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2023-04-19gnu: r-dmrseq: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.18.1.
2023-04-19gnu: r-beachmat: Update to 2.14.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-beachmat): Update to 2.14.2.
2023-04-19gnu: r-gdsfmt: Update to 1.34.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.34.1.
2023-04-19gnu: r-ebimage: Update to 4.40.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ebimage): Update to 4.40.1.
2023-04-19gnu: r-enrichplot: Update to 1.18.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.18.4.
2023-04-19gnu: r-structuralvariantannotation: Update to 1.14.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-structuralvariantannotation): Update to 1.14.1.
2023-04-19gnu: r-rhdf5: Update to 2.42.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.42.1.
2023-04-19gnu: openmw-scenegraph: Fix build.Efraim Flashner
* gnu/packages/graphics.scm (openmw-scenegraph)[outputs]: Only use 'out' output. [arguments]: Delete inherited 'copy-plugins phase.
2023-04-19gnu: repo2docker: Add missing inputs.Efraim Flashner
* gnu/packages/jupyter.scm (repo2docker)[inputs]: Add python-iso8601, python-chardet.
2023-04-19gnu: kwin: Update skipped test list.Efraim Flashner
* gnu/packages/kde-plasma.scm (kwin)[arguments]: Update custom 'check phase with new list of skipped tests.
2023-04-19gnu: kwin: Rewrite skipped tests to be more readable.Efraim Flashner
* gnu/packages/kde-plasma.scm (kwin)[arguments]: Rewrite skipped tests in custom 'check phase to be easier to read.
2023-04-19gnu: emacs-osm: Do not mix home-page and origin.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-osm)[source]<origin>: Do not use home-page value as origin.
2023-04-19gnu: emacs-osm: Update to 0.11.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-osm): Update to 0.11.
2023-04-19gnu: emacs-marginalia: Update to 1.2.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-marginalia): Update to 1.2.
2023-04-19gnu: emacs-envrc: Add DIRENV as an input.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-envrc)[arguments]<#:phases>: Set direnv executable location. <#:tests?, #:test-command>: Tentatively run tests, without success. At least, they do not complain "direnv" executable is nowhere to be found. [inputs]: Add DIRENV.
2023-04-19gnu: emacs-envrc: Update to 0.5.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-envrc): Update to 0.5.
2023-04-19gnu: emacs-cape: Update to 0.15.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-cape): Update to 0.15.
2023-04-19gnu: emacs-autothemer: Run tests.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-autothemer)[arguments]: Run tests.
2023-04-19gnu: emacs-autothemer: Update to 0.2.17.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-autothemer): Update to 0.2.17.
2023-04-19gnu: Add texlive-totpages.Matthieu Lemerre
* gnu/packages/tex.scm (texlive-totpages): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2023-04-19gnu: texlive-latex-lastpage: Replace with texlive-lastpage.Nicolas Goaziou
* gnu/packages/tex.scm (texlive-lastpage): New variable. (texlive-latex-lastpage): Deprecate variable.
2023-04-19gnu: texlive-latex-totcount: Replace with texlive-totcount.Nicolas Goaziou
* gnu/packages/tex.scm (texlive-totcount): New variable. (texlive-latex-totcount): Deprecate package.
2023-04-19gnu: texlive-latex-acronym: Replace with texlive-acronym.Nicolas Goaziou
* gnu/packages/tex.scm (texlive-latex-acronym): Deprecate package. (texlive-acronym): New variable.
2023-04-19gnu: texlive-latex-bigfoot: Replace with texlive-bigfoot.Nicolas Goaziou
* gnu/packages/tex.scm (texlive-bigfoot): New variable. (texlive-latex-bigfoot): Deprecate package. (texlive-pstool): Use new variable.
2023-04-19gnu: Add texlive-relsize.Nicolas Goaziou
* gnu/packages/tex.scm (texlive-relsize): New variable.
2023-04-19gnu: Add texlive-ncctools.Nicolas Goaziou
* gnu/packages/tex.scm (texlive-ncctools): New variable.
2023-04-19gnu: r-with-tests: Update to 4.2.3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-with-tests): Update to 4.2.3.
2023-04-19snippets: tempel: Simplify git-commit-mode detection.Nicolas Graves
* etc/snippets/tempel/text-mode: Simplify git-commit-mode detection. Signed-off-by: Andrew Tropin <andrew@trop.in>
2023-04-19gnu: emacs-next: Update to 29.0.90.Liliana Marie Prikler
* gnu/packages/emacs.scm (emacs-next): Update to 29.0.90.
2023-04-19gnu: qemu: Update to 7.2.1.Maxim Cournoyer
* gnu/packages/virtualization.scm (qemu): Update to 7.2.1.
2023-04-19gnu: audacity: Update to 3.3.0-beta-1.Maxim Cournoyer
* gnu/packages/audio.scm (audacity): Update to 3.3.0-beta-1. [source]: Delete trailing #t in snippet. [arguments]: Update fix-cmake-rpath phase. Reported-by: tschilptschilp23 on #guix.
2023-04-19gnu: remmina: Update to 1.4.29.TakeV
* gnu/packages/vnc.scm (remmina): Update to 1.4.29. [inputs]: Add PYTHON-MINIMAL-WRAPPER. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2023-04-19gnu: usbutils: Use G-Expressions.Bruno Victal
* gnu/packages/linux.scm (usbutils): Use G-Expressions. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-04-19gnu: usbutils: Make package description different from synopsis.mikadoZero
* gnu/packages/linux.scm (usbutils)[description]: Change package description. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-04-19gnu: Add kitsas.Saku Laesvuori
* gnu/packages/finance.scm (kitsas): New variable. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2023-04-19ssh: Silence remote daemon messages when sending store items.Ludovic Courtès
Fixes <https://issues.guix.gnu.org/61839>. Previously, when running 'guix-daemon --debug' on the remote machine, lots of debugging outputs would be printed to stderr; since the client wouldn't read it, we could eventually reach a deadlock where the 'guix repl' process would be stuck writing to stderr while the client is stuck waiting on its stdout. * guix/ssh.scm (store-import-channel)[import]: Parameterize 'current-build-output-port'.
