gnu: librsvg@2.40: Depend on the default Pango version.

This avoids conflicts where, say, gtk+ would pull pango@1.44 whereas
mate-control-center would additionally pull pango@1.42 via librsvg@2.40
on i686-linux.

* gnu/packages/gnome.scm (librsvg-2.40)[arguments]: In
'remove-failing-tests' phase, remove two additional tests.
[inputs]: Change PANGO-1.42 to PANGO.

gnu: Add texlive-latex-luatex.

When TeX Live was updated to version 2021 the ‘lualatex’ format started
being generated with the LuaHBTeX engine, but the ‘lualatex’ command still
uses the LuaTeX engine. This causes the command to fail:

  user@popigai:~$ lualatex hello.tex
  This is LuaTeX, Version 1.13.0 (TeX Live 2021/GNU Guix)
  restricted system commands enabled.

  ---! lualatex.fmt was written by luahbtex
  (Fatal format file error; I'm stymied)user@popigai:~$

The correct way to fix this problem would be either to change texlive-bin
to make ‘lualatex’ use the LuaHBTeX engine, or to change texlive-latex-base
to generate ‘lualatex.fmt’ with LuaTeX. Both options would rebuild large
parts of the world.

Ricardo Wurmus suggested creating a new package to provide ‘lualatex.fmt’
for LuaTeX as a workaround. This is what this package does.

Fixes https://issues.guix.gnu.org/51252.

* gnu/packages/tex.scm (texlive-latex-luatex): New variable.

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

gnu: gtranslator: Fix URL.

Reported by Vivien Kraus.

* gnu/packages/gnome.scm (gtranslator)[source]: Change
'version-major+minor' to 'version-major'.

gnu: Add libnftnl/fixed.

* gnu/packages/linux.scm (libnftnl/fixed): New variable.

Merge remote-tracking branch 'origin/master' into core-updates-frozen

gnu: python-bwapy: Remove sanity-check.

* gnu/packages/bioinformatics.scm (python-bwapy)[arguments]: Add phase
'relax-requirements to accept a slightly older version of wheel; remove the
'sanity-check phase.

gnu: Remove python2-plastid.

* gnu/packages/bioinformatics.scm (python2-plastid): Remove variable.

gnu: Remove python2-twobitreader.

* gnu/packages/bioinformatics.scm (python2-twobitreader): Remove variable.

gnu: python-bbknn: Fix sanity-check phase.

* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase
'do-not-fail-to-find-sklearn, which prevents the 'sanity-check phase from
failing.

gnu: python-bbknn: Add missing input.

* gnu/packages/bioinformatics.scm (python-bbknn)[propagated-inputs]: Add
python-scikit-learn.

gnu: velvet: Add missing TeX package.

* gnu/packages/bioinformatics.scm (velvet)[native-inputs]: Add
texlive-fonts-ec.

gnu: velvet: Remove trailing #T.

* gnu/packages/bioinformatics.scm (velvet)[arguments]: Remove trailing #T from
build phases.

gnu: python-bwapy: Remove pre-built object files.

* gnu/packages/bioinformatics.scm (python-bwapy)[source]: Remove all .o files
in a snippet.

gnu: metabat: Remove trailing #T.

* gnu/packages/bioinformatics.scm (metabat)[arguments]: Remove trailing #T
from build phases.

gnu: clapack: Pass -fcommon to compiler.

* gnu/packages/maths.scm (clapack)[arguments]: Set CFLAGS.

gnu: clapack: Remove trailing #T.

* gnu/packages/maths.scm (clapack)[arguments]: Remove trailing #T from build
phases.

gnu: tla2tools: Remove remaining reference to %output.

This is a follow-up to commit 7e6ee16d498f48b7bb74fefe5d3d67c62b5baa9d.

* gnu/packages/java.scm (tla2tools)[arguments]: Remove remaining reference to
%output.

gnu: kraken2: Remove reference to %outputs.

* gnu/packages/bioinformatics.scm (kraken2)[arguments]: Remove reference to
%outputs by using a gexp.

gnu: methyldackel: Remove reference to %outputs.

* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove reference
to %outputs by using a gexp.

gnu: phast: Remove reference to %outputs.

* gnu/packages/bioinformatics.scm (phast)[arguments]: Remove reference to
%outputs by using a gexp.