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.
gnu: Add r-org-dm-eg-db. * gnu/packages/bioinformatics.scm (r-org-dm-eg-db): New variable.
gnu: Add r-org-ce-eg-db. * gnu/packages/bioinformatics.scm (r-org-ce-eg-db): New variable.
gnu: Add r-org-hs-eg-db. * gnu/packages/bioinformatics.scm (r-org-hs-eg-db): New variable.
Do not check package freshness during upgrade. 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.
publish: Move 'query-path-info' call where it belongs. * guix/scripts/publish.scm (narinfo-string): Remove 'path-info' parameter and add 'store' parameter. Call 'query-path-info'. (render-narinfo): Adjust accordingly.
gnu: lsh: lshd now supports X11 forwarding. Reported by myglc2 <myglc2@gmail.com>. * gnu/packages/lsh.scm (lsh)[inputs]: Add XAUTH. [arguments]: Modify 'XAUTH_PROGRAM' macro in 'server_x11.c'.
gnu: lsh: Use 'modify-phases'. * gnu/packages/lsh.scm (lsh)[arguments]: Use 'modify-phases' instead of 'alist-cons-before'.
gnu: services: Install policies for polkit service. * 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.
mplayer: Use 'modify-phases'. * gnu/packages/video.scm (mplayer)[arguments]: Use 'modify-phases'. [source]: Use https. [home-page]: Use https.