branch core-updates updated (9c4ce3a -> 2718a9c)

[Marius Bakke]

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

      from  9c4ce3a   gnu: perl-test-trap: Update to 0.3.2.
      adds  3837108   gnu: bcftools: Fix building on aarch64.
      adds  06f31e5   gnu: diamond: Update to 0.9.10.
      adds  6550e5a   gnu: signify: Update to 22.
      adds  dca82ae   gnu: p11-kit: Update to 0.23.8.
      adds  be69176   gnu: fish-guix: Use new download URL.
      adds  425d66f   gnu: Add emacs-highlight-symbol.
      adds  2434f5c   gnu: Add dssi.
      adds  6230e15   gnu: Fix memcached service startup.
      adds  8343d37   gnu: cgit: Don't build cgit's special 'git:src' input.
      adds  953a12f   gnu: hdf4: Fix building on aarch64.
      adds  d534f3a   gnu: r-mzr: Fix building on aarch64 and armhf.
      adds  2f7966c   gnu: font-google-noto: Use font-build-system.
      adds  c12562e   gnu: cpphs: Update to 1.20.8.
      adds  f99a57d   gnu: Add ghc-strict.
      adds  867ed97   gnu: Add ghc-stmonadtrans.
      adds  be04f80   gnu: Add ghc-edit-distance.
      adds  3f8b8e7   gnu: Add ghc-boxes.
      adds  96f23b6   gnu: Add ghc-equivalence.
      adds  adcb306   gnu: pspp: Update to 0.11.0.
      adds  ca48a34   gnu: Add ghc-data-hash.
      adds  a623fd7   gnu: Add ghc-murmur-hash.
      adds  212ae09   gnu: Add ghc-edisonapi.
      adds  1eced2a   gnu: Add ghc-edisoncore.
      adds  005a08e   gnu: Add ghc-fail.
      adds  298af2a   gnu: Add ghc-monadplus.
      adds  e0ca14c   gnu: Add ghc-geniplate-mirror.
      adds  af4db69   gnu: Add ghc-gitrev.
      adds  e664200   gnu: Add ltris.
      adds  ab1bd28   gnu: connman: Update to 1.35.
      adds  d0b13d7   gnu: fossil: Update to 2.2.
      adds  f207984   gnu: Add gpick.
      adds  e2a4c13   gnu: cbatticon: Update to 1.6.6.
      adds  f886e7c   gnu: limnoria: Update to 2017.08.03.
      adds  f37995f   gnu: python-cryptography: Update to 2.0.3.
      adds  f73f1f0   gnu: python-cryptography-vectors: Update to 2.0.3.
      adds  84a5263   gnu: Add liblinebreak.
      adds  d6ef422   gnu: Add fbreader.
      adds  e3b861c   gnu: python-cython: Update to 0.26.
      adds  a6d0544   gnu: cuirass: Update to 0.0.1-7.6f85bc0.
      adds  721e198   gnu: Add mgba.
      adds  aacefef   gnu: american-fuzzy-lop: Add support for non-Intel 
architectures.
      adds  a71fd67   gnu: american-fuzzy-lop: Update to 2.49b.
      adds  5f96f30f  gnu: Add r-interactivedisplaybase.
      adds  4a007ff   gnu: Add r-annotationhub.
      adds  33ce12e   gnu: Add r-auc.
      adds  c69d27d   gnu: Add r-calibrate.
      adds  2bdb5c3   gnu: Add r-shape.
      adds  4847a62   gnu: Add r-globaloptions.
      adds  2856369   gnu: Add r-circlize.
      adds  5cc79c9   gnu: Add r-powerlaw.
      adds  eb60149   gnu: Add r-png.
      adds  0548660   gnu: Add r-compare.
      adds  d3c67e1   gnu: Add r-dendextend.
      adds  e0268ff   gnu: Add r-getoptlong.
      adds  f2e974e   gnu: Add r-fastmatch.
      adds  a7f0faa   gnu: Add r-ff.
      adds  49c9c29   gnu: Add r-ffbase.
      adds  18a16ce   gnu: Add r-prettyunits.
      adds  71be51d   gnu: Add r-reshape.
      adds  c9c6f4b   gnu: Add r-progress.
      adds  ac84020   gnu: Add r-ggally.
      adds  3349fae   gnu: Add r-proxy.
      adds  bc0081e   gnu: Add r-sp.
      adds  b723ded   gnu: Add r-rook.
      adds  e389d10   gnu: Add r-rmtstat.
      adds  6427e62   gnu: Add r-lmoments.
      adds  28476b4   gnu: Add r-distillery.
      adds  58db98c   gnu: Add r-extremes.
      adds  062b6db   gnu: Add r-lmtest.
      adds  d6b156d   gnu: Add r-inline.
      adds  8c72b83   gnu: Add r-bbmle.
      adds  97cb349   gnu: r-trimcluster: Update license.
      adds  b31e4a9   gnu: Add r-emdbook.
      adds  d4a1e91   gnu: Add r-fastseg.
      adds  212f612   gnu: Add r-qvalue.
      adds  a3e36d3   gnu: Add r-lpsolve.
      adds  521e070   gnu: Add r-limsolve.
      adds  6b4a9ae   gnu: Add r-fitdistrplus.
      adds  8d22007   gnu: Add r-energy.
      adds  abcb849   gnu: Add r-suppdists.
      adds  05e8a3e   gnu: Add r-ksamples.
      adds  f30ff28   gnu: mariadb: Update to 10.1.26 [fixes 
CVE-2017-{3636,3641,3653}].
      adds  8a39e4a   gnu: sassc: Update to 3.4.5.
      adds  bf3fa99   gnu: Add r-methylkit.
      adds  dd75a9a   gnu: Add ogre.
      adds  42d0d13   gnu: Add mygui.
      adds  e9a599c   gnu: Add OpenMW.
      adds  c9aa261   gnu: services: Nginx configs can reference store
      adds  f2d7a49   web: Check for the existance of SSL related files.
      adds  821f187   gnu: address@hidden: Update to 4.4.83.
      adds  1e07076   gnu: address@hidden: Update to 4.9.44.
      adds  2d72ddf   gnu: linux-libre: Update to 4.12.8.
      adds  9fa0c0e   gnu: libmspack: Update to 0.6 [fixes 
CVE-2017-{6419,11423}].
      adds  d016b60   gnu: wireshark: Update to 2.4.0.
      adds  d80a47f   gnu: libnl: Add "doc" output.
      adds  3eb7c00   gnu: libnl: Add "python2" and "python3" outputs.
      adds  ae5947b   gnu: Add libfabric.
      adds  a099570   gnu: openmpi: Add RDMA and libfabric support.
      adds  961012a   gnu: Add missing import.
      adds  52d445f   gnu: Add rss-bridge.
      adds  623cc34c  gnu: rpm: Update to 4.13.0.1.
      adds  2c7321e   gnu: libconfuse: Update to 3.2.1.
      adds  2559401   gnu: youtube-dl: Update to 2017.08.18.
      adds  842e0e4   Simplify remouting with MS_PRIVATE in sandbox build
      adds  ed464f4   nix: Remove unused function.
      adds  c5361b7   gnu: Add rtl-sdr.
      adds  1286ff6   gnu: giac-xcas: Update to 1.2.3-57.
      adds  26ca43b   gnu: freeipmi: Update to 1.5.7.
      adds  de5a235   gnu: kde-framework: Update to 5.37.0.
      adds  d983a1c   gnu: libksysguard: Update to 5.10.4.
      adds  c5a856d   gnu: xf86-video-siliconmotion: Fix building on aarch64.
      adds  cc81f1c   gnu: freerdp: Revert to version 1.1.
      adds  598b548   gnu: freerdp: Update inputs.
      adds  94793c1   gnu: perl-crypt-openssl-bignum: Update to 0.08.
      adds  7c94a35   gnu: totem-pl-parser: Update to 3.10.8.
      adds  69d0674   gnu: shotwell: Update to 0.26.3.
      adds  9d086c0   gnu: gjs: Update to 1.48.6.
      adds  32d00d7   gnu: libgnome-games-support: Update to 1.2.2.
      adds  d95d6d9   gnu: gnome-keyring: Update to 3.20.1.
