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2021-12-05gnu: openbox: Use 'librsvg-for-system'.Ludovic Courtès
* gnu/packages/openbox.scm (openbox)[inputs]: Use 'librsvg-for-system' unconditionally.
2021-12-05gnu: mate: Depend on 'librsvg-for-system'.Ludovic Courtès
* gnu/packages/mate.scm (engrampa)[inputs]: Replace LIBRSVG by LIBRSVG-FOR-SYSTEM. (libmatekbd)[inputs]: Likewise. (mate-panel)[inputs]: Likewise. (mate-screensaver)[inputs]: Likewise. (mate-utils)[inputs]: Likewise. (mate-control-center)[inputs]: Likewise. (eom)[inputs]: Likewise, and remove duplicate [license]: Remove unnecessary list.
2021-12-05gnu: librsvg@2.40: Depend on the default Pango version.Ludovic Courtès
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.
2021-12-05gnu: Add texlive-latex-luatex.Thiago Jung Bauermann
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>
2021-12-05gnu: gtranslator: Fix URL.Ludovic Courtès
Reported by Vivien Kraus. * gnu/packages/gnome.scm (gtranslator)[source]: Change 'version-major+minor' to 'version-major'.
2021-12-05gnu: Add libnftnl/fixed.Ricardo Wurmus
* gnu/packages/linux.scm (libnftnl/fixed): New variable.
2021-12-05Merge remote-tracking branch 'origin/master' into core-updates-frozenRicardo Wurmus
2021-12-05gnu: python-bwapy: Remove sanity-check.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bwapy)[arguments]: Add phase 'relax-requirements to accept a slightly older version of wheel; remove the 'sanity-check phase.
2021-12-05gnu: Remove python2-plastid.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-plastid): Remove variable.
2021-12-05gnu: Remove python2-twobitreader.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-twobitreader): Remove variable.
2021-12-05gnu: python-bbknn: Fix sanity-check phase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase 'do-not-fail-to-find-sklearn, which prevents the 'sanity-check phase from failing.
2021-12-05gnu: python-bbknn: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bbknn)[propagated-inputs]: Add python-scikit-learn.
2021-12-05gnu: velvet: Add missing TeX package.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (velvet)[native-inputs]: Add texlive-fonts-ec.
2021-12-05gnu: velvet: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (velvet)[arguments]: Remove trailing #T from build phases.
2021-12-05gnu: python-bwapy: Remove pre-built object files.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bwapy)[source]: Remove all .o files in a snippet.
2021-12-05gnu: metabat: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (metabat)[arguments]: Remove trailing #T from build phases.
2021-12-05gnu: clapack: Pass -fcommon to compiler.Ricardo Wurmus
* gnu/packages/maths.scm (clapack)[arguments]: Set CFLAGS.
2021-12-05gnu: clapack: Remove trailing #T.Ricardo Wurmus
* gnu/packages/maths.scm (clapack)[arguments]: Remove trailing #T from build phases.
2021-12-05gnu: tla2tools: Remove remaining reference to %output.Ricardo Wurmus
This is a follow-up to commit 7e6ee16d498f48b7bb74fefe5d3d67c62b5baa9d. * gnu/packages/java.scm (tla2tools)[arguments]: Remove remaining reference to %output.
2021-12-05gnu: kraken2: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kraken2)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-05gnu: methyldackel: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-05gnu: phast: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (phast)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-05gnu: libsbml: Remove references to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (libsbml)[arguments]: Remove references to %build-inputs by using a gexp.
2021-12-05gnu: ataqv: Remove references to %outputs and %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ataqv)[arguments]: Remove references to %outputs and %build-inputs by using a gexp.
2021-12-05gnu: adapterremoval: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (adapterremoval)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-05gnu: bbmap: Remove reference to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Remove reference to %build-inputs by using a gexp.
2021-12-05gnu: intervaltree: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (intervaltree)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-05gnu: biobambam2: Remove reference to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (biobambam2)[arguments]: Remove reference to %build-inputs by using a gexp.
2021-12-05gnu: sjcount: Remove reference to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove reference to %build-inputs by using a gexp.
