.Brendan Tildesley
* gnu/packages/gnome.scm (moka-icon-theme)[propagated-inputs]: New field. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07gnu: moka-icon-theme: Simplify package definition.Brendan Tildesley
* gnu/packages/gnome.scm (moka-icon-theme): Inherit faba-icon-theme to avoid duplicating similar package definition. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07gnu: Add faba-icon-theme.Brendan Tildesley
* gnu/packages/gnome.scm (faba-icon-theme): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07gnu: electrum: Update to 3.0.Carlo Zancanaro
gnu/packages/finance.scm (electrum): Update to 3.0. [inputs]: Change to python3 inputs. [arguments]: Remove python-2. Disable tests. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07gnu: Add python-jsonrpclib-pelix.Carlo Zancanaro
* gnu/packages/python.scm (python-jsonrpclib-pelix, python2-jsonrpclib-pelix): New variables. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07refresh: Account for hidden packages.Ludovic Courtès
Suggested by Marius Bakke <mbakke@fastmail.com> in <https://bugs.gnu.org/29177>. * guix/scripts/refresh.scm (all-packages): Pass #:select? to 'fold-packages'.
2017-11-07packages: 'fold-packages' takes #:select? parameter.Ludovic Courtès
* gnu/packages.scm (fold-packages): Add #:select? parameter and honor it.
2017-11-07compile: Fix VPATH builds.Ludovic Courtès
Fixes <https://bugs.gnu.org/29091>. Reported by Eric Bavier <bavier@cray.com>. * guix/build/compile.scm (relative-file): New procedure. (load-files): Use it before calling 'file-name->module-name'. (compile-files): Likewise before calling 'scm->go'. * guix/build/pull.scm (build-guix): Remove 'with-directory-excursion' and file name hack from ce33c3af76b0e5c68cc42dddf2b9c4b017386fd8. Pass OUT to 'all-scheme-files'.
2017-11-07Fix ambiguous imports.Ludovic Courtès
* gnu/packages/ocaml.scm: Hide 'zip' from (srfi srfi-1). * guix/git.scm: Select 'mkdir-p' from (guix build utils).
2017-11-06gnu: nnn: Update to 1.5.Efraim Flashner
* gnu/packages/admin.scm (nnn): Update to 1.5.
2017-11-06gnu: libuninameslist: Update to 20170807.Efraim Flashner
* gnu/packages/fontutils.scm (libuninameslist): Update to 20170807.
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