branch core-updates updated (a19da40 -> 02c73ad)

[Leo Famulari]

lfam pushed a change to branch core-updates
in repository guix.

      from  a19da40   gnu: perl-www-curl: Fix build failure.
      adds  2dfa907   gnu: weechat: Update to 1.6.
      adds  41e94ad   nls: Update 'fr' translation.
      adds  d6465ef   gnu: gajim: License is "version 3 only".
      adds  0f6b6cb   gnu: gajim: Update to 0.16.6.
      adds  8e3017c   gnu: windowmaker: Update to 0.95.7.
      adds  02cfea6   gnu: musl: Fix CVE-2016-8859.
      adds  bd1b1e0   gnu: gnumeric: Use 'glib-or-gtk-build-system'.
      adds  9c798f9   gnu: Add whois.
      adds  c201b28   gnu: red-eclipse: Update to 1.5.6.
      adds  405be8d   gnu: efl: Update to 1.18.2.
      adds  8c00b83   services: nginx: Virtual hosts are first-class 
configuration items.
      adds  3b5783f   gnu: Add guile-bytestructures
      adds  d3c4f3b   gnu: Add hdf-eos2.
      adds  d91025e   gnu: Add coda.
      adds  ffde82c   system: grub: Use Guile-{RSVG,Cairo} instead of Inkscape 
+ ImageMagick.
      adds  e9a19bd   gnu: address@hidden: Update to 4.1.35.
      adds  8ce84bf   svg: Autoload Guile-RSVG and Guile-Cairo.
      adds  301d73f   build: 'guilemoduledir' honors $GUILE_EFFECTIVE_VERSION.
      adds  4b12fe5   gnu: coda: Remove bundled libraries.
      adds  47a04fc   gnu: mupdf: Fix CVE-2016-8674.
      adds  3de764f   gnu: gtk+-2: Update to 2.24.31 [fixes CVE-2013-7447].
      adds  6c18c4f   gnu: elfutils: Update to 0.167.
      adds  a98470b   import cran: Use URL for Bioconductor 3.4.
      adds  f987580   gnu: emacs-emms-player-mpv: Update to 0.0.10.
      adds  557a4b8   gnu: Add r-kernsmooth.
      adds  9beba74   gnu: r-annotate: Update to 1.52.0.
      adds  6faa2a4   gnu: r-geneplotter: Update to 1.52.0.
      adds  1e66e71   gnu: r-genefilter: Update to 1.56.0.
      adds  e1db8dd   gnu: r-deseq2: Update to 1.14.0.
      adds  55cd914   gnu: r-annotationforge: Update to 1.16.0.
      adds  700c780   gnu: r-rbgl: Update to 1.50.0.
      adds  558d02c   gnu: r-gseabase: Update to 1.36.0.
      adds  816599c   gnu: r-category: Update to 2.40.0.
      adds  ae6899b   gnu: r-gostats: Update to 2.40.0.
      adds  b87b41a   gnu: r-shortread: Update to 1.32.0.
      adds  1265d38   gnu: r-systempiper: Update to 1.8.1.
      adds  c9b5046   gnu: r-grohmm: Update to 1.8.0.
      adds  f0b297e   gnu: r-biocgenerics: Update to 0.20.0.
      adds  5c7b04e   gnu: r-biocinstaller: Update to 1.24.0.
      adds  22c5d73   gnu: r-dnacopy: Update to 1.48.0.
      adds  b120c5f   gnu: r-s4vectors: Update to 0.12.0.
      adds  7f354da   gnu: r-iranges: Update to 2.8.0.
      adds  dece310   gnu: r-genomeinfodb: Update to 1.10.0.
      adds  5e48005   gnu: r-edger: Update to 3.16.0.
      adds  37d96f1   gnu: r-variantannotation: Update to 1.20.0.
      adds  753bc32   gnu: r-limma: Update to 3.30.0.
      adds  1d04858   gnu: r-xvector: Update to 0.14.0.
      adds  92a740a   gnu: r-genomicranges: Update to 1.26.1.
      adds  464870c   gnu: r-biobase: Update to 2.34.0.
      adds  e45dc05   gnu: r-annotationdbi: Update to 1.36.0.
