gnu: linux-libre@4.4: Update to 4.4.28.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.28.

gnu: mumps: Upgrade to 5.0.2.

* gnu/packages/maths.scm (mumps): Upgrade to 5.0.2.
[arguments]: Properly return boolean from install phase.

guix hash: Interpret '-' as standard input.

* guix/scripts/hash.scm (guix-hash)[file-hash]: Special-case "-".
* tests/guix-hash.sh: Add test.
* doc/guix.texi (Invoking guix hash): Document it.

daemon: Do not error out when deduplication fails due to ENOSPC.

This solves a problem whereby if /gnu/store/.links had enough entries,
ext4's directory index would be full, leading to link(2) returning
ENOSPC.

* nix/libstore/optimise-store.cc (LocalStore::optimisePath_): Upon
ENOSPC from link(2), print a message and return instead of throwing a
'SysError'.

daemon: Improve the SQLite wrapper API.

In particular, this eliminates a bunch of boilerplate code.

Also integrates these Nix commits:

  80da7a6 Probably fix SQLITE_BUSY errors
  37a337b throwSQLiteError(): Check for SIGINT so we don't loop forever

Co-authored-by: Ludovic Courtès <ludo@gnu.org>

daemon: Factor out SQLite handling.

* nix/libstore/local-store.cc: Move SQLite code to...
* nix/libstore/sqlite.cc, nix/libstore/sqlite.hh: ... here.  New files.
* nix/local.mk (libstore_a_SOURCES): Add sqlite.cc.
(libstore_headers): Add sqlite.hh.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>

daemon: Turn retrying SQLite transactions into a higher-order function.

* nix/libstore/local-store.cc (retry_sqlite, end_retry_sqlite): Remove.
(retrySQLite): New template.
(LocalStore::registerFailedPath, LocalStore::hasPathFailed)
(LocalStore::queryFailedPaths, LocalStore::clearFailedPaths)
(LocalStore::queryPathInfo, LocalStore::isValidPath_)
(LocalStore::queryValidPaths, LocalStore::queryAllValidPaths)
(LocalStore::queryReferrers, LocalStore::queryValidDerivers)
(LocalStore::queryDerivationOutputs)
(LocalStore::queryDerivationOutputNames)
(LocalStore::queryPathFromHashPart, LocalStore::registerValidPaths)
(LocalStore::invalidatePathChecked): Use it.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>

gnu: vim: Update to 8.0.0051.

* gnu/packages/vim.scm (vim): Update to 8.0.0051.
[source]: Change to github release archive.

gnu: python-twobitreader: Update to 3.1.4.

* gnu/packages/bioinformatics.scm (python-twobitreader, python2-twobitreader):
Update to 3.1.4.

gnu: python-twobitreader: Disable the test suite.

The tests were silently skipped with Python 3.4. With Python 3.5, this caused
the build of python-twobitreader to fail.

* gnu/packages/bioinformatics.scm (python-twobitreader,
python2-twobitreader)[arguments]: Disable the tests.

gnu: Add emacs-org-trello.

* gnu/packages/emacs.scm (emacs-org-trello): New variable.

gnu: python-wsgiproxy2: Disable the test suite.

* gnu/packages/python.scm (python-wsgiproxy2, python2-wsgiproxy2)[arguments]:
Disable the tests.

gnu: python-beautifulsoup4: Update to 4.5.1.

* gnu/packages/python.scm (python-beautifulsoup4, python2-beautifulsoup4):
Update to 4.5.1.

gnu: python-beautifulsoup4: Run the test suite.

* gnu/packages/python.scm (python-beautifulsoup4)[arguments]: Add field
run python-2 -> python-3 conversion script and test suite.
(python2-beautifulsoup4)[arguments]: Specify use of python-2.

gnu: python-feedparser: Disable the test suite.

The tests were silently skipped with Python 3.4. With Python 3.5, this caused
the build of python-feedparser to fail.

* gnu/packages/python.scm (python-feedparser, python2-feedparser)[arguments]:
Disable the tests.

gnu: libwebp: Fix CVE-2016-9085.

* gnu/packages/patches/libwebp-CVE-2016-9085.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/image.scm (libwebp)[source]: Use it.

gnu: libwebp: Update to 0.5.1.

* gnu/packages/image.scm (libwebp): Update to 0.5.1.

gnu: Add emacs-request.

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

gnu: Add qwt.

* gnu/packages/qt.scm (qwt): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add r-mutationalpatterns.

* gnu/packages/bioinformatics.scm (r-mutationalpatterns): New variable.