gnu: gemma: Fix building on non-Intel architectures.

* gnu/packages/patches/gemma-intel-compat.patch: New file.
* gnu/packages/bioinformatics.scm (gemma)[source]: Add patch.
[arguments]: Add NO_INTEL_COMPAT flag on non-Intel architectures.
* gnu/local.mk (dist_patch_DATA): Register patch.

gnu: gajim: Update to 0.16.8.

* gnu/packages/messaging.scm (gajim): Update to 0.16.8.
[source]: Remove patch.
* gnu/packages/patches/gajim-CVE-2016-10376.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

gnu: diamond: Update to 0.9.9.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.9.

gnu: blast+: Update to 2.6.0.

* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0.
[origin]: Remove bundled pcre.
[arguments]: Replace paths in run_with_lock.c.  Configure with pcre.
[inputs]: Add pcre, perl, python.

gnu: linux-libre: Update to 4.12.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.12.
(%linux-libre-hash): Update hash.
* gnu/packages/aux-files/linux-libre/4.11-i686.conf,
gnu/packages/aux-files/linux-libre/4.11-x86_64.conf: Delete files.
* gnu/packages/aux-files/linux-libre/4.12-i686.conf,
gnu/packages/aux-files/linux-libre/4.12-x86_64.conf: New files.
* Makefile.am (AUX_FILES): Update accordingly.

gnu: qt: Update to 5.9.1.

* gnu/packages/qt.scm (qtbase, qtsvg, qtimageformats, qtx11extras)
(qtxmlpatterns, qtdeclarative, qtconnectivity, qtwebsockets, qtsensors)
(qtmultimedia, qtwayland, qtserialport, qtserialbus, qtwebchannel)
(qtlocation, qttools, qtscript, qtquickcontrols, qtquickcontrols2)
(qtgraphicaleffects, qtgamepad, qtscxml, qtpurchasing, qtcanvas3d)
(qtcharts, qtdatavis3d, qtwebkit): Update to 5.9.1.
(qtwebkit)[source]: Change to official qt location.

gnu: python-pylint: Update to 1.7.2.

* gnu/packages/python.scm (python-pylint): Update to 1.7.2.
[native-inputs]: Add PYTHON-PYTEST and PYTHON-PYTEST-RUNNER.

gnu: python-astroid: Update to 1.5.3.

* gnu/packages/python.scm (python-astroid): Update to 1.5.3.
[properties]: Declare python2 variant.
(python2-astroid)[propagated-inputs]: Add PYTHON2-BACKPORTS-FUNCTOOLS-LRU-CACHE,
PYTHON2-ENUM34 and PYTHON2-SINGLEDISPATCH.

gnu: python-pyopenssl: Update to 17.1.0.

* gnu/packages/python.scm (python-pyopenssl, python2-pyopenssl): Update to 17.1.0.
[source]: Remove patch.
[native-inputs]: Add PYTHON-PRETEND.
[arguments]<#:phases>: Disable the network test here instead of via a patch.
Also disable one new test.
* gnu/packages/patches/python-pyopenssl-skip-network-test.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

gnu: python-cryptography: Update to 1.9.

* gnu/packages/python.scm (python-cryptography-vectors): Update to 1.9.
(python-cryptography): Update to 1.9.
[propagated-inputs]: Remove PYTHON-PACKAGING.

gnu: python-cffi: Update to 1.10.0.

* gnu/packages/python.scm (python-cffi): Update to 1.10.0.
[arguments]<#:phases>: Patch distutils.ccompiler call to use "gcc". Patch
another hard-coded cc invocation. Adjust `py.test` invocation per README.

gnu: python-cffi: Really enable tests.

* gnu/packages/python.scm (python-cffi, python2-cffi)[arguments]: Replace
'check' phase with custom expression. Change to 'modify-phases' syntax.

gnu: re2: Update to 2017-07-01.

* gnu/packages/regex.scm (re2): Update to 2017-07-01.

gnu: ibus: Update to 1.5.16.

* gnu/packages/ibus.scm (ibus): Update to 1.5.16.

gnu: cdogs-sdl: Update to 0.6.5.

* gnu/packages/games.scm (cdogs-sdl): Update to 0.6.5.
[inputs]: Add mesa.
[home-page]: Use HTTPS.

gnu: nnn: Update to 1.2.

* gnu/packages/admin.scm (nnn): Update to 1.2.

gnu: gcr: Correct patch.

* gnu/packages/patches/gcr-disable-failing-tests.patch: Correct
erroneously committed file.

This is a follow-up to commit 85c774808fc13a0adc603784b2358a7c285c4822.

packages: Mark 'replacement' as an "innate" field.

Suggested by Mark H Weaver
at <https://lists.gnu.org/archive/html/guix-devel/2017-06/msg00355.html>.

* guix/packages.scm (<package>)[replacement]: Mark as "innate".
* gnu/packages/base.scm (glibc-2.25-patched, glibc-2.24)
(glibc-2.23, glibc-2.22, glibc-2.21, glibc-locales): Remove
'replacement' field, which was set to #f.
* gnu/packages/commencement.scm (perl-boot0): Likewise.
* gnu/packages/fontutils.scm (graphite2/fixed): Likewise.
* gnu/packages/ghostscript.scm (ghostscript/fixed): Likewise.
* gnu/packages/gnupg.scm (libgcrypt-1.7.8): Likewise.
* gnu/packages/guile.scm (guile-2.0/fixed, guile-2.2): Likewise.
* gnu/packages/icu4c.scm (icu4c/fixed): Likewise.
* gnu/packages/image.scm (libpng-apng): Likewise.
* gnu/packages/make-bootstrap.scm (%guile-static): Likewise.
* gnu/packages/pcre.scm (pcre/fixed): Likewise.
* gnu/packages/perl.scm (perl/fixed): Likewise.
* gnu/packages/ruby.scm (ruby-2.3, ruby-2.2, ruby-2.1)
(ruby-1.8): Likewise.
* gnu/packages/tls.scm (gnutls-3.5.13, gnutls/guile-2.2): Likewise.
* gnu/packages/xml.scm (expat-2.2.1): Likewise.

gnu: wine: Add stable release.

* gnu/packages/wine.scm (wine): Refer to stable release instead of development
  one.
(wine-next): New variable.

gnu: Add emacs-emamux.

* gnu/packages/emacs.scm (emacs-emamux): New variable.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>