      adds  9405333   gnu: r-biomart: Update to 2.30.0.
      adds  89559a1   gnu: r-biocparallel: Update to 1.8.0.
      adds  47d39b6   gnu: r-biostrings: Update to 2.42.0.
      adds  c0ccef4   gnu: r-rsamtools: Update to 1.26.1.
      adds  08da08d   gnu: r-summarizedexperiment: Update to 1.4.0.
      adds  4ab32f0   gnu: r-genomicalignments: Update to 1.10.0.
      adds  6a45fd9   gnu: r-rtracklayer: Update to 1.34.0.
      adds  b17aac0   gnu: r-genomicfeatures: Update to 1.26.0.
      adds  d1b1587   gnu: r-go-db: Update to 3.4.0.
      adds  3587b46   gnu: r-graph: Update to 1.52.0.
      adds  30ec4de   gnu: r-topgo: Update to 2.26.0.
      adds  3d74c04   gnu: r-bsgenome: Update to 1.42.0.
      adds  acf6f7e   gnu: r-impute: Update to 1.48.0.
      adds  e92dd6f   gnu: r-seqpattern: Update to 1.6.0.
      adds  51c3c49   gnu: r-genomation: Update to 1.6.0.
      adds  21d6c7a   gnu: r-seqlogo: Update to 1.40.0.
      adds  809251e   gnu: r-motifrg: Update to 1.18.0.
      adds  da22da8   gnu: r-zlibbioc: Update to 1.20.0.
      adds  53ca52f   gnu: r-rhtslib: Update to 1.6.0.
      adds  e357bec   gnu: r-bamsignals: Update to 1.6.0.
      adds  59198f8   gnu: r-genomationdata: Update to 1.6.0.
      adds  19262a7   gnu: opensmtpd: Fix 'license' field.
      adds  1df790d   gnu: Add psyclpc.
      adds  7bc7ffc   gnu: Add x265.
      adds  d505801   gnu: ffmpeg: Add x265 support.
      adds  e3cb00d   gnu: gst-plugins-bad: Add x265 support.
      adds  8f5f6c9   gnu: vlc: Add x265 support.
      adds  d2a9b53   gnu: notmuch: Update to 0.23.1.
      adds  7a6213c   gnu: offlineimap: Install documentation.
      adds  f9c3396   gnu: yubico.scm: Rename to security-token.scm.
      adds  07b1fb8   gnu: security-token: Use 'license:' prefix.
      adds  b2a2232   gnu: python-certifi: Update to 2016.8.31.
      adds  e95ae7c   guix package: Display generation diffs.
      adds  39df253   gnu: mupdf: Modify CVE-2016-8674 patch to apply to 1.9a.
      adds  c70271e   gnu: bioperl-minimal: Update to 1.7.0.
      adds  8e1369f   gnu: r-rmarkdown: Update to 1.1.
      adds  7397cd9   gnu: armadillo: Update to 7.500.0.
      adds  062737a   gnu: r-rcpparmadillo: Update to 0.7.500.0.0.
      adds  a46cc72   gnu: r-seqinr: Update to 3.3-3.
      adds  2ffcd66   gnu: r-curl: Update to 2.2.
      adds  e1c2b7e   gnu: r-jsonlite: Update to 1.1.
      adds  9e087a1   gnu: r-colorspace: Update to 1.2-7.
      adds  03f72a1   gnu: r-matrix: Update to 1.2-7.1.
      adds  c2a9e99   gnu: r-stringi: Update to 1.1.2.
      adds  2d9da70   gnu: r-reshape2: Update to 1.4.2.
      adds  e0a9093   gnu: r-evaluate: Update to 0.10.
      adds  bff4dc6   gnu: r-r6: Update to 2.2.0.
      adds  e762280   gnu: r-acepack: Update to 1.4.0.
      adds  130410d   gnu: r-cluster: Update to 2.0.5.
      adds  72263db   gnu: r-foreign: Update to 0.8-67.
      adds  41bc22a   gnu: r-backports: Update to 1.0.4.
      adds  cf738e9   gnu: r-snow: Update to 0.4-2.
      adds  4f2ebc1   gnu: r-codetools: Update to 0.2-15.
