* gnu/packages/ruby.scm (ruby-lumberjack): Update to 1.0.10.
[native-inputs]: Add 'ruby-timecop'.

* gnu/packages/ruby.scm (ruby-arel): Update to 7.1.4.

* gnu/packages/ruby.scm (ruby-rake-compiler): Update to 1.0.1.

* gnu/packages/ruby.scm (ruby-hoe): Update to 3.15.2.

* gnu/packages/ruby.scm (ruby-rspec-core): Update to 3.5.4.

* gnu/packages/ruby.scm (bundler): Update to 1.13.6.

* gnu/packages/ruby.scm (ruby-yard): Update to 0.9.5-1.d816482a.
[source]: Update source URL.
[arguments]: Remove unneeded substitutions.  Change test target.
* gnu/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch (New
file)
* gnu/local.mk (dist_patch_DATA): Add it.

* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.4.0.

* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.4.0.

* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.4.0.

* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.4.0.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.31.

* gnu/packages/linux.scm (%linux-libre-version, %linux-libre-hash)
(linux-libre): Update to 4.8.7.

* gnu/packages/guile.scm (guile-aspell): New variable.

* gnu/packages/wordnet.scm (wordnet)[arguments]: Remove
-fno-builtin-strcpy.
[native-inputs]: New field.

* gnu/packages/python.scm (python-pillow, python2-pillow): Update to 3.3.3.

This phase is no longer needed as upstream has merged the fix in the
current release.

* gnu/packages/statistics.scm (r-rmarkdown)[arguments]: Remove build
phase "copy-files-without-mode".

* gnu/packages/inkscape.scm (inkscape)[arguments]: Use modify-phases
syntax.

* gnu/packages/vim.scm (vim, vim-full): Update to 8.0.0073.

* gnu/build/linux-container.scm (mount-file-systems): 'mounts' is now a
list of <file-system> objects instead of a list of lists ("specs").
Add call to 'file-system->spec' as the argument to 'mount-file-system'.
(run-container, call-with-container): Adjust docstring accordingly.
* gnu/system/file-systems.scm (spec->file-system): New procedure.
* gnu/system/linux-container.scm (container-script)[script]: Call
'spec->file-system' inside gexp.
* guix/scripts/environment.scm (launch-environment/container): Remove
call to 'file-system->spec'.
* tests/containers.scm ("call-with-container, mnt namespace")
("call-with-container, mnt namespace, wrong bind mount"): Pass a list of
<file-system> objects.

* gnu/system/linux-container.scm (container-script)[script]: Use
'source-module-closure' in 'with-imported-modules' form.

* gnu/packages/package-management.scm (guix-devel): Update to commit
324a2ba5.

* gnu/packages/maths.scm (gmsh): Update to 2.14.1.
[source]: Use new uri.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

* gnu/packages/music.scm (milkytracker)[source]: Update source uri.
[home-page]: Change to new domain.

Reported-by: ng0 <ng0@we.make.ritual.n0.is>

* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.6-4.

* gnu/packages/mail.scm (claws-mail): Update to 3.14.1.

* gnu/packages/pdf.scm(pdfposter): New variable.

* gnu/packages/pdf.scm (python2-pypdf): New variable.

* gnu/packages/pdf.scm (python-pypdf2, python2-pypdf2): New variables.

This is a followup to bc3c41ce.

* tests/cpan.scm ("cpan->guix-package"): Add #:verify-certificate?
parameter in 'url-fetch' mock.
* tests/cran.scm ("description->package"): Likewise.

Partly addresses <http://bugs.gnu.org/24703>.
Reported by Mark H Weaver <mhw@netris.org>.

* gnu/packages/patches/gcc-strmov-store-file-names.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gcc.scm (gcc-5)[sources](patches): Add it.
(gcc-6)[sources](patches): Add it.

Reported by Frederick Muriithi <fredmanglis@gmail.com>.

* guix/scripts/lint.scm (tls-certificate-error-string): New procedure.
(validate-uri): Use it.
(current-vulnerabilities*): Catch 'tls-certificate-error' and print a
warning.

* gnu/packages/kde.scm (kdevelop-pg-qt): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

* gnu/packages/kde.scm (libkomparediff2): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

* gnu/packages/libusb.scm (hidapi)[license]: Actually call
'non-copyleft'.

* doc/guix.texi (Invoking guix import): Document elpa.gnu.org
signatures.

* gnu/packages/vim.scm (vifm): New variable.

* gnu/packages/patches/libxslt-CVE-2016-4738.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/xml.scm (libxslt)[replacement]: New field.
(libxslt/fixed): New variable.

* gnu/packages/databases.scm (postgresql): Update to 9.5.5.
[home-page]: Use https.

* gnu/packages/databases.scm (mariadb): Update to 10.1.19.