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2023-10-05gnu: r-activepathways: Update to 2.0.2....* gnu/packages/bioconductor.scm (r-activepathways): Update to 2.0.2. Ricardo Wurmus
2023-10-05gnu: r-valr: Update to 0.7.0....* gnu/packages/bioconductor.scm (r-valr): Update to 0.7.0. [propagated-inputs]: Add r-lifecycle. Ricardo Wurmus
2023-10-05gnu: r-biomartr: Update to 1.0.5....* gnu/packages/bioconductor.scm (r-biomartr): Update to 1.0.5. Ricardo Wurmus
2