      adds  89242ea   gnu: r-irlba: Update to 2.1.2.
      adds  fd54f65   gnu: r-r-utils: Update to 2.4.0.
      adds  a8e893b   gnu: r-matrixstats: Update to 0.51.0.
      adds  aba6463   gnu: r: Update to 3.3.1.
      adds  8caeb11   gnu: Add autossh.
      adds  5d73e30   gnu: Add lci.
       new  02c73ad   Merge branch 'master' into core-updates

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 configure.ac                                       |    9 +-
 doc/guix.texi                                      |   50 +-
 gnu/build/svg.scm                                  |   71 ++
 gnu/local.mk                                       |   12 +-
 gnu/packages/bioinformatics.scm                    |  222 ++--
 gnu/packages/elf.scm                               |    4 +-
 gnu/packages/emacs.scm                             |    4 +-
 gnu/packages/enlightenment.scm                     |    4 +-
 gnu/packages/games.scm                             |   70 +-
 gnu/packages/gnome.scm                             |    2 +-
 gnu/packages/gnustep.scm                           |    4 +-
 gnu/packages/gstreamer.scm                         |    3 +-
 gnu/packages/gtk.scm                               |    4 +-
 gnu/packages/guile.scm                             |   81 ++
 gnu/packages/irc.scm                               |    6 +-
 gnu/packages/linux.scm                             |    9 +-
 gnu/packages/lolcode.scm                           |   58 +
 gnu/packages/mail.scm                              |   36 +-
 gnu/packages/maths.scm                             |   86 +-
 gnu/packages/messaging.scm                         |   45 +-
 gnu/packages/musl.scm                              |    1 +
 gnu/packages/networking.scm                        |   39 +
 gnu/packages/patches/coda-use-system-libs.patch    |   46 +
 gnu/packages/patches/hdf-eos2-build-shared.patch   |   25 +
 gnu/packages/patches/hdf-eos2-fortrantests.patch   |  329 +++++
 gnu/packages/patches/hdf-eos2-remove-gctp.patch    |   55 +
 .../patches/linux-libre-4.1-CVE-2016-5195.patch    |   99 --
 gnu/packages/patches/mupdf-CVE-2016-8674.patch     |  165 +++
 gnu/packages/patches/musl-CVE-2016-8859.patch      |   81 ++
 .../notmuch-emacs-25-compatibility-fix.patch       |   46 -
 gnu/packages/pdf.scm                               |    3 +-
 gnu/packages/psyc.scm                              |   82 ++
 gnu/packages/python.scm                            |    4 +-
 gnu/packages/{yubico.scm => security-token.scm}    |    8 +-
 gnu/packages/ssh.scm                               |   26 +
 gnu/packages/statistics.scm                        |   94 +-
 gnu/packages/video.scm                             |   34 +
 gnu/packages/web.scm                               |    8 +-
 gnu/services/web.scm                               |   92 +-
 gnu/system/grub.scm                                |   41 +-
 guix/import/cran.scm                               |    4 +-
 guix/scripts/package.scm                           |   18 +-
 guix/ui.scm                                        |   28 +
 po/guix/fr.po                                      | 1349 +++++++++++---------
 44 files changed, 2427 insertions(+), 1030 deletions(-)
 create mode 100644 gnu/build/svg.scm
 create mode 100644 gnu/packages/lolcode.scm
 create mode 100644 gnu/packages/patches/coda-use-system-libs.patch
 create mode 100644 gnu/packages/patches/hdf-eos2-build-shared.patch
 create mode 100644 gnu/packages/patches/hdf-eos2-fortrantests.patch
 create mode 100644 gnu/packages/patches/hdf-eos2-remove-gctp.patch
 delete mode 100644 gnu/packages/patches/linux-libre-4.1-CVE-2016-5195.patch
 create mode 100644 gnu/packages/patches/mupdf-CVE-2016-8674.patch
 create mode 100644 gnu/packages/patches/musl-CVE-2016-8859.patch
 delete mode 100644 
gnu/packages/patches/notmuch-emacs-25-compatibility-fix.patch
 rename gnu/packages/{yubico.scm => security-token.scm} (94%)