gnu: Remove python2-rpy2.
Python 2 is no longer supported.
* gnu/packages/python.scm (python2-rpy2): Remove variable.
gnu: python-rpy2: Update to 2.9.0.
* gnu/packages/python.scm (python-rpy2): Update to 2.9.0.
[arguments]: Run tests before install phase; add build phase "fix-tests".
[propagated-inputs]: Add python-jinja2 and python-pytz.
[inputs]: Add r-ggplot2, r-rsqlite, r-dplyr, r-dbplyr, and python-numpy.
gnu: python-rpy2: Update license.
* gnu/packages/python.scm (python-rpy2)[license]: Correct GPLv3+ to GPLv2+;
list additional licenses.
gnu: Add r-dbplyr.
* gnu/packages/statistics.scm (r-dbplyr): New variable.
gnu: retux: Update to 1.3.5.
* gnu/packages/games.scm (retux): Update to 1.3.5.
gnu: python-tmx: Update to 1.10.
* gnu/packages/game-development.scm (python-tmx): Update to 1.10.
gnu: python-sge-pygame: Update to 1.5.1.
* gnu/packages/game-development.scm (python-sge-pygame,
python2-sge-pygame): Update to 1.5.1.
gnu: python-pyjwt: Update to 1.5.2 [fixes CVE-2017-11424].
* gnu/packages/python.scm (python-pyjwt): Update to 1.5.2.
[source]: Add snippet to remove pre-compiled files.
[native-inputs]: Change PYTHON-PYTEST to PYTHON-PYTEST-3.0.
gnu: Add emacs-idris-mode.
* gnu/packages/emacs.scm (emacs-idris-mode): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
gnu: Add emacs-prop-menu.
* gnu/packages/emacs.scm (emacs-prop-menu): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
gnu: knot: Update to 2.5.4.
* gnu/packages/dns.scm (knot): Update to 2.5.4.
gnu: Add pt-scotch32.
* gnu/packages/maths.scm (pt-scotch32): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
gnu: Add "scotch32".
* gnu/packages/maths.scm (scotch32): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
gnu: bioinformatics: Work around more "dotless @INC" build failures.
* gnu/packages/bioinformatics.scm (ncbi-vdb, sra-tools)[arguments]: Add
'set-perl-search-path' phase.
gnu: ruby-2.2.7: Fix CVE-2017-{0899,0900,0901,0902}.
* gnu/packages/patches/ruby-2.2.7-rubygems-2613-ruby22.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/ruby.scm (ruby-2.2.7)[source]: Use it.
gnu: ruby-2.3.4: Fix CVE-2017-{0899,0900,0901,0902}.
* gnu/packages/patches/ruby-2.3.4-rubygems-2613-ruby23.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/ruby.scm (ruby-2.3.4)[source]: Use it.
gnu: ruby-2.4.1: Fix CVE-2017-{0899,0900,0901,0902}.
* gnu/packages/patches/ruby-rubygems-2612-ruby24.patch,
gnu/packages/patches/ruby-rubygems-2613-ruby24.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/ruby.scm (ruby-2.4.1)[source]: Use them.
gnu: metabat: Update to 2.11.3.
* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.3.
[source]: Use git-fetch. Remove boost-related patch.
* gnu/packages/patches/metabat-fix-boost-issue.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
gnu: vlc: Fix build and clean up expression.
Commit 3e0c54bf4de0b5e9d77271613287457dbcd64103 touches 'configure.ac' which
in turn regenerates 'po/Makefile.in.in' with the wrong SHELL and breaks
install. While at it, consolidate the other patching phases and remove
unneeded inputs.
* gnu/packages/video.scm (vlc)[arguments]: Consolidate patching phases into a
'patch-source' phase and run it immediately after unpack.
[native-inputs]: Remove AUTOCONF, AUTOMAKE and LIBTOOL.