      adds  cd5db77   gnu: gnome-control-center: Update to 3.24.3.
      adds  1f9c235   gnu: gnome-shell: Update to 3.24.3.
      adds  8c0c0c4   gnu: python-pygit2: Update to 0.26.0.
      adds  d9f15d7   gnu: newsbeuter: Fix CVE-2017-12904.
      adds  865aacc   gnu: Remove libgames-support.
      adds  00d9124   gnu: lz4: Use recommended home page.
      adds  b7585ca   gnu: lz4: Update to 1.8.0.
      adds  e121be1   gnu: python-netaddr: Update to 0.7.19.
      adds  d79013f   maint: Create an ISO9660 installation image in the 
'release' target.
      adds  acabbd5   doc: Mention how to use emacs-debbugs.
      adds  2905926   doc: Update Database services in detailed node list.
      adds  af73566   pack: Add "none" compressor.
      adds  7b87132   gnu: libreoffice: Update to 5.3.5.2.
      adds  0c2e2b6   gnu: address@hidden: Update to 2.6.11 [security fixes].
      adds  36ed934   gnu: address@hidden: Update to 3.5.1.
      adds  6a84ec8   gnu: Add libinfinity.
      adds  97291c0   gnu: gobby: Update to 0.5.0.
      adds  2941b34   gnu: grub-efi-bootloader: Specialize grub-install 
invocation.
      adds  63ad9b8   gnu: gnome: Propagate more packages.
      adds  50631fe   gnu: gobby: Re-add Gobby 0.4.
      adds  a9dbefd   gnu: gnome: Propagate font-dejavu.
      adds  96d36f3   gnu: Add gnome-default-applications.
      adds  17cddc1   gnu: Add r-annotationfilter.
      adds  92a1cb9   gnu: powertabeditor: Update to 2.0.0-alpha10.
      adds  a8cd352   gnu: r-minimal: Work around failure to embed reference to 
"which".
      adds  6d7d9d9   gnu: graphicsmagick: Fix CVE-2017-{12935,12936,12937}.
      adds  a02967d   guix download: Support retrieving local file without the 
URI scheme.
      adds  3fa1b08   gnu: limnoria: Update to 2017.08.18.
      adds  29a3325   gnu: bundler: Update to 1.15.4.
      adds  bda6c35   gnu: pspp: Update to 1.0.0.
      adds  1dbd343   gnu: vifm: Update to 0.9.
      adds  e904de7   gnu: gnurl: Update to 7.55.1.
       new  2718a9c   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:
 HACKING                                            |  10 +
 Makefile.am                                        |   3 +-
 doc/guix.texi                                      |  95 ++-
 gnu/bootloader/grub.scm                            |  16 +-
 gnu/local.mk                                       |  12 +-
 gnu/packages/admin.scm                             |   4 +-
 gnu/packages/algebra.scm                           |   4 +-
 gnu/packages/bioinformatics.scm                    | 195 ++++-
 gnu/packages/ci.scm                                |  28 +-
 gnu/packages/compression.scm                       |  13 +-
 gnu/packages/connman.scm                           |   4 +-
 gnu/packages/cran.scm                              | 782 ++++++++++++++++++++-
 gnu/packages/crypto.scm                            |   4 +-
 gnu/packages/databases.scm                         |   5 +-
 gnu/packages/debug.scm                             |  27 +-
 gnu/packages/ebook.scm                             |  82 +++
 gnu/packages/emacs.scm                             |  32 +
 gnu/packages/fonts.scm                             |  27 +-
 gnu/packages/freeipmi.scm                          |   4 +-
 gnu/packages/game-development.scm                  |  85 +++
 gnu/packages/games.scm                             | 100 +++
 gnu/packages/gnome.scm                             |  96 ++-
 gnu/packages/gnunet.scm                            |   4 +-
 gnu/packages/gobby.scm                             |  85 ++-
 gnu/packages/graphics.scm                          |  71 ++
 gnu/packages/ham-radio.scm                         |  52 ++
 gnu/packages/haskell.scm                           | 304 +++++++-
 gnu/packages/image.scm                             |  71 ++
 gnu/packages/imagemagick.scm                       |   6 +-
