* gnu/packages/admin.scm (intel-gpu-tools): New variable.

* gnu/packagages/emacs.scm (emacs-symon): Update to 20160630 (this is
the latest tag available from the upstream).
[source]: Use github instead of melpa.
[home-page]: Update.

Signed-off-by: Alex Kost <alezost@gmail.com>

Suggested-by Ivan Vilata i Balaguer <ivan@selidor.net>.
Fixes <https://bugs.gnu.org/26367

>.

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

Signed-off-by: Alex Kost <alezost@gmail.com>

* gnu/packages/emacs.scm (emacs-debbugs): Update to 0.14.

* gnu/packages/linux.scm (perf)[inputs]: Add libiberty.

* gnu/packages/ratpoison.scm (ratpoison): Update to 1.4.9.
[inputs]: Remove libxinerama. Add libxrandr.

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

The only version of webkit supported by guitarix is unmaintained and contains a
large number of security vulnerabilities, and should be removed from Guix.

* gnu/packages/audio.scm (guitarix)[inputs]: Remove webkitgtk/gtk+-2.

* gnu/packages/version-control.scm (myrepos)[arguments]: Use
'modify-phases' syntax.

* gnu/packages/version-control.scm (myrepos): Update to 1.20170129.
[source]: Source tarballs have been removed from Github, use
git-download to download from upstream repository.
[home-page]: Use https.

* gnu/packages/games.scm (gnubik): Update to 2.4.3.

* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.3.

Fixes CVE-2016-{9602,9603} and CVE-2017-{2615,2620,2630,5667,5931}.

* gnu/packages/qemu.scm (qemu): Update to 2.8.1.
* gnu/packages/patches/qemu-CVE-2017-2615.patch,
gnu/packages/patches/qemu-CVE-2017-2620.patch,
gnu/packages/patches/qemu-CVE-2017-2630.patch,
gnu/packages/patches/qemu-CVE-2017-5667.patch,
gnu/packages/patches/qemu-CVE-2017-5931.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.

* gnu/packages/suckless.scm (surf): Update to 2.0.
[inputs]: Replace webkitgtk/gtk+-2 with webkitgtk.

* tests/size.scm ("store-profile with multiple items"): New test.

* guix/scripts/size.scm (display-profile, profile->page-map): Don't use
'_' as a 'match' pattern variable.

That way the closure of flann:out is down from 1 GiB
to 290 MiB.

* gnu/packages/maths.scm (flann)[outputs]: New field.
[arguments]: Add 'set-octave-directory' phase.

* gnu/packages/webkit.scm (webkitgtk): Update to 2.16.1.

Armadillo versions 7.800 and onwards are licensed under the Apache License
2.0.

* gnu/packages/maths.scm (armadillo)[license]: Change to ASL 2.0.

* gnu/packages/regex.scm (re2): Update to 2017-04-01.

* gnu/packages/image-viewers.scm (feh): Update to 2.18.3.

* gnu/packages/libusb.scm (libusb): Update to 1.0.21.
[home-page]: Update to new URL.

* gnu/packages/libusb.scm (libmtp): Update to 1.1.13.

* gnu/packages/statistics.scm (r-sourcetools): Update to 0.1.6.

* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-6.

This package is no longer useful, because upstream does not keep the tarballs
of older releases.  We use the bundled armadillo sources in the
r-rccparmadillo package instead.

* gnu/packages/maths.scm (armadillo-for-rcpparmadillo): Remove variable.

* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.700.0.0.
[source]: Do not delete bundled armadillo sources, because upstream no longer
hosts previous versions.
[propagated-inputs]: Remove "armadillo-for-rcpparmadillo".
[arguments]: Remove because we no longer need to link with the armadillo
library.
* gnu/packages/bioinformatics.scm (r-deseq2)[arguments]: Remove because we no
longer need to link with armadillo library.

* gnu/packages/maths.scm (armadillo): Update to 7.800.2.

* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.1.

* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.1.

* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.2.

* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.2.

* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.3.

* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.13.

* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.4.

* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.2.

* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.10.1.

* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.2.

* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.4.

* gnu/packages/bioinformatics.scm (r-seqminer): Update to 5.7.

* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.2.