| Age | Commit message (Expand) | Author |
|---|
| 2021-12-07 | gnu: subread: Update to 2.0.3.•••* gnu/packages/bioinformatics.scm (subread): Update to 2.0.3.
| Ricardo Wurmus |
| 2021-12-07 | gnu: subread: Update home page..•••* gnu/packages/bioinformatics.scm (subread)[home-page]: Use new home page.
| Ricardo Wurmus |
| 2021-12-07 | gnu: subread: Pass -fcommon to compiler.•••* gnu/packages/bioinformatics.scm (subread)[arguments]: Add -fcommon to flags.
| Ricardo Wurmus |
| 2021-12-07 | gnu: python-pytest-console-scripts: Update to 1.2.1.•••* gnu/packages/python-check.scm (python-pytest-console-scripts): Update to
1.2.1.
| Ricardo Wurmus |
| 2021-12-07 | gnu: Add python-pytest-rerunfailures.•••* gnu/packages/python-check.scm (python-pytest-rerunfailures): New variable.
| Ricardo Wurmus |
| 2021-12-07 | gnu: mcl: Add -fcommon to compiler flags.•••* gnu/packages/machine-learning.scm (mcl)[arguments]: Set CFLAGS.
| Ricardo Wurmus |
| 2021-12-07 | gnu: python-cytoolz: Update to 0.11.2.•••* gnu/packages/python-xyz.scm (python-cytoolz): Update to 0.11.2.
[source]: Add snippet.
| Ricardo Wurmus |
| 2021-12-07 | gnu: hisat: Update to 0.1.6.•••* gnu/packages/bioinformatics.scm (hisat): Update to 0.1.6.
| Ricardo Wurmus |
| 2021-12-07 | gnu: hisat: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove trailing #T from
build phase.
| Ricardo Wurmus |
| 2021-12-07 | gnu: hisat: Remove invalid characters.•••* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove curly quotes.
| Ricardo Wurmus |
| 2021-12-07 | gnu: crossmap: Update to 0.6.1.•••* gnu/packages/bioinformatics.scm (crossmap): Update to 0.6.1.
[source]: Add snippet to remove generated files.
| Ricardo Wurmus |
| 2021-12-07 | gnu: Remove python2-bx-python.•••* gnu/packages/bioinformatics.scm (python2-bx-python): Delete variable.
| Ricardo Wurmus |
| 2021-12-07 | gnu: python-bx-python: Update to 0.8.12.•••* 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.
| Ricardo Wurmus |
| 2021-12-07 | gnu: Remove pbtranscript-tofu.•••Upstream has disappeared and it depends on Python 2, which is no longer
supported.
* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove variable.
| Ricardo Wurmus |
| 2021-12-07 | gnu: python-pyfit-sne: Update to 1.2.1.•••* gnu/packages/bioinformatics.scm (python-pyfit-sne): Update to 1.2.1.
[arguments]: Disable tests explicitly.
| Ricardo Wurmus |
| 2021-12-06 | gnu: helm: Fix build with GCC 9 and later.•••* 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.
| Pierre Langlois |
| 2021-12-06 | gnu: patchwork: Adjust for python-build-system change.•••This is a follow-up to commit db5646d957895944007c1bb44fcd998ea392f168, et.al.
* gnu/packages/patchutils.scm (patchwork)[arguments]: Adapt one more
site-packages call.
| Marius Bakke |
| 2021-12-06 | gnu: f-seq: Update name of commons-cli JAR.•••* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Use new name of
commons-cli JAR.
| Ricardo Wurmus |
| 2021-12-06 | gnu: f-seq: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Remove trailing #T from
build phase.
| Ricardo Wurmus |
| 2021-12-06 | gnu: f-seq: Simplify snippet.•••* gnu/packages/bioinformatics.scm (f-seq)[source]: Simplify snippet.
| Ricardo Wurmus |
| 2021-12-06 | gnu: osinfo-db-next: Fix uri.•••* gnu/packages/virtualization.scm (osinfo-db-next)[source]: Fix URI.
| Mathieu Othacehe |
| 2021-12-06 | gnu: python-kivy: Add missing dependencies.•••* 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.
| Ludovic Courtès |
| 2021-12-06 | gnu: Add python-kivy-garden.•••* gnu/packages/python-xyz.scm (python-kivy-garden): New variable.
| Ludovic Courtès |
| 2021-12-06 | gnu: fpm2: Build with '-fcommon'.•••* gnu/packages/password-utils.scm (fpm2)[arguments]: Add #:configure-flags.
| Ludovic Courtès |
| 2021-12-06 | gnu: xnee: Build with '-fcommon'.•••* gnu/packages/xnee.scm (xnee)[arguments]: New field.
| Ludovic Courtès |
| 2021-12-05 | gnu: libsoup: Simplify inputs.•••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.
| Ludovic Courtès |
| 2021-12-05 | gnu: librsvg: Simplify inputs.•••Obtained by running "guix style --input-simplification=always".
