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>

services: mpd: Remove the mpd-file field.

Since MPD switches user, the pid-file must be in a writable dir.  This
is now always /var/run/mpd/(user)/pid.

* gnu/services/audio.scm (mpd-service-type): Add a activation-service
extension.
(<mpd-configuration>)[pid-file]: Remove.
(mpd-service): Rename to...
(mpd-shepherd-service): ... this.
(mpd-file-name, mpd-service-activation): New procedure.
* doc/guix.texi (Audio Services): Document the changes.

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.

gnu: vlc: Recover lost phase.

This is a followup to eb1f2420d5d72bb5d178a744cffb4978c7446286.

* gnu/packages/video.scm (vlc)[arguments]: Run the fix-livemedia-utils-prefix
phase before configure.

gnu: gd: Replace with 2.2.5.

Fixes CVE-2017-6362 and CVE-2017-7890.

* gnu/packages/gd.scm (gd)[replacement]: New field.
(gd-2.2.5): New variable.
* gnu/packages/php.scm (gd-for-php): Remove variable
(php)[inputs]: Replace GD-FOR-PHP with GD-2.2.5.
* gnu/packages/patches/gd-CVE-2017-7890.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

gnu: claws-mail: Update to 3.15.1.

* gnu/packages/mail.scm (claws-mail): Update to 3.15.1.