gnu: Add r-pdist.

* gnu/packages/cran.scm (r-pdist): New variable.

gnu: Update coq-interval to 3.3.0.

* gnu/packages/ocaml.scm (coq-interval): Update to 3.3.0.
[inputs]: Add coq-bignums.

gnu: Add coq-bignums.

* gnu/packages/ocaml.scm (coq-bignums): New variable.

gnu: Update coq-coquelicot to 3.0.1.

* gnu/packages/ocaml.scm (coq-coquelicot): Update to 3.0.1.

gnu: Update coq-mathcomp to 1.6.2.

* gnu/packages/ocaml.scm (coq-mathcomp): Update to 1..6.2.

gnu: Update coq-flocq to 2.6.0.

* gnu/packages/ocaml.scm (coq-flocq): Update to 2.6.0.

gnu: Update coq to 8.7.0.

* gnu/packages/ocaml.scm (coq): Update to 8.7.0.
[build-system]: Use ocaml-build-system.
[inputs]: Add python-2.
[arguments]: Disable two failing tests.

gnu: camlp5: install META file.

* gnu/packages/ocaml.scm (camlp5) [phases]: New install-meta phase.

gnu: lame: Update to 3.100.

* gnu/packages/mp3.scm (lame): Update to 3.100.
[source]: Don't hard-code version.

gnu: python-pyqt: Update to 5.9.

* gnu/packages/qt.scm (python-pyqt): Update to 5.9.

gnu: python-sip: Update to 4.19.3.

* gnu/packages/qt.scm (python-sip): Update to 4.19.3.

gnu: rest: Update to 0.8.1.

* gnu/packages/gnome.scm (rest): Update to 0.8.1.

gnu: gnome-disk-utility: Update to 3.26.1.

* gnu/packages/gnome.scm (gnome-disk-utility): Update to 3.26.1.
[build-system]: Use meson-build-system.
[native-inputs]: Add gtk+:bin.

gnu: perl-geo-ip: Update to 1.51.

* gnu/packages/networking.scm (perl-geo-ip): Update to 1.51.

Use HTTPS for bioconductor.org.

* doc/guix.texi (Invoking guix import, Invoking guix refresh): Use HTTPS for
bioconductor.org URLs.
* gnu/packages/bioinformatics.scm (r-annotate, r-geneplotter, r-genefilter)
(r-deseq2, r-dexseq, r-annotationforge, r-rbgl, r-gseabase, r-category)
(r-gostats, r-shortread, r-biocgenerics, r-biocinstaller, r-biocviews)
(r-biocstyle, r-bioccheck, r-s4vectors, r-iranges, r-genomeinfodbdata)
(r-genomeinfodb, r-xvector, r-genomicranges, r-biobase, r-annotationdbi)
(r-biomart, r-biocparallel, r-biostrings, r-rsamtools, r-delayedarray)
(r-summarizedexperiment, r-genomicalignments, r-rtracklayer)
(r-genomicfeatures, r-graph, r-topgo, r-bsgenome, r-impute, r-seqpattern)
(r-seqlogo, r-motifrg, r-bamsignals, r-mutationalpatterns, r-tximport)
(r-rhdf5, r-chipseq, r-sva, r-affy, r-vsn, r-mzid, r-msnid)
(r-interactivedisplaybase, r-annotationhub)[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene)
(r-go-db, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db)
(r-org-ce-eg-db, r-org-dm-eg-db, r-org-mm-eg-db)
(r-bsgenome-hsapiens-ucsc-hg19, r-bsgenome-mmusculus-ucsc-mm9)
(r-bsgenome-mmusculus-ucsc-mm10, r-txdb-mmusculus-ucsc-mm10-knowngene)
(r-bsgenome-celegans-ucsc-ce6, r-bsgenome-celegans-ucsc-ce10)
(r-bsgenome-dmelanogaster-ucsc-dm3, r-copyhelper)[source, home-page]:
Likewise.
* gnu/packages/statistics.scm (r-rcurl)[source]: Likewise.
* guix/build-system/r.scm (bioconductor-uri): Likewise.
* guix/import/cran.scm (%cran-url, bioconductor-package?)
(bioconductor-data-package?, bioconductor-experiment-package?): Likewise.

gnu: schismtracker: Update to 20170910.

* gnu/packages/music.scm (schismtracker): Update to 20170910.

gnu: Fix the hashes of mutated GitHub archives.

Fixes <https://bugs.gnu.org/28745>.

* gnu/packages/audio.scm (csound): Fix hash.
* gnu/packages/engineering.scm (fritzing): Likewise.
* gnu/packages/erlang.scm (erlang): Likewise.
* gnu/packages/fonts.scm (font-google-material-design-icons): Likewise.
* gnu/packages/graphics.scm (ogre): Likewise.
* gnu/packages/java.scm (java-plexus-interpolation, antlr3): Likewise.
* gnu/packages/serialization.scm (yaml-cpp): Likewise.
* gnu/packages/version-control.scm (libgit2): Likewise.

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

gnu: libvirt: Fix CVE-2017-1000256.

* gnu/packages/patches/libvirt-CVE-2017-1000256.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/virtualization.scm (libvirt)[source]: Use it.

gnu: mysql: Update to 5.7.20.

* gnu/packages/databases.scm (mysql): Update to 5.7.20.

gnu: webkitgtk: Update to 2.18.1.

* gnu/packages/webkit.scm (webkitgtk): Update to 2.18.1.