gnu: Add missing import in bioinformatics.scm.

This is a followup to 1baee94.

* gnu/packages/bioinformatics.scm: Add missing import.

guix system: Restore load path after running the activation script.

Fixes <http://bugs.gnu.org/22753>.
Reported by Mark H Weaver <mhw@netris.org>.

* guix/scripts/system.scm (save-load-path-excursion): New variable.
(upgrade-shepherd-services): Add comment about the issue.
(switch-to-system): Use 'save-load-path-excursion' around
'primitive-load' call.

store: Clarify documentation of 'valid-path?'.

* guix/store.scm (valid-path?): Improve docstring.
* doc/guix.texi (The Store): Update accordingly.

publish: Do not publish nars for invalid store items.

Before that, /nar requests could succeed if the requested store item
exists but is invalid (although such requests were unlikely because the
corresponding narinfo request would have failed.)

* guix/scripts/publish.scm (render-nar): Add 'store' parameter.  Use
'valid-path?' instead of 'file-exists?'.
(make-request-handler): Adjust 'render-nar' call accordingly.
* tests/publish.scm ("/nar/invalid"): New test.

gnu: Add kyotocabinet.

* gnu/packages/databases.scm (kyotocabinet): New variable.

gnu: Add libBigWig.

* gnu/packages/bioinformatics.scm (libbigwig): New variable.

gnu: guile-json: Update to 0.5.0.

* gnu/packages/guile.scm (guile-json): Update to 0.5.0.

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

gnu: ardour: Update to 4.7.

* gnu/packages/audio.scm (ardour): Update to 4.7.

gnu: xdg-utils: Propagate xprop and xset.

Fixes <http://bugs.gnu.org/22755>.

* gnu/packages/freedesktop.scm (xdg-utils): Propagate xprop and xset.

doc: Improve recent changes in "Binary Installation".

This amends part of c8e2688.

* doc/guix.texi (Binary Installation): Improve wording of some parts.
Fix Upstart example.  Remove incorrect paragraph about locales.
Reinstate bit about reproducing the binary tarball.

doc: Clarify who can run 'guix pull'.

Suggested by Chris Marusich <cmmarusich@gmail.com>.

* doc/guix.texi (Invoking guix pull): Add paragraph explaining that any
user can run 'guix pull'.

gnu: libssh: Update to 0.7.3 [fixes CVE-2016-0739].

* gnu/packages/patches/libssh-CVE-2014-0017.patch: Delete file.
* gnu/packages/patches/libssh-0.6.5-CVE-2016-0739.patch: New file.
* gnu-system.am (dist_patch_DATA): Adjust accordingly.
* gnu/packages/ssh.scm (libssh): Update to 0.7.3.
  (libssh-0.5): Rename to...
  (libssh-0.6): ... this.  Update to 0.6.5.
  [source]: Add patch for CVE-2016-0739.
  (guile-ssh)[inputs]: Use libssh-0.6.

Modified-By: Mark H Weaver <mhw@netris.org>

gnu: libssh2: Update to 1.7.0 [fixes CVE-2016-0787].

* gnu/packages/ssh.scm (libssh2): Update to 1.7.0.
  (libssh2-1.4): New variable.
* gnu/packages/curl.scm (curl)[inputs]: Use libssh4-1.4.

Modified-By: Mark H Weaver <mhw@netris.org>

doc: Add details for binary installation.

* doc/guix.texi (Binary Installation): Provide some more details for binary
  installation, in particular automatic starting of the daemon.

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

doc: Fix minor typos and add missing words.

* 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: gdb: Update to 7.11.

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

gnu: kde-frameworks: Update to 5.19.0.

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

gnu: r-topgo: Add missing input.

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

gnu: Add r-graph.

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

gnu: Add r-org-mm-eg-db.

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