 gnu/packages/irc.scm                               |   4 +-
 gnu/packages/java.scm                              |  42 +-
 gnu/packages/kde-frameworks.scm                    | 311 ++++----
 gnu/packages/kde.scm                               |   6 +-
 gnu/packages/libreoffice.scm                       |   4 +-
 gnu/packages/linux.scm                             |  91 ++-
 gnu/packages/maths.scm                             |  11 +-
 gnu/packages/mpi.scm                               |   2 +
 gnu/packages/music.scm                             |  59 +-
 gnu/packages/networking.scm                        |  38 +-
 gnu/packages/package-management.scm                |   8 +-
 .../patches/bcftools-regidx-unsigned-char.patch    |  16 +
 .../patches/graphicsmagick-CVE-2017-12935.patch    |  28 +
 .../patches/graphicsmagick-CVE-2017-12936.patch    |  16 +
 .../patches/graphicsmagick-CVE-2017-12937.patch    |  28 +
 gnu/packages/patches/lz4-fix-test-failures.patch   | 136 ----
 .../patches/newsbeuter-CVE-2017-12904.patch        |  34 +
 .../patches/python-cython-fix-tests-32bit.patch    |  27 -
 .../python-pygit2-disable-network-tests.patch      |  79 +--
 gnu/packages/patches/rpm-CVE-2014-8118.patch       |  25 -
 gnu/packages/patches/vinagre-revert-1.patch        |  56 ++
 gnu/packages/patches/vinagre-revert-2.patch        | 448 ++++++++++++
 .../xf86-video-siliconmotion-fix-ftbfs.patch       | 171 +++++
 gnu/packages/python.scm                            |  23 +-
 gnu/packages/rdesktop.scm                          | 108 +--
 gnu/packages/ruby.scm                              |   4 +-
 gnu/packages/shells.scm                            |   2 +-
 gnu/packages/statistics.scm                        |  17 +-
 gnu/packages/syndication.scm                       |   2 +
 gnu/packages/tls.scm                               |   8 +-
 gnu/packages/version-control.scm                   |  52 +-
 gnu/packages/video.scm                             |   4 +-
 gnu/packages/vim.scm                               |  40 +-
 gnu/packages/web.scm                               |  85 ++-
 gnu/packages/wm.scm                                |   4 +-
 gnu/packages/xorg.scm                              |   3 +-
 gnu/services/databases.scm                         |  17 +-
 gnu/services/web.scm                               | 164 ++---
 gnu/system/examples/bare-bones.tmpl                |   4 +-
 gnu/system/examples/desktop.tmpl                   |   7 +-
 gnu/system/examples/lightweight-desktop.tmpl       |   7 +-
 gnu/tests/databases.scm                            |  10 +-
 guix/scripts/download.scm                          |   5 +-
 guix/scripts/pack.scm                              |  18 +-
 nix/libstore/build.cc                              |   8 +-
 nix/libutil/util.cc                                |  15 -
 nix/libutil/util.hh                                |   6 -
 tests/guix-download.sh                             |   5 +-
 77 files changed, 3645 insertions(+), 834 deletions(-)
 create mode 100644 gnu/packages/ham-radio.scm
 create mode 100644 gnu/packages/patches/bcftools-regidx-unsigned-char.patch
 create mode 100644 gnu/packages/patches/graphicsmagick-CVE-2017-12935.patch
 create mode 100644 gnu/packages/patches/graphicsmagick-CVE-2017-12936.patch
 create mode 100644 gnu/packages/patches/graphicsmagick-CVE-2017-12937.patch
 delete mode 100644 gnu/packages/patches/lz4-fix-test-failures.patch
 create mode 100644 gnu/packages/patches/newsbeuter-CVE-2017-12904.patch
 delete mode 100644 gnu/packages/patches/python-cython-fix-tests-32bit.patch
 delete mode 100644 gnu/packages/patches/rpm-CVE-2014-8118.patch
 create mode 100644 gnu/packages/patches/vinagre-revert-1.patch
 create mode 100644 gnu/packages/patches/vinagre-revert-2.patch
 create mode 100644 
gnu/packages/patches/xf86-video-siliconmotion-fix-ftbfs.patch