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2023-04-26gnu: cppcheck: Skip failing test....* gnu/packages/patches/check.scm (cppcheck)[source]: Add patch. * gnu/packages/patches/cppcheck-disable-char-signedness-test.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. Efraim Flashner
2023-04-26gnu: graphviz: Remove version 2.38....This is a follow-up to commit 370cb92eaa089af19c08d9a7b4f5a96ac5b27716 . * gnu/packages/graphviz.scm: Drop imported modules. (graphviz-2.38): Remove package. Andreas Enge
2023-04-25gnu: lcov: Update to 1.16....* gnu/packages/code.scm (lcov): Update to 1.16. Ludovic Courtès
2023-04-25gnu: perl-io-compress: Update to 2.204....* gnu/packages/perl-compression.scm (perl-io-compress): Update to 2.204. Ludovic Courtès
2023-04-25gnu: perl-compress-raw-bzip2: Update to 2.204....* gnu/packages/perl-compression.scm (perl-compress-raw-bzip2): Update to 2.204. Ludovic Courtès
2023-04-25gnu: perl-compress-raw-zlib: Update to 2.204....* gnu/packages/perl-compression.scm (perl-compress-raw-zlib): Update to 2.204. [arguments]: Remove. Ludovic Courtès
2023-04-25gnu: gnutls: Don't embed a phase inside another phase....* gnu/packages/tls.scm (gnutls)[arguments]: Adjust powerpc-linux phase 'increase-test-timeout to not be embedded inside another phase. Efraim Flashner
2023-04-25gnu: mpdevil: Add missing input....* gnu/packages/mpd.scm (mpdevil)[native-inputs]: Add gettext-minimal. Efraim Flashner
2023-04-25gnu: presage: Build with c++-14....* gnu/packages/fcitx.scm (presage)[arguments]: Adjust configure-flags to use c++-14 cor CFLAGS and CXXFLAGS. Efraim Flashner
2023-04-25gnu: libpst: Fix python detection....* gnu/packages/mail.scm (libpst)[arguments]: Add a phase to detect newer versions of python3. [native-inputs]: Add autoconf, automake, gettext-minimal, libool. Efraim Flashner
2023-04-25gnu: perl-data-dumper: Update to 2.183....* gnu/packages/perl.scm (perl-data-dumper): Update to 2.183. Ricardo Wurmus
2023-04-25gnu: cwltool: Use pyproject-build-system...."setup.py install is deprecated. Use build and pip and other standards-based tools." It then falls back to attempting to install packages via pip. * gnu/packages/bioinformatics.scm (cwltool)[build-system]: Use pyproject-build-system. Ricardo Wurmus
2023-04-25gnu: python-schema-salad: Use pyproject-build-system....The python-build-system fails with "setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer." This, in turn, causes all Python packages to be ignored and "pip install" to be invoked for them. * gnu/packages/bioinformatics.scm (python-schema-salad)[build-system]: Use pyproject-build-system. Ricardo Wurmus
2023-04-25gnu: gfeeds: Add missing gettext-minimal....* gnu/packages/syndication.scm (gfeeds)[inputs]: Add gettext-minimal. Liliana Marie Prikler
2023-04-25gnu: syndication-domination: Update to 1.0-1-7592032....* gnu/packages/syndication.scm (syndication-domination): Update to 1.0-1-7592032. Liliana Marie Prikler
2023-04-25gnu: evolution: Update to 3.46.4....* gnu/packages/gnome.scm (evolution): Update to 3.46.4. Liliana Marie Prikler
2023-04-25gnu: evolution-data-server: Update to 3.46.4....* gnu/packages/gnome.scm (evolution-data-server): Update to 3.46.4. Liliana Marie Prikler
