* doc/guix.texi (Invoking guix size): Update example.

Suggested by Martin Castillo <castilma@uni-bremen.de>.
Fixes <https://bugs.gnu.org/31456>.

* doc/guix.texi (Invoking guix size): Clarify that 'guix size' looks for
ungrafted packages.  Clarify that it can be passed several package
specifications.

* gnu/packages/nano.scm: Update to 2.9.7.

* gnu/packages/patches/python-statsmodels-fix-tests.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/statistics.scm (python-statsmodels)[source]: Remove patches.
[arguments]: Disable tests; adjust build phases; add build phase
"patch-for-scipy" to fix runtime error.

* gnu/packages/ftp.scm (libfilezilla): Update to 0.12.2.

* gnu/packages/inkscape.scm (inkscape)[arguments]<#:make-flags>: Delete.
<#:phases>[patch-icon-cache-generator]: Add phase.

* gnu/packages/games.scm (wesnoth): Update to 1.14.1.
[source]: Remove wesnoth-fix-std-bad-cast.patch.
* gnu/packages/patches/wesnoth-fix-std-bad-cast.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Unregister it.

* gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm6): New variable.

* gnu/package/guile.scm (guile-simple-zmq): New variable.

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

Fixes <https://bugs.gnu.org/31450>.
Reported by Martin Castillo <castilma@uni-bremen.de>.

* guix/gexp.scm (gexp->derivation): Pass #:deprecation-warnings to
'imported-modules'.
(imported-files): Add #:deprecation-warnings and pass #:env-vars to
'gexp->derivation'.
(imported-modules): Add #:deprecation-warnings and pass it to
'imported-files'.

Previously things like:

  guix pack -R guile guile-json

would lead to a profile without Guile-JSON, and to an 'etc/profile' that
does not define 'GUILE_LOAD_PATH'.

* guix/scripts/pack.scm (wrapped-package)[build]: Link top-level entries
of PACKAGE into OUTPUT.

* gnu/packages/image-processing.scm (opencv)[properties]:  Add a
lint-hidden-cve property and add three CVEs to be ignored.

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

* doc/guix.texi (Invoking guix lint): Add cpe-version to example.
(Invoking guix lint): Add example for lint-hidden-cve.

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

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

* gnu/services/games.scm: Export wesnothd-configuration?, not the
non-existent wesnoth-configuration?.

* gnu/packages/password-utils.scm (pass-rotate): New variable.

Prior to this change, libguile-dbi.so was unable to find
libguile-dbd-sqlite3.so.

* gnu/packages/guile.scm (guile-dbi-bootstrap): New variable.
(guile-dbd-sqlite3)[propagated-inputs]: Remove guile-dbi.
[native-inputs]: Add guile-dbi-bootstrap.
(guile-dbi)[inputs]: Add guile-dbd-sqlite3.
[arguments]: Set RPATH using #:make-flags.

* gnu/packages/pdf.scm (mupdf): Update to 1.13.0.
[source]: Remove patches.
* gnu/packages/patches/mupdf-build-with-latest-openjpeg.patch,
gnu/packages/patches/mupdf-CVE-2017-17858.patch,
gnu/packages/patches/mupdf-CVE-2018-6544.patch,
gnu/packages/patches/mupdf-CVE-2018-1000051.patch: Remove files.
* gnu/local.mk (dist_patch_DATA): Remove them.

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

* gnu/packages/haskell.scm (ghc-containers): New variable.

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

* gnu/packages/haskell.scm (ghc-array): New variable.

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

* gnu/packages/haskell-check.scm (ghc-quickcheck-2.9): New variable.

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

Reported by Efraim Flashner.

* gnu/packages/printers.scm (robocut)[native-inputs]: Replace QTTOOLS
with QTBASE, which is where 'qmake' lives.

Reported by uniq10.

* build-aux/test-env.in: Check whether FILE exists before invoking 'guix
download'.

* gnu/packages/networking.scm (speedtest-cli): Update to 2.0.0.

* gnu/packages/version-control.scm (myrepos)[source]: Add patch.
* gnu/packages/patches/myrepos-CVE-2018-7032.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.

* gnu/packages/image-viewers.scm (viewnior): Update to 1.7.
[source]: Update source uri.
[build-system]: Switch to meson-build-system.
[arguments]: Remove custom 'autogen and 'skip-gtk-update-icon-cache
phases, add 'patch-source phase.  Skip tests.
[native-inputs]: Remove automake, autoconf, intltool, gnome-common,
libtool, which, add gettext-minimal.
[home-page]: Update home-page.

* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.9-43.

* gnu/packages/printers.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.

Fixes <https://bugs.gnu.org/28446>.
Reported by Mark H Weaver <mhw@netris.org>.

* gnu/packages.scm (find-packages-by-name): Use 'version-prefix?'
instead of 'string-prefix?'.

* guix/utils.scm (version-prefix?): New procedure.
* tests/utils.scm ("version-prefix?"): New test.

Previously the test suite would fail to run 'ppmquant', though it would
silently ignore it.

* gnu/packages/maths.scm (hypre)[native-inputs]: Add PERL.

* gnu/packages/golang.scm (go-1.10): Update to 1.10.2.

* gnu/packages/golang.scm (go-1.9): Update to 1.9.6.

* gnu/packages/bootloaders.scm (make-u-boot-package): Install "u-boot".

* gnu/packages/bootloaders.scm (u-boot-cubieboard): New variable.

Libmad is not used by gst-plugins-ugly since 1.12.0.

* gnu/packages/gstreamer.scm (gst-plugins-ugly)[inputs]: Remove libmad.

MPD already depends on FFmpeg, which uses LAME for MP3 decoding.

gnu/packages/mpd.scm (mpd)[inputs]: Remove LIBMAD.

* gnu/packages/libreoffice.scm (libreoffice): Update to 5.4.7.1.

* gnu/packages/wine.scm (wine-staging): Update to 3.8.