2023-04-19substitute: Download nar from another server upon ETIMEDOUT.Ludovic Courtès
Previously, 'guix substitute' would fail abruptly with something like: guix substitute: warning: while fetching https://ci.guix.gnu.org/nar/lzip/…-example: server is somewhat slow guix substitute: warning: try `--no-substitutes' if the problem persists guix substitute: error: connect*: Connection timed out substitution of /gnu/store/…-example failed * guix/scripts/substitute.scm (network-error?): Add ETIMEDOUT.
2023-04-19services: agetty: 'term-console' succeeds by default.Ludovic Courtès
Previously, on a typical setup without "console=ttyS0" or similar in 'kernel-arguments', the 'term-console' Shepherd service would always be marked as failing to start. This is undesirable because it raises a false alarm: the service is expected to do nothing in this case. This patch instead marks it as succeeding and logs a message explaining it's doing nothing. * gnu/services/base.scm (agetty-shepherd-service): In 'start' method, succeed when TTY is #f and print a message.
2023-04-19environment: Really auto-load (guix scripts pack).Ludovic Courtès
Fixes a performance regression on cache hits introduced in b31ea797edb4f6e8c14e8fe790da1319607c5cb1, whereby (guix scripts pack) would be loaded eagerly during startup, leading hundreds of (gnu packages *) modules to be loaded. Fixes <https://issues.guix.gnu.org/62899>. * guix/scripts/environment.scm: Autoload (gnu build install). (%options): Add indirection when calling 'symlink-spec-option-parser' so that (guix scripts pack) is auto-loaded only when needed.
2023-04-19gnu: Add converseen.Nicolas Goaziou
* gnu/packages/image.scm (converseen): New variable. * gnu/packages/patches/converseen-hide-non-free-pointers.patch: * gnu/packages/patches/converseen-hide-updates-checks.patch: New files. * gnu/local.mk: Register files above.
2023-04-19gnu: python-anyio: Update to 3.6.2.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-anyio): Update to 3.6.2.
2023-04-19gnu: font-meera-inimai: Use gexps and remove labels.Maxim Cournoyer
* gnu/packages/fonts.scm (font-meera-inimai) [native-inputs]: Remove labels. [arguments]: Use gexps.
2023-04-19gnu: python-fonttools-full: Rename to python-fonttools.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-fonttools): Rename to... (python-fonttools-minimal): ... this. (python-fonttools-full): Adjust references to base package. Rename to... (python-fonttools): ... this. (python-matplotlib): * gnu/packages/fontutils.scm (python-cu2qu) [propagated-inputs]: Rename python-fonttools-full to python-fonttools. (python-ufolib2, python-defcon-bootstrap): Likewise. * gnu/packages/pdf.scm (weasyprint): Likewise. * gnu/packages/fonts.scm (font-meera-inimai) Adjust for renamed python-fonttools-minimal. * gnu/packages/fontutils.scm (python-cffsubr): Likewise. (python-compreffor, python-cu2qu, python-fontmath, python-fontpens-bootstrap) (python-fontparts-bootstrap, python-glyphsets, python-mutatormath) (python-ufoprocessor, graphite2, python-ufolib2) (python-defcon-bootstrap): Likewise. * gnu/packages/graphics.scm (python-booleanoperations): Likewise.
2023-04-19gnu: python-fonttools: Update to 4.39.3.Maxim Cournoyer
This should have been already merged but was left out in a conflict resolution. * gnu/packages/python-xyz.scm (python-fonttools): Update to 4.39.3.
2023-04-19gnu: python-scikit-build: Update to 0.17.1.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-scikit-build): Update to 0.17.1. [source]: Update URI. [arguments]: Update check phase override. [native-inputs]: Add python-hatchling, python-hatch-fancy-pypi-readme and python-hatch-vcs. [propagated-inputs]: Add python-tomli.
2023-04-19gnu: Add python-hatch-fancy-pypi-readme.Maxim Cournoyer
* gnu/packages/python-build.scm (python-hatch-fancy-pypi-readme): New variable.
2023-04-19gnu: gfeeds: Update to 2.2.0.Maxim Cournoyer
* gnu/packages/syndication.scm (gfeeds): Update to 2.2.0. [phases]: Fix skip-icon-cache phase. Use search-input-file in wrap-gfeeds.
2023-04-19gnu: python-pytest-trio: Update to 0.8.0.Maxim Cournoyer
* gnu/packages/python-check.scm (python-pytest-trio): Update to 0.8.0. [arguments]: New relax-requirements phase. Delete extraneous add-installed-pythonpath call. Disable two new tests.
2023-04-19gnu: python-aiohttp: Update to 3.8.4.Maxim Cournoyer
* gnu/packages/python-web.scm (python-aiohttp): Update to 3.8.4. [arguments]: Adjust comments in fix-tests phase. Skip/ignore more tests in check phase. Remove extraneous or (it wouldn't have worked with invoke anyway). [propagated-inputs]: Add python-asynctest. Remove python-typing-extensions.
2023-04-19gnu: python-pyzmq: Disable two tests to fix build.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-pyzmq) [arguments]: Rename disable-draft-test to disable-problematic-tests, and disable two extra tests.
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