2023-04-25gnu: adapterremoval: Update to 2.3.3....* gnu/packages/bioinformatics.scm (adapterremoval): Update to 2.3.3. [arguments]: Simplify. [inputs]: Reformat. Ricardo Wurmus
2023-04-25gnu: ocaml-lwt: Add ocaml4.07 variant....* gnu/packages/ocaml.scm (ocaml-lwt)[properties]: New field. (ocaml4.07-lwt): New variable. Efraim Flashner
2023-04-25gnu: perl-crypt-openssl-rsa: Update to 0.33....* gnu/packages/tls.scm (perl-crypt-openssl-rsa): Update to 0.33. Efraim Flashner
2023-04-25gnu: bedtools-2.18: Fix build....* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Fix operators in 'compatibility phase. Ricardo Wurmus
2023-04-25gnu: hisat: Build with GCC 10....* gnu/packages/bioinformatics.scm (hisat)[native-inputs]: Add gcc-10. Ricardo Wurmus
2023-04-25gnu: kallisto: Update to 0.48.0....* gnu/packages/bioinformatics.scm (kallisto): Update to 0.48.0. [arguments]: Remove trailing #T from build phase. Ricardo Wurmus
2023-04-25gnu: bpp-core: Build with GCC 10....* gnu/packages/bioinformatics.scm (bpp-core)[native-inputs]: Add gcc-10. Ricardo Wurmus
2023-04-25gnu: vcflib: Update to 1.0.9....* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.9. [source]: Update snippet. [inputs]: Add curl, pybind11, and wfa2-lib. [arguments]: Adjust and reformat. Ricardo Wurmus
2023-04-25gnu: tabixpp: Update to 1.1.2....* gnu/packages/bioinformatics.scm (tabixpp): Update to 1.1.2. [source]: Simplify snippet. [inputs]: Add curl. [arguments]: Simplify and reformat. Ricardo Wurmus
2023-04-25gnu: Add wfa2-lib....* gnu/packages/bioinformatics.scm (wfa2-lib): New variable. Ricardo Wurmus
2023-04-25gnu: biber: Fix build with new Perl....* gnu/packages/patches/biber-adapt-perl-5.36.patch: Backport patch from upstream's 760e6e4ec08a3097f7e6136331541a7b8c1c9df7. * gnu/packages/tex.scm (biber): Use it. * gnu/local.mk (dist_patch_DATA): Register it. Signed-off-by: Andreas Enge <andreas@enge.fr> Josselin Poiret
2023-04-25gnu: gcc: Do not build gcov on MinGW....* gnu/packages/gcc.scm (gcc-configure-flags-for-triplet): Disable gcov when targetting mingw. Co-authored-by: Ludovic Courtès <ludo@gnu.org> Vivien Kraus
2023-04-25gnu: nerd-dictation: Add package variants....* gnu/packages/machine-learning.scm (nerd-dictation)[inputs]: Remove. (nerd-dictation-gexp): New procedure. (nerd-dictation/xdotool, nerd-dictation/sox-xdotool) (nerd-dictation/sox-ydotool, nerd-dictation/sox-wtype): New variables Signed-off-by: Ludovic Courtès <ludo@gnu.org> Nicolas Graves
2023-04-25gnu: ghc-8.10: Avoid testsuite timeouts on i686....* gnu/packages/haskell.scm (ghc-8.10)[arguments]: Add new phase 'skip-failing-tests-i686-cuirass. Lars-Dominik Braun
2023-04-25gnu: lofreq: Set file timestamps to 1980s....This keeps Python from complaining: "ZIP does not support timestamps before 1980". * gnu/packages/bioinformatics.scm (lofreq)[arguments]: Add build phase 'set-source-file-times-to-1980. Ricardo Wurmus
2023-04-25gnu: lofreq: Drop input labels....* gnu/packages/bioinformatics.scm (lofreq)[inputs]: Drop package labels. Ricardo Wurmus
2023-04-25gnu: ivar: Update to 1.4.2....* gnu/packages/bioinformatics.scm (ivar): Update to 1.4.2. [arguments]: Remove -Werror flag. Ricardo Wurmus