2021-12-05gnu: sjcount: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove trailing #T from build phases.
2021-12-05gnu: dropseq-tools: Remove reference to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove reference to %build-inputs by using a gexp.
2021-12-05gnu: dropseq-tools: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove trailing #T from build phases... [source]: ...and from the snippet.
2021-12-05gnu: python-django-netfields: Update to 1.2.4.Marius Bakke
* gnu/packages/django.scm (python-django-netfields): Update to 1.2.4.
2021-12-05gnu: python-django: Update to 3.2.9.Marius Bakke
* gnu/packages/django.scm (python-django): Update to 3.2.9.
2021-12-05gnu: drbd-utils: Update to 9.19.1.Marius Bakke
* gnu/packages/cluster.scm (drbd-utils): Update to 9.19.1.
2021-12-05gnu: emacs-peg: Update to 0.10.3.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-peg): Update to 0.10.3.
2021-12-05gnu: tbb: Update to 2021.4.0.Marius Bakke
* gnu/packages/tbb.scm (tbb): Update to 2021.4.0.
2021-12-05gnu: Adjust for python-build-system behavior change.Marius Bakke
Commit cb72f9a773e0931ee3758c851d96007ded034e4c changed the semantics of SITE-PACKAGES, but did not adjust all callers. * gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Adjust for missing trailing slash. * gnu/packages/maths.scm (nomad-optimizer)[arguments]: Likewise. * gnu/packages/patchutils.scm (patchwork)[arguments]: Likewise.
2021-12-05gnu: python-pyvcf: Fix bytecode compilation.Marius Bakke
* gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Add phase to patch sample script.
2021-12-05gnu: python-whisper: Update to 1.1.8.Marius Bakke
* gnu/packages/monitoring.scm (python-whisper): Update to 1.1.8.
2021-12-05gnu: python-mailman-hyperkitty: Update to 1.2.0.Marius Bakke
* gnu/packages/mail.scm (python-mailman-hyperkitty): Update to 1.2.0. [source](patches): Remove.
2021-12-05gnu: python-hyperkitty: Update to 1.3.5.Marius Bakke
* gnu/packages/mail.scm (python-hyperkitty): Update to 1.3.5. [arguments]: Add pythonpath in test invokation. [propagated-inputs]: Add PYTHON-MISTUNE-NEXT. Change from PYTHON-DJANGO-2.2 to PYTHON-DJANGO. [native-inputs]: Add PYTHON-LXML.
2021-12-05gnu: Add python-mistune-next.Marius Bakke
* gnu/packages/python-xyz.scm (python-mistune-next): New variable.
2021-12-05gnu: python-django-haystack: Update to 3.1.1.Marius Bakke
* gnu/packages/django.scm (python-django-haystack): Update to 3.1.1. [arguments]: Adjust substitution.
2021-12-05gnu: python-alembic: Update to 1.7.5.Marius Bakke
* gnu/packages/databases.scm (python-alembic): Update to 1.7.5. [propagated-inputs]: Remove PYTHON-IMPORTLIB-RESOURCES.
2021-12-05gnu: ganeti: Add the output directory on GUIX_PYTHONPATH.Marius Bakke
This is a follow-up to commit 1ed567c8721ec2810fdb70f1c6fc8396a705d503. * gnu/packages/virtualization.scm (ganeti)[arguments]: Adjust wrap phase to include Ganetis own site-packages on $GUIX_PYTHONPATH.
2021-12-05gnu: python-webassets: Patch for Python 3.9.Marius Bakke
* gnu/packages/python-web.scm (python-webassets)[arguments]: Add substitution.
2021-12-05gnu: python-django-mailman3: Update to 1.3.7.Marius Bakke
* gnu/packages/mail.scm (python-django-mailman3): Update to 1.3.7.
2021-12-05gnu: python-mailmanclient: Update to 3.3.3.Marius Bakke
* gnu/packages/mail.scm (python-mailmanclient): Update to 3.3.3.
2021-12-05gnu: python-django-url-filter: Adjust phase order.Marius Bakke
* gnu/packages/django.scm (python-django-url-filter)[arguments]: Move substitution to after the unpack phase, so that it does not end up in the egg info.
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