gnu: emacs-org-journal: Disable failing tests.

* gnu/packages/emacs-xyz.scm (emacs-org-journal)
[arguments]: Add disable-failing-tests phase.

Change-Id: I466cb46613a7048ccbda66cd7855001a04871891

gnu: emacs-ess: Disable flaky "command-without-trailing-newline-test" test.

* gnu/packages/statistics.scm [arguments]: Add new disable-etests syntax in
'skip-failing-tests phase, and use it to disable the
'command-without-trailing-newline-test' test.

Change-Id: I99f52685691d86dc633fe6061f9ef3332159eb4e

gnu: wfmash: Update to 0.12.5.

* gnu/packages/bioinformatics.scm (wfmash): Update to 0.12.5.
(source): Use git-fetch. Update git repository URL.
(arguments): In check phase, symlink to "../source/data" and change wfmash
invocation arguments.
(home-page): Update URL.

Change-Id: I78f228f06a6a12e6904a58a12fd4201743e84d72

gnu: python-graph-tool: Update to 2.59.

* gnu/packages/graph.scm (python-graph-tool): Update to 2.59.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: I08ecb5fe76183fa980fedf2408fc1df93ebbc63d

gnu: guix-build-coordinator: Update to 0-95.dc04b74.

* gnu/packages/package-management.scm (guix-build-coordinator): Update to
0-95.dc04b74.

Change-Id: I89d968e72188428d40906a7d55533dfd25c7ec25

gnu: bffe: Update to 0-3.1c12da4.

* gnu/packages/package-management.scm (bffe): Update to 0-3.1c12da4.

Change-Id: I90a4231961aed434c2b4ffa07189b85e108b5c46

gnu: nsq: Fix build on i686-linux.

As seen in https://ci.guix.gnu.org/build/3329277/details

* gnu/packages/high-availability.scm (nsq)[arguments]<#:phases>{check}:
Skip '-race' option during tests on i686-linux.

Change-Id: I952d7187443835d5fbcb74f0ae09b923bd6bdb29

gnu: Add emacs-vhdl-mode.

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

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Modified-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Change-Id: I7e261fc25ae011c20f22e1078ae40bacff3a6947

gnu: Add emacs-pde.

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

Change-Id: Icab5d8acf9d441bb4a832a82e75432d64cc77ba7

gnu: perl-b-keywords: Update to 1.26.

* gnu/packages/perl.scm (perl-b-keywords): Update to 1.26.

Change-Id: I3fdb9acf9f257ff9583179e29b2e6a26104b7e0d

build: perl: Accept Gexps for #:module-build-flags.

* guix/build-system/perl.scm (perl-build) [module-build-flags]: Accept gexps.

Change-Id: If1daa4d9a8cf97824b75f2113f4d7d83256463ce

gnu: emacs: Patch awk, find, sed and sh commands.

Before this change, using Emacs in a pure environment, e.g. 'guix shell --pure
emacs', would cause problems such as:

  jka-compr-insert-file-contents: Uncompression program ‘sh’ not found

And other problems were found requiring the other tools.

* gnu/packages/emacs.scm (emacs-minimal) [arguments]: Extend the
patch-program-file-names phase.
[inputs]: Add findutils, gawk and sed.

Series-changes: 2
 - Patch references in place instead of wrapping via PATH

Change-Id: Ifb4fe2fc12ddc9eae387adb3da3f7821fab78e65

gnu: qt-creator: Update to 12.0.1.

* gnu/packages/qt.scm (qt-creator): Update to 12.0.1.
[source]: Adjust snippet for the upstream removal of bundled libraries under
the unittest directory.
[arguments]: Also wrap kcachegrind tool in wrap-bin phase.
[inputs]: Add kcachegrind.

Change-Id: I63616d532be2f1a603fcee0841f493d83a138302

gnu: kcachegrind: Update to 23.08.4.

* gnu/packages/kde.scm (kcachegrind): Update to 23.08.4.

Change-Id: I5cd0401c61325b274bfcb5c4bc914d8fe0325388

gnu: mpv: Propagate most libraries.

This is needed when packages lookup the mpv library via pkg-config, such as
done by plasmatube.

Prior to this change, the following would fail (this is what CMake's
'pkg_check_modules' does):

  $ guix shell --pure pkg-config mpv \
    -- pkg-config --print-errors --short-errors --exists mpv
  Package 'wayland-client', required by 'mpv', not found

* gnu/packages/video.scm (mpv)
[inputs]: Move alsa-lib, ffmpeg, jack-1, libass, libbluray, libcaca,
libcdio-paranoia, libdvdnav, libjpeg-turbo, libplacebo, libva, libvdpau,
libx11, libxext, libxinerama, libxpresent, libxrandr, libxscrnsaver, lua-5.2,
mesa, pulseaudio, shaderc, wayland, wayland-protocols, zimg and zlib to...
[propagated-inputs]: ... here.

Change-Id: Ia0cd4e33a8b4df4b060546c979d00be0b2b3977e

gnu: libdvdnav: Propagate libdvdread.

* gnu/packages/video.scm (libdvdnav) [inputs]: Move libdvdread to...
[propagated-inputs]: ... here.

Change-Id: Ifea887985f27ed1dec2c56ce2f5291862f011bed

gnu: libplacebo: Propagate lcms, shaderc and vulkan-loader.

* gnu/packages/video.scm (libplacebo)
[inputs]: Move lcms, shaderc and vulkan-loader to...
[propagated-inputs]: ... here.

Change-Id: If426be3b4e32632bb775485e0a8c517e09ccbeaf

gnu: ktextaddons: Update to 1.5.3.

* gnu/packages/kde-frameworks.scm (ktextaddons): Update to 1.5.3.
[inputs]: Add kio, ksyntaxhighlighting and sonnet.

Change-Id: I2c09d28f90dfcd43bf3081e2174405837798b29f

gnu: pulseaudio-qt: Update to 1.4.0.

* gnu/packages/kde-frameworks.scm (pulseaudio-qt): Update to 1.4.0.

Change-Id: I6a7a60a6da03af5591724596509292e09616ca7d

gnu: kdav: Update to 5.114.0.

* gnu/packages/kde-frameworks.scm (kdav): Update to 5.114.0.

Change-Id: Ieceba23a043909cd88018e3f2e310d0483c7f3f8