* doc/guix.texi (Shepherd Services): Add missing words.
  (Invoking guix system): Fix typo.
  (Service Types and Services): Fix typo.
* doc/contributing.texi (Submitting Patches): Fix typo.

Signed-off-by: Andreas Enge <andreas@enge.fr>

* gnu/packages/gdb.scm (gdb): Update to 7.11.

* gnu/packages/kde-frameworks.scm (kwindowsystem): Update to 5.19.0.
(extra-cmake-modules): Update to 5.19.0.

* gnu/packages/bioinformatics.scm (r-topgo)[propagated-inputs]: Add
  "r-graph".

* gnu/packages/bioinformatics.scm (r-graph): New variable.

* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): New variable.

* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): New variable.

* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): New variable.

* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): New variable.

Fixes <http://bugs.gnu.org/22740>.
Reported by Andreas Enge <andreas@enge.fr>.

* gnu/packages.scm (waiting, ftp-open*, check-package-freshness): Remove.
* guix/scripts/package.scm (options->installable): Adjust accordingly.
* emacs/guix-main.scm (package->manifest-entry*): Likewise.

* guix/scripts/publish.scm (narinfo-string): Remove 'path-info'
parameter and add 'store' parameter.  Call 'query-path-info'.
(render-narinfo): Adjust accordingly.

Reported by myglc2 <myglc2@gmail.com>.

* gnu/packages/lsh.scm (lsh)[inputs]: Add XAUTH.
[arguments]: Modify 'XAUTH_PROGRAM' macro in 'server_x11.c'.

* gnu/packages/lsh.scm (lsh)[arguments]: Use 'modify-phases' instead of
'alist-cons-before'.

* gnu/services/desktop.scm (polkit-etc-files): Add the polkit package
  itself to the list of packages to scan for .policy files.  This add
  support for pkexec.

* gnu/packages/video.scm (mplayer)[arguments]: Use 'modify-phases'.
[source]: Use https.
[home-page]: Use https.

* gnu/packages/video.scm (mplayer)[inputs]: Add libass, libmpeg2,
  libvdpau, libx264, opus.

* gnu/packages/ssh.scm (dropbear): Update to 2015.71.

* gnu/packages/guile.scm (guile-next): Use the "2.2" directory for the
  load paths.

* gnu/services/herd.scm (report-action-error): Add missing newlines in
messages.

Reported by Leo Famulari <leo@famulari.name>
and Ben Woodcroft <b.woodcroft@uq.edu.au>
at <http://bugs.gnu.org/22752>.

* guix/scripts/refresh.scm: Remove unneeded and harmful import of (guix
import gem).

* doc/guix.texi (Version Numbers): Add example for VCS version numbers.

* gnu/packages/xfce.scm (xfce4-xkb-plugin): New variable.
  (xfce)[propagated-inputs]: Add it.

* gnu/packages/freedesktop.scm (telepathy-logger)[arguments]: Disable parallel
tests.

* gnu/packages/ldc.scm (rdmd): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

* gnu/packages/freedesktop.scm (modem-manager)[source]: Use HTTPS URL.

* gnu/packages/mpd.scm (mpd): Update t0 0.19.12.

* gnu/packages/mpd.scm (ncmpcpp): Update to 0.7.3.
[inputs]: Add icu4c.

* gnu/packages/mpd.scm (ncmpcpp)[arguments]: Use 'modify-phases'.

Fixes <http://bugs.gnu.org/22633>.

* gnu/build/vm.scm (load-in-linux-vm): Only pass "-enable-kvm" flag to qemu
  if "/dev/kvm" is present.
* gnu/system/vm.scm (common-kvm-options): Same as above.

* gnu/packages/pkg-config.scm (%pkg-config)[source]: Add non-HTTPS URL.

* guix/grafts.scm (graft-derivation): Name 'name' a keyword parameter.
* guix/packages.scm (package-derivation, package-cross-derivation):
Adjust accordingly.
* tests/grafts.scm ("graft-derivation"): Likewise.
* tests/packages.scm ("package-derivation, indirect grafts"): Likewise.

* guix/derivations.scm (<graft>, graft-derivation, %graft?)
(set-grafting): Move to...
* guix/grafts.scm: ... here.  New file.
* guix/gexp.scm, guix/packages.scm, tests/packages.scm,
guix/scripts/build.scm: Use it.
* Makefile.am (MODULES): Add it.
(SCM_TESTS): Add tests/grafts.scm.
* tests/derivations.scm ("graft-derivation"): Move to...
* tests/grafts.scm: ... here.  New file.

* gnu/packages/qt.scm (python2-pyqt-4): Delete variable. It depends on Qt 4,
  which does not receive security updates any more.

* gnu/packages/kde.scm (qjson): Move from here...
* gnu/packages/qt.scm (qjson): ...to here.
* gnu/packages/pumpio.scm: Drop inclusion of (gnu packages kde).
* gnu/packages/kde.scm: Delete file.
* gnu-system.am (GNU_SYSTEM_MODULES): Unregister it.
* gnu/packages/rdf.scm (soprano): Delete variable.

KDE 4 relies on Qt 4, which does not receive security updates any more.

* gnu/packages/statistics.scm (python-patsy)[properties]: New field.
(python2-patsy): Use 'strip-python2-variant'.

* gnu/packages/statistics.scm (python-patsy, python2-patsy): Update to 0.4.1.

Fixes <http://bugs.gnu.org/22607>.
Reported by myglc2 <myglc2@gmail.com>.

Remove possibilities to install/delete packages to/from a system profile
both for "Package List" and "Package Info" buffers.

* emacs/guix-profiles.el (guix-system-profile-regexp): New variable.
(guix-system-profile?): New procedure.
* emacs/guix-ui-package.el (guix-package-info-insert-output): Do not
display "Install"/"Delete" button for a system profile.
(guix-package-assert-non-system-profile): New procedure.
(guix-package-execute-actions): Use it.

* emacs/guix-buffer.el (guix-buffer-set): Set 'guix-buffer-item' early,
  so that it can be used during displaying entries.  For example, this
  allows us to use a value of the current guix profile when package
  entries are inserted in a "List" or "Info" buffer.

* emacs/guix-ui-package.el (guix-installed-user-packages)
(guix-installed-system-packages): New commands.
* doc/emacs.texi (Emacs Commands): Document them.

* gnu/packages/patches/qemu-CVE-2015-8619.patch,
  gnu/packages/patches/qemu-CVE-2016-1981.patch,
  gnu/packages/patches/qemu-CVE-2016-2197.patch,
  gnu/packages/patches/qemu-usb-ehci-oob-read.patch: New files.
* gnu-system.am (dist_patch_DATA): Add them.
* gnu/packages/qemu.scm (qemu)[source]: Add patches.