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2022-10-03gnu: r-ggtree: Update to 3.4.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ggtree): Update to 3.4.4.
2022-10-03gnu: r-treeio: Update to 1.20.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-treeio): Update to 1.20.2.
2022-10-03gnu: r-scaledmatrix: Update to 1.4.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-scaledmatrix): Update to 1.4.1.
2022-10-03gnu: r-diffbind: Update to 3.6.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.6.4.
2022-10-03gnu: r-zellkonverter: Update to 1.6.5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.6.5.
2022-10-03gnu: r-limma: Update to 3.52.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-limma): Update to 3.52.4.
2022-10-03gnu: r-genomicfeatures: Update to 1.48.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.48.4.
2022-10-03gnu: r-genomeinfodb: Update to 1.32.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.32.4.
2022-10-03gnu: r-gage: Update to 2.46.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gage): Update to 2.46.1.
2022-10-03gnu: r-complexheatmap: Update to 2.12.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-complexheatmap): Update to 2.12.1.
2022-10-03gnu: r-chipseeker: Update to 1.32.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.32.1. [propagated-inputs]: Add r-ggvenndiagram.
2022-10-03gnu: r-biostrings: Update to 2.64.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.64.1.
2022-10-03gnu: r-annotationforge: Update to 1.38.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.38.1.
2022-10-03gnu: r-dearseq: Update to 1.8.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dearseq): Update to 1.8.4.
2022-10-03doc: Mention sourcing system profile when chrooting.Maxim Cournoyer
* doc/guix.texi (Chrooting into an existing system): Add sourcing of system profile along user profile.
2022-10-03gnu: Remove ocaml-craml.Maxim Cournoyer
The package doesn't build from source and is unmaintained according to its maintainer: https://github.com/realworldocaml/craml/pull/8#issuecomment-529235628. * gnu/packages/ocaml.scm (ocaml-craml): Delete variable.
2022-10-03gnu: r-spams: Update to 2.6.1.Maxim Cournoyer
* gnu/packages/statistics.scm (r-spams): Update to 2.6.1. [source]: Migrate from gforge.inria.fr to gitlab.inria.fr, fetching from git. [phases]: Use gexps. {patch-paths, mkdist}: New phases. {no-mtune}: Delete trailing #t. [native-inputs]: New field. [home-page]: Update URL.
2022-10-03gnu: ocaml-dose3: Migrate from gforce.inria.fr.Maxim Cournoyer
* gnu/packages/ocaml.scm (ocaml-dose3) [source]: Fetch from git from inill's gitlab instance.
2022-10-03gnu: Remove unused scotch patches.Maxim Cournoyer
* gnu/packages/patches/scotch-build-parallelism.patch: Delete file. * gnu/packages/patches/scotch-integer-declarations.patch: Likewise. * gnu/local.mk (dist_patch_DATA): De-register them.
2022-10-03gnu: mpfi: Update to 1.5.4-1.b982534.Maxim Cournoyer
* gnu/packages/multiprecision.scm (mpfi): Update to 1.5.4-1.b982534. [source]: Fetch from git and use latest commit available. [tests?]: Delete argument, enabling test suite. [phases]: New argument. [native-inputs]: New field.
2022-10-03gnu: mpfi: Use gexps and remove input labels.Maxim Cournoyer
* gnu/packages/multiprecision.scm (mpfi) [source]: Re-indentation. [configure-flags]: Use gexps. [native-inputs]: Remove labels.
2022-10-03gnu: isl: Remove outdated comment.Maxim Cournoyer
* gnu/packages/gcc.scm (isl) [source]: Remove outdated comment.
2022-10-03gnu: gappa: Honor TESTS?.Maxim Cournoyer
* gnu/packages/algebra.scm (gappa) [phases] {check}: Honor TESTS?.
2022-10-03gnu: gappa: Update to 1.4.1.Maxim Cournoyer
* gnu/packages/algebra.scm (gappa): Update to 1.4.1. [source]: Fetch from git. [arguments]: Use gexps. [phases]: Delete trailing #t. [native-inputs]: New field.
2022-10-03gnu: gmp-ecm: Update to 7.0.5.Maxim Cournoyer
* gnu/packages/algebra.scm (gmp-ecm): Update to 7.0.5. [source]: Fetch from git from gitlab.inria.fr. [arguments]: Use gexps. [phases] {patch-paths}: New phase [native-inputs]: New field. [home-page]: Update URL.
2022-10-03gnu: gf2x: Update to 1.3.0.Maxim Cournoyer
* gnu/packages/algebra.scm (gf2x): Update to 1.3.0.
2022-10-03gnu: gf2x: Migrate from gforge.inria.fr to gitlab.inria.fr.Maxim Cournoyer
* gnu/packages/algebra.scm (gf2x) [source]: Fetch from git, adjust URL. [native-inputs]: Add autoconf, automake and libtool. [home-site]: Update URL.
2022-10-03gnu-maintenance: Remove retired 'gforge.inria.fr' site.Maxim Cournoyer
* guix/gnu-maintenance.scm (html-updatable-package?): Remove "gforge.inria.fr".
