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2021-12-07gnu: python-dendropy: Update to 4.5.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.5.1. [arguments]: Skip failing tests.
2021-12-07gnu: python-cooler: Use python-cytoolz-for-cooler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace python-cytoolz with python-cytoolz-for-cooler.
2021-12-07gnu: Add python-cytoolz-for-cooler.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-cytoolz-for-cooler): New variable.
2021-12-07gnu: python-sparse: Update to 0.13.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-sparse): Update to 0.13.0.
2021-12-07gnu: python-dask: Update to 2021.11.2.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dask): Update to 2021.11.2. [source]: Fetch from github. [arguments]: Remove phase 'disable-broken-tests.
2021-12-07gnu: python-dask: Run tests conditionally.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dask)[arguments]: Respect TESTS? option.
2021-12-07gnu: python-dask: Add missing input for tests.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dask)[native-inputs]: Add python-pytest-rerunfailures.
2021-12-07gnu: phylip: Update to 3.697.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (phylip): Update to 3.697.
2021-12-07gnu: phylip: Pass -fcommon to compiler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (phylip)[arguments]: Set CFLAGS.
2021-12-07gnu: phylip: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (phylip)[arguments]: Remove trailing #T from build phases.
2021-12-07gnu: subread: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (subread)[arguments]: Remove trailing #T from build phases.
2021-12-07gnu: subread: Update to 2.0.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (subread): Update to 2.0.3.
2021-12-07gnu: subread: Update home page..Ricardo Wurmus
* gnu/packages/bioinformatics.scm (subread)[home-page]: Use new home page.
2021-12-07gnu: subread: Pass -fcommon to compiler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (subread)[arguments]: Add -fcommon to flags.
2021-12-07gnu: python-pytest-console-scripts: Update to 1.2.1.Ricardo Wurmus
* gnu/packages/python-check.scm (python-pytest-console-scripts): Update to 1.2.1.
2021-12-07gnu: Add python-pytest-rerunfailures.Ricardo Wurmus
* gnu/packages/python-check.scm (python-pytest-rerunfailures): New variable.
2021-12-07gnu: mcl: Add -fcommon to compiler flags.Ricardo Wurmus
* gnu/packages/machine-learning.scm (mcl)[arguments]: Set CFLAGS.
2021-12-07gnu: python-cytoolz: Update to 0.11.2.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-cytoolz): Update to 0.11.2. [source]: Add snippet.
2021-12-07gnu: hisat: Update to 0.1.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat): Update to 0.1.6.
2021-12-07gnu: hisat: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove trailing #T from build phase.
2021-12-07gnu: hisat: Remove invalid characters.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove curly quotes.
2021-12-07gnu: crossmap: Update to 0.6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.6.1. [source]: Add snippet to remove generated files.
2021-12-07gnu: Remove python2-bx-python.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-bx-python): Delete variable.
2021-12-07gnu: python-bx-python: Update to 0.8.12.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.8.12. [propagated-inputs]: Remove python-six. [arguments]: Remove. Tests are still not run, though.
2021-12-07gnu: Remove pbtranscript-tofu.Ricardo Wurmus
Upstream has disappeared and it depends on Python 2, which is no longer supported. * gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove variable.
2021-12-07gnu: python-pyfit-sne: Update to 1.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyfit-sne): Update to 1.2.1. [arguments]: Disable tests explicitly.
2021-12-06gnu: helm: Fix build with GCC 9 and later.Pierre Langlois
* gnu/packages/music.scm (helm)[origin]: Add patch. * gnu/packages/patches/helm-fix-gcc-9-build.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
2021-12-06gnu: patchwork: Adjust for python-build-system change.Marius Bakke
This is a follow-up to commit db5646d957895944007c1bb44fcd998ea392f168, et.al. * gnu/packages/patchutils.scm (patchwork)[arguments]: Adapt one more site-packages call.
2021-12-06gnu: f-seq: Update name of commons-cli JAR.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Use new name of commons-cli JAR.
2021-12-06gnu: f-seq: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Remove trailing #T from build phase.
2021-12-06gnu: f-seq: Simplify snippet.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (f-seq)[source]: Simplify snippet.
2021-12-06gnu: osinfo-db-next: Fix uri.Mathieu Othacehe
* gnu/packages/virtualization.scm (osinfo-db-next)[source]: Fix URI.
2021-12-06gnu: python-kivy: Add missing dependencies.Ludovic Courtès
* gnu/packages/python-xyz.scm (python-kivy)[arguments]: Add 'set-home' phase. [inputs]: Add PYTHON-DOCUTILS, PYTHON-KIVY-GARDEN, and PYTHON-PYGMENTS. [synopsis, description]: Tweak.
2021-12-06gnu: Add python-kivy-garden.Ludovic Courtès
* gnu/packages/python-xyz.scm (python-kivy-garden): New variable.
2021-12-06gnu: fpm2: Build with '-fcommon'.Ludovic Courtès
* gnu/packages/password-utils.scm (fpm2)[arguments]: Add #:configure-flags.
2021-12-06gnu: xnee: Build with '-fcommon'.Ludovic Courtès
* gnu/packages/xnee.scm (xnee)[arguments]: New field.
2021-12-05gnu: libsoup: Simplify inputs.Ludovic Courtès
Obtained by running "guix style --input-simplification=always" and by using 'modify-inputs' instead of list primitives. * gnu/packages/gnome.scm (libsoup-minimal, libsoup-minimal-2, libsoup): Simplify inputs.
2021-12-05gnu: librsvg: Simplify inputs.Ludovic Courtès
Obtained by running "guix style --input-simplification=always". * gnu/packages/gnome.scm (librsvg, librsvg-2.40): Simplify inputs.
2021-12-05gnu: gtk+: Simplify inputs.Ludovic Courtès
Obtained by running: guix style --input-simplification=always gtk+ gtk+@2 * gnu/packages/gtk.scm (gtk+-2, gtk+): Simplify inputs.
2021-12-05gnu: gtk+@2: Use 'librsvg-for-system'.Ludovic Courtès
* gnu/packages/gtk.scm (gtk+-2)[propagated-inputs]: Use 'librsvg-for-system' unconditionally.
2021-12-05gnu: libsoup: Remove unneeded dependency on PHP.Ludovic Courtès
* gnu/packages/gnome.scm (libsoup-minimal)[native-inputs]: Remove PHP.
2021-12-05gnu: gtk+: Use 'librsvg-for-system'.Ludovic Courtès
This brings back SVG support on non-x86_64 platforms. * gnu/packages/gtk.scm (gtk+)[inputs]: Use 'librsvg-for-system' unconditionally. [arguments]: In 'disable-failing-tests' phase, remove conditional substitutions aimed for non-x86_64 targets lacking librsvg support. * gnu/packages/gnome.scm (libhandy)[arguments]: Likewise, remove 'skip-test-that-requires-svg' phase.
2021-12-05gnu: emacs: Use 'librsvg-for-system'.Ludovic Courtès
* gnu/packages/emacs.scm (emacs)[inputs]: Use 'librsvg-for-system' unconditionally.
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
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