* gnu/packages/gnome.scm (librsvg, librsvg-2.40): Simplify inputs.
| Ludovic Courtès |
| 2021-12-05 | gnu: gtk+: Simplify inputs.•••Obtained by running:
guix style --input-simplification=always gtk+ gtk+@2
* gnu/packages/gtk.scm (gtk+-2, gtk+): Simplify inputs.
| Ludovic Courtès |
| 2021-12-05 | gnu: gtk+@2: Use 'librsvg-for-system'.•••* gnu/packages/gtk.scm (gtk+-2)[propagated-inputs]: Use
'librsvg-for-system' unconditionally.
| Ludovic Courtès |
| 2021-12-05 | gnu: libsoup: Remove unneeded dependency on PHP.•••* gnu/packages/gnome.scm (libsoup-minimal)[native-inputs]: Remove PHP.
| Ludovic Courtès |
| 2021-12-05 | gnu: gtk+: Use 'librsvg-for-system'.•••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.
| Ludovic Courtès |
| 2021-12-05 | gnu: emacs: Use 'librsvg-for-system'.•••* gnu/packages/emacs.scm (emacs)[inputs]: Use 'librsvg-for-system'
unconditionally.
| Ludovic Courtès |
| 2021-12-05 | gnu: openbox: Use 'librsvg-for-system'.•••* gnu/packages/openbox.scm (openbox)[inputs]: Use 'librsvg-for-system'
unconditionally.
| Ludovic Courtès |
| 2021-12-05 | gnu: mate: Depend on 'librsvg-for-system'.•••* 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.
| Ludovic Courtès |
| 2021-12-05 | 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.
| Ludovic Courtès |
| 2021-12-05 | 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>
| Thiago Jung Bauermann |
| 2021-12-05 | gnu: gtranslator: Fix URL.•••Reported by Vivien Kraus.
* gnu/packages/gnome.scm (gtranslator)[source]: Change
'version-major+minor' to 'version-major'.
| Ludovic Courtès |
| 2021-12-05 | gnu: Add libnftnl/fixed.•••* gnu/packages/linux.scm (libnftnl/fixed): New variable.
| Ricardo Wurmus |
| 2021-12-05 | Merge remote-tracking branch 'origin/master' into core-updates-frozen | Ricardo Wurmus |
| 2021-12-05 | 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.
| Ricardo Wurmus |
| 2021-12-05 | gnu: Remove python2-plastid.•••* gnu/packages/bioinformatics.scm (python2-plastid): Remove variable.
| Ricardo Wurmus |
| 2021-12-05 | gnu: Remove python2-twobitreader.•••* gnu/packages/bioinformatics.scm (python2-twobitreader): Remove variable.
| Ricardo Wurmus |
| 2021-12-05 | 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.
| Ricardo Wurmus |
| 2021-12-05 | gnu: python-bbknn: Add missing input.•••* gnu/packages/bioinformatics.scm (python-bbknn)[propagated-inputs]: Add
python-scikit-learn.
| Ricardo Wurmus |
| 2021-12-05 | gnu: velvet: Add missing TeX package.•••* gnu/packages/bioinformatics.scm (velvet)[native-inputs]: Add
texlive-fonts-ec.
| Ricardo Wurmus |
| 2021-12-05 | gnu: velvet: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (velvet)[arguments]: Remove trailing #T from
build phases.
| Ricardo Wurmus |
| 2021-12-05 | gnu: python-bwapy: Remove pre-built object files.•••* gnu/packages/bioinformatics.scm (python-bwapy)[source]: Remove all .o files
in a snippet.
| Ricardo Wurmus |
| 2021-12-05 | gnu: metabat: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (metabat)[arguments]: Remove trailing #T
from build phases.
| Ricardo Wurmus |
| 2021-12-05 | gnu: clapack: Pass -fcommon to compiler.•••* gnu/packages/maths.scm (clapack)[arguments]: Set CFLAGS.
| Ricardo Wurmus |
| 2021-12-05 | gnu: clapack: Remove trailing #T.•••* gnu/packages/maths.scm (clapack)[arguments]: Remove trailing #T from build
phases.
| Ricardo Wurmus |