2022-10-03news: Add 'pt' translation.Thiago Jung Bauermann
* etc/news.scm: Add Portuguese translation of entry about the --with-source option being recursive. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2022-10-03etc: teams: Add news.scm to translations team scope.Thiago Jung Bauermann
* etc/teams.scm.in (translations)[#:scope]: Add etc/news.scm. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2022-10-03gnu: emacs-ag: Do not propagate the-silver-searcher.Michael Rohleder
* gnu/packages/emacs-xyz.scm (emacs-ag)[phases]: Add phase substitute-ag-path to avoid propagating ag. [inputs]: Add the-silver-searcher. [propagated-inputs]: Remove the-silver-searcher. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-10-03gnu: emacs-ag: Use gexps.Michael Rohleder
* gnu/packages/emacs-xyz.scm (emacs-ag)[phases]: Use gexps. {install-info}: Adjust for gexps. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-10-02gnu: python-louvain: Fix test.Greg Hogan
* gnu/packages/graph.scm (python-louvain)[source]: Add patch. * gnu/packages/patches/python-louvain-fix-test.patch: New file. * gnu/local.mk (dist_patch_DATA): Register patch. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-10-02gnu: python-setools: Update to 4.4.0.Greg Hogan
* gnu/packages/selinux.scm (python-setools): Update to 4.4.0. [source, home-page]: Update url. [inputs]: Add python-pyqt. [native-inputs]: Add python-cython. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-10-02gnu: python-cfn-lint: Update to 0.65.0.Greg Hogan
* gnu/packages/python-web.scm (python-cfn-lint): Update to 0.65.0. [arguments]<#:phases>: Add 'skip-network-test. [propagated-inputs]: Add python-importlib-resources, python-jschema-to-python, python-sarif-om. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-10-02gnu: Add python-sarif-om.Greg Hogan
* gnu/packages/python-web.scm (python-sarif-om): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-10-02gnu: Add python-jschema-to-python.Greg Hogan
* gnu/packages/python-web.scm (python-jschema-to-python): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-10-02gnu: python-aws-sam-translator: Update to 1.51.0.Greg Hogan
* gnu/packages/python-web.scm (python-aws-sam-translator): Update to 1.51.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-10-02gnu: python-networkx: Update to 2.8.6.Greg Hogan
* gnu/packages/python-xyz.scm (python-networkx): Update to 2.8.6. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-10-02gnu: Add texlive-generic-xstring.Wiktor Żelazny
* gnu/packages/tex.scm (texlive-generic-xstring): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-10-02gnu: emacs-telega: Use tdlib-1.8.0Giovanni Biscuolo
emacs-telega is compatible with the latest TDLib major release 1.8.0 * gnu/packages/emacs-xyz.scm: (emacs-telega) Use tdlib-1.8.0 instead of latest tdlib Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-10-02gnu: Add tdlib-1.8.0.Giovanni Biscuolo
This is needed for emacs-telega 0.8.3 * gnu/packages/messaging.scm (tdlib-1.8.0): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-10-02gnu: ffmpeg@4: Build against SDL2 2.0 so 'ffplay' gets built.Ludovic Courtès
Fixes <https://issues.guix.gnu.org/58090>. Reported by Zhu Zihao <all_but_last@163.com>. * gnu/packages/sdl.scm (sdl2-2.0): New variable. * gnu/packages/video.scm (ffmpeg-4)[inputs]: New field.
2022-10-02read-print: Fix indentation rule for 'match-lambda*'.Ludovic Courtès
Fixes <https://issues.guix.gnu.org/58040>. Reported by Maxime Devos <maximedevos@telenet.be>. * guix/read-print.scm (%special-forms): Set 'match-lambda*' parameter count to 1.
2022-10-02doc: Update the URL of ISC DHCP.Ludovic Courtès
* doc/guix.texi (Networking Services): Update ISC DHCP URL.
2022-10-02transformations: Switch to SRFI-71.Ludovic Courtès
* guix/transformations.scm (package-with-source) (evaluate-source-replacement-specs): Use SRFI-71 'let' instead of 'let-values'.
2022-10-02gnu: emacs-scratch-el: Update source and homepage.Michael Rohleder
* gnu/packages/emacs-xyz.scm (emacs-scratch-el)[source, homepage]: Update URL. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-10-02gnu: pantalaimon: Update to 0.10.5.Michael Rohleder
* gnu/packages/matrix.scm (pantalaimon): Update to 0.10.5. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-10-02gnu: python-matrix-nio: Update to 0.20.0.Michael Rohleder
* gnu/packages/matrix.scm (python-matrix-nio): Update to 0.20.0. [native-inputs]: Add python-pytest-asyncio. [propagated-inputs]: Changed python-jsonschema to python-jsonschema-next. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-10-02gnu: python-aiohttp-socks: Update to 0.7.1.Michael Rohleder
* gnu/packages/python-web.scm (python-aiohttp-socks): Update to 0.7.1. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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