2023-04-25gnu: propeller-gcc-4: Use MODIFY-INPUTS....* gnu/packages/embedded.scm (propeller-gcc-4)[native-inputs]: Use MODIFY-INPUTS and drop package label. Ricardo Wurmus
2023-04-25gnu: propeller-gcc-4: Use G-expression....* gnu/packages/embedded.scm (propeller-gcc-4)[arguments]: Use G-expression because the parent GCC package uses them too. Ricardo Wurmus
2023-04-25gnu: trurl: Correct inputs....* gnu/packages/curl.scm (trurl): Replace non-existant input curl-7.84.0 by curl, which is version 7.85.0. Andreas Enge
2023-04-25Merge remote-tracking branch 'origin/master' into core-updatesAndreas Enge
2023-04-25gnu: python-asyncssh: Update to 2.13.1....Includes fix for python-cryptography>=39 disallowing SHA-1 signatures, which caused the testsuite to fail. * gnu/packages/ssh.scm (python-asyncssh): Update to 2.13.1. Lars-Dominik Braun
2023-04-25gnu: alacritty: Patch reference to xdg-open....* gnu/packages/terminals.scm (alacritty)[arguments]: Add a phase to add an absolute reference to xdg-open. [inputs]: Add xdg-utils. Efraim Flashner
2023-04-25gnu: emacs-eshell-syntax-highlighting: Update to 0.5....* gnu/packages/emacs-xyz.scm (emacs-eshell-syntax-highlighting): Update to 0.5. Nicolas Goaziou
2023-04-25gnu: nethack: Update to 3.6.7....* gnu/packages/games.scm (nethack): Update to 3.6.7. Nicolas Goaziou
2023-04-25gnu: Add trurl....* gnu/packages/curl.scm (trurl): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Sharlatan Hellseher
2023-04-25gnu: emacs-auctex: Update to 13.2.0....* gnu/packages/emacs-xyz.scm (emacs-auctex): Update to 13.2.0. Nicolas Goaziou
2023-04-25gnu: Add emacs-xonsh-mode....* gnu/packages/emacs-xyz.scm (emacs-xonsh-mode): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Joseph LaFreniere
2023-04-25gnu: python-importlib-resources: Update to 5.12.0....* gnu/packages/python-xyz.scm (python-importlib-resources): Update to 5.12.0. [build-system]: Use pyproject-build-system. [arguments]: Add phase to avoid "pip install". [native-inputs]: Remove python-toml; add python-flake8, python-pytest, python-pytest-black, python-pytest-checkdocs, python-pytest-cov, python-pytest-enabler, python-pytest-flake8, python-pytest-mypy, and python-setuptools-57. [propagated-inputs]: Add python-zipp. Ricardo Wurmus
2023-04-25gnu: guix-build-coordinator: Update to 0-79.6a4e827....* gnu/packages/package-management.scm (guix-build-coordinator): Update to 0-79.6a4e827. Christopher Baines
2023-04-25gnu: schismtracker: Update to 20221201....* gnu/packages/music.scm (schismtracker): Update to 20221201. [source]: Convert snippet to gexp. [arguments]: Convert to gexp, add configure flags for FLAC and Wayland support. [inputs]: Remove libx11, libxext, and sdl; add flac and sdl2. Signed-off-by: Christopher Baines <mail@cbaines.net> Antero Mejr
2023-04-25gnu: python-anyio: Upgrade to 3.6.2....* gnu/packages/python-xyz.scm (python-anyio): Upgrade to 3.6.2. Lars-Dominik Braun
2023-04-25Revert "gnu: python-pytest-trio: Update to 0.8.0."...Not compatible with python-trio 0.8. This reverts commit 27a4bfbd07022ebabc352a419c7588fcfc881d88. Lars-Dominik Braun