gnu: hdf5: Add output for fortran interface.

* gnu/packages/maths.scm (hdf5) [native-inputs]: Add gfortran.
  [outputs]: Add "fortran".
  [arguments]: Enable Fortran compilation; add "/lib" directory of the fortran
  output to the runpath of the Fortran libs; add a 'split phase to move
  all Fortran-related files to the the Fortran output store location.

gnu: python2-larch: Enable tests.

* gnu/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/python.scm (python2-larch)[source]: Use it.
[arguments]: Move 'check' phase to before 'build' phase.

gnu: python2-ttystatus: Enable tests.

* gnu/packages/python.scm (python2-ttystatus)[arguments]: Replace 'check'
phase with custom function.

gnu: python2-cliapp: Enable tests.

* gnu/packages/python.scm (python2-cliapp)[arguments]: Replace 'check' phase
with custom function.

gnu: linux-libre: Update to 4.12.10.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.12.10.
(%linux-libre-hash): Update hash.

gnu: linux-libre@4.9: Update to 4.9.46.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.46.

gnu: linux-libre@4.4: Update to 4.4.85.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.85.

gnu: libxml2/fixed: Use patches from inherited package.

This is a followup to 76fed2b3c4e3703d1ad81c4330edd94d551b6334.

* gnu/packages/xml.scm (libxml2/fixed)(patches): Inherit patches from LIBXML2.

gnu: graphicsmagick: Fix CVE-2017-{13775,13776,13777}.

* gnu/packages/imagemagick.scm (graphicsmagick)[source]: Add patches.
* gnu/packages/patches/graphicsmagick-CVE-2017-13775.patch,
gnu/packages/patches/graphicsmagick-CVE-2017-13776+CVE-2017-13777.patch:
New files.
* gnu/local.mk (dist_patch_DATA): Register them.

gnu: efl: Update to 1.20.3.

* gnu/packages/enlightenment.scm (efl): Update to 1.20.3.

gnu: Fix current-guix.

Without this change, I get errors like:
  ERROR: In procedure string-drop:
  ERROR: Value out of range 0 to 35: 51

* gnu/packages/package-management.scm (current-guix): Pass exactly the same
  path to git-predicate and local-file, to ensure that the select? function is
  compatible.

gnu: sddm: Update to 0.15.0.

* gnu/packages/display-managers.scm (sddm): Update to 0.15.0.
[source]: Update tarball name.
[inputs]: Add ELOGIND.
[arguments]: Adjust #:configure-flags for elogind support. Add phase to
patch hard-coded loginctl reference.

gnu: libxml2: Fix CVE-2017-{0663,7375,7376,9047,9048,9049,9050}.

* gnu/packages/patches/libxml2-CVE-2017-0663.patch,
gnu/packages/patches/libxml2-CVE-2017-7375.patch,
gnu/packages/patches/libxml2-CVE-2017-7376.patch,
gnu/packages/patches/libxml2-CVE-2017-9047+CVE-2017-9048.patch,
gnu/packages/patches/libxml2-CVE-2017-9049+CVE-2017-9050.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/xml.scm (libxml2)[replacement]: New field.
(libxml2/fixed): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: postgresql: Update to 9.6.5.

* gnu/packages/databases.scm (postgresql): Update to 9.6.5.

Release-notes: https://www.postgresql.org/docs/9.6/static/release-9-6-5.html

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.