branch core-updates updated (55174e6 -> 64461ba)

[Marius Bakke]

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

      from  55174e6   Merge branch 'master' into core-updates
      adds  497fc04   gnu: mash: Fetch sources from git.
      adds  5c1f35e   gnu: mash: Update to 2.1.
      adds  b58d9e4   gnu: metabat: Fetch sources from git.
      adds  9d94ca0   gnu: minced: Fetch sources from git.
      adds  6052264   gnu: minced: Update to 0.3.2.
      adds  a2b9d6a   gnu: pplacer: Fetch sources from git.
      adds  1a20bca   gnu: r-seqgl: Fetch sources from git.
      adds  4257c10   gnu: kentutils: Fetch sources from git.
      adds  55698df   gnu: libgff: Fetch sources from git.
      adds  2b773a9   gnu: sra-tools: Fetch sources from git.
      adds  ea68b3f   pull: Add missing monadic 'return'.
      adds  b44b1f0   gnu: hplip: Remove bundled non-free blobs.
      adds  5e242b0   gnu: pyicoteo: Fetch sources from git.
      adds  4715d4a   gnu: raxml: Fetch sources from git.
      adds  d9ba126   gnu: python2-biom-format: Fix build.
      adds  b9d0c35   gnu: raxml: Update to 8.2.12.
      adds  019fcdf   gnu: seqtk: Fetch sources from git.
      adds  63f3255   gnu: seqtk: Update to 1.3.
      adds  37e285b   gnu: preseq: Fetch sources from git.
      adds  67caa4b   gnu: preseq: Update to 2.0.3.
      adds  273df99   gnu: vsearch: Fetch source from git.
      adds  6236524   gnu: sortmerna: Fetch sources from git.
      adds  e0a8fc8   gnu: snap-aligner: Fetch sources from git.
      adds  7145f4e   gnu: ritornello: Fetch sources from git.
      adds  3b88806   gnu: ritornello: Update to 2.0.1.
      adds  f3f34b1   gnu: filevercmp: Fetch sources from git.
      adds  e2f3638   gnu: Add spread-sheet-widget.
      adds  ed33049   gnu: pspp: Update to 1.2.0.
      adds  e0f1aa2   gnu: tadbit: Fetch sources from git.
      adds  3398dfb   gnu: ncbi-vdb: Fetch sources from git.
      adds  6a7d9ee   gnu: ncbi-vdb: Use INVOKE and end phases on #T.
      adds  4031e7f   gnu: ngs-sdk: Fetch sources from git.
      adds  c098c49   gnu: sailfish: Fetch sources from git.
      adds  e438c96   gnu: fraggenescan: Use INVOKE.
      adds  c527d36   gnu: java-picard-1.113: Use INVOKE.
      adds  31c41a8   gnu: vsearch: Remove custom autogen phase.
      adds  e35dce0   gnu: mash: Remove custom autoconf phase.
      adds  0881d62   gnu: newick-utils: Remove custom autoconf phase.
      adds  1794164   gnu: muscle: Use INVOKE.
      adds  2e2d885   gnu: sra-tools: Use INVOKE.
      adds  8b685c4   gnu: taxtastic: Use INVOKE.
      adds  e78e54d   gnu: emboss: Use INVOKE.
      adds  3da3ced   gnu: ngs-sdk: Use INVOKE.
      adds  8d3eaa9   gnu: ngs-sdk: Update to 2.9.3.
      adds  8740885   gnu: ncbi-vdb: Update to 2.9.3.
      adds  b173334   gnu: plink-ng: Fetch sources from git.
      adds  15c9609   gnu: sra-tools: Update to 2.9.3.
      adds  86c6928   gnu: vsearch: Update to 2.9.1.
      adds  9f527c9   gnu: sailfish: Use INVOKE.
      adds  a954293   gnu: seek: Use INVOKE.
      adds  ce49fdc   gnu: roary: Use INVOKE.
      adds  a1e83a9   gnu: pplacer-scripts: Use INVOKE.
      adds  9c30cba   gnu: pcc: Use INVOKE.
      adds  ec618c2   gnu: cmus: Use INVOKE.
      adds  4e82946   gnu: cmus: Fetch sources from git.
      adds  9ab90ea   gnu: pd: Remove custom autoconf phase.
      adds  69cb939   gnu: libmusicbrainz: Use INVOKE.
      adds  195e081   gnu: Add python-pyelftools.
      adds  9870b9f   gnu: python-ilinkedlist: Update to 0.3.1.
      adds  ec86863   services: elogind: Fix spelling errors of left value 
fields in elogind config file.
      adds  8fa9ace   doc: Add index entries.
      adds  988b78b   gnu: Add fstrcmp.
      adds  e340725   gnu: kodi: Update to 18.0b5.
      adds  2705780   gnu: Add emacs-clang-format.
      adds  41d2b7f   gnu: PostgreSQL 9: Update to 9.6.11 [fixes 
CVE-2018-16850].
      adds  e4b62e2   gnu: wxmaxima: Update to 18.10.1.
      adds  b1b82ae   gnu: powertabeditor: Use INVOKE.
      adds  1b12b57   gnu: powertabeditor: Fetch sources from git.
      adds  97f33b0   gnu: guile-newt: Update to revision 1.
      adds  2cce23b   gnu: Add xmlrpc-c.
      adds  ddd925f   gnu: Add emacs-gtk-look.
      adds  2eaaadb   gnu: r-with-tests: Use INVOKE.
      adds  cee9ab2   gnu: r-with-tests: Update to 3.5.1.
       new  64461ba   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:
 doc/guix.texi                                      |   6 +
 gnu/local.mk                                       |   2 +-
 gnu/packages/bioinformatics.scm                    | 512 ++++++++++-----------
 gnu/packages/c.scm                                 |   5 +-
 gnu/packages/cups.scm                              |   6 +-
 gnu/packages/databases.scm                         |   4 +-
 gnu/packages/emacs.scm                             |  75 +++
 gnu/packages/gtk.scm                               |  27 ++
 gnu/packages/guile.scm                             |   6 +-
 gnu/packages/kodi.scm                              |  70 ++-
 gnu/packages/maths.scm                             |  10 +-
 gnu/packages/music.scm                             |  79 ++--
 .../patches/hplip-remove-imageprocessor.patch      | 232 ++++++++++
 .../patches/vsearch-unbundle-cityhash.patch        |   6 +-
 ...xmaxima-do-not-use-old-gnuplot-parameters.patch |  26 --
 gnu/packages/python.scm                            |  29 +-
 gnu/packages/statistics.scm                        |  17 +-
 gnu/packages/xml.scm                               |  38 ++
 gnu/services/desktop.scm                           |   8 +-
 guix/scripts/pull.scm                              |   2 +-
 20 files changed, 781 insertions(+), 379 deletions(-)
 create mode 100644 gnu/packages/patches/hplip-remove-imageprocessor.patch
 delete mode 100644 
gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch