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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.
2017-11-06gnu: u-boot: Only install 'MLO' output if it exists.Efraim Flashner
* gnu/packages/bootloaders.scm (u-boot)[arguments]: Add 'MLO' to uboot-files only if it has been built.
2017-11-06system: vm: Use 2^32 - 1 as hash size.Mathieu Othacehe
* gnu/system/vm.scm (operating-system-uuid): Use 2^32 - 1 instead of 2^32 as hash size. On some 32 bit system (ARM for example), 2^32 exceeds hash max size (ULONG_MAX = 2^32 - 1).
2017-11-06bootloaders: uboot: Add .img and MLO files to binary outputs.Mathieu Othacehe
* gnu/packages/bootloaders.scm (make-u-boot-package): Add .img and MLO files as binary output.
2017-11-06linux: Add omap2plus generic kernel.Mathieu Othacehe
* gnu/packages/linux.scm (linux-libre-arm-omap2plus): New exported variable.
2017-11-06gnu: uboot: Fix same-arch? check.Mathieu Othacehe
* gnu/packages/bootloaders.scm (make-u-boot-package): Compare %current-system to system associated to given triplet. Comparing a system and a triplet didn't make sense.
2017-11-06gnu: perl-test-www-mechanize-psgi: Update source uri.Efraim Flashner
* gnu/packages/web.scm (perl-test-www-mechanize-psgi)[source]: Update to new source uri.
2017-11-06gnu: dtc: Build python bindings.Efraim Flashner
* gnu/packages/bootloaders.scm (dtc)[native-inputs]: Add swig. [inputs]: Add python-2. [arguments]: Remove 'NO_PYTHON' from make-flags, add 'SETUP_PREFIX' to set python bindings prefix.
2017-11-06gnu: dtc: Update to 1.4.5.Efraim Flashner
* gnu/packages/bootloaders.scm (dtc): Update to 1.4.5. [arguments]: Add NO_PYTHON flag to make-flags.
2017-11-06gnu: libxres: Update to 1.2.0.Efraim Flashner
* gnu/packages/xorg.scm (libxres): Update to 1.2.0.
2017-11-06gnu: youtube-dl: Update to 2017.11.06.Tobias Geerinckx-Rice
* gnu/packages/video.scm (youtube-dl): Update to 2017.11.06.
2017-11-06gnu: aria2: Update to 1.33.0.Efraim Flashner
* gnu/packages/bittorrent.scm (aria2): Update to 1.33.0.
2017-11-06gnu: emacs-undo-tree: Parameterize source uri.Efraim Flashner
* gnu/packages/emacs.scm (emacs-undo-tree)[source]: Replace hard-coded version with version parameter.
2017-11-05gnu: borg: Update to 1.1.2.Leo Famulari
* gnu/packages/backup.scm (borg): Update to 1.1.2. [arguments]: Disable another test in the 'check' phase.
2017-11-05gnu: netsurf: Update to 3.7.Eric Bavier
For compatibility, dependents must be updated at the same time. * gnu/packages/web.scm (libcss): Update to 0.7.0 (nsgenbind): Update to 0.5. (netsurf): Update to 3.7. [arguments]: Fix binary name in .desktop. Adjust "docs" directory name. * gnu/packages/patches/netsurf-system-utf8proc.patch: Adjust to new source.
2017-11-05gnu: libnspsl: Update to 0.1.2.Eric Bavier
* gnu/packages/web.scm (libnspsl): Update to 0.1.2.
2017-11-05gnu: libnsgif: Update to 0.2.0.Eric Bavier
* gnu/packages/web.scm (libnsgif): Update to 0.2.0.
2017-11-05gnu: libsvgtiny: Update to 0.1.6.Eric Bavier
* gnu/packages/web.scm (libsvgtiny): Update to 0.1.6.
2017-11-05gnu: libdom: Update to 0.3.2.Eric Bavier
* gnu/packages/web.scm (libdom): Update to 0.3.2.
2017-11-05gnu: libwapcaplet: Update to 0.4.0.Eric Bavier
* gnu/packages/web.scm (libwapcaplet): Update to 0.4.0.
2017-11-05gnu: hubbub: Update to 0.3.4.Eric Bavier
* gnu/packages/web.scm (hubbub): Update to 0.3.4.
2017-11-05gnu: netsurf-buildsystem: Update to 1.6.Eric Bavier
* gnu/packages/web.scm (netsurf-buildsystem): Update to 1.6.
2017-11-05gnu: emacs-evil: Update to 1.2.13.ng0
* gnu/packages/emacs.scm (emacs-evil): Update to 1.2.13. (source): Adjust URL to new upstream location on github. (home-page): likewise. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2017-11-05gnu: emacs-slime: Use correct Texinfo commands in the description.ng0
Previously the description had "@{something}" in it which is never valid Texinfo. This commit changes it to use "@command{something}" to render the full description. * gnu/packages/emacs.scm (emacs-slime)[description]: Correct Texinfo usage. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2017-11-05gnu: emacs-undo-tree: Update to 0.6.6.ng0
* gnu/packages/emacs (emacs-undo-tree): Update to 0.6.6. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2017-11-05gnu: emacs-which-key: Update to 3.0.2.ng0
* gnu/packages/emacs.scm (emacs-which-key): Update to 3.0.2. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2017-11-05gnu: emacs-neotree: Update to 0.5.2.ng0
* gnu/packages/emacs.scm (emacs-neotree): Update to 0.5.2. [source](uri): Adjust URL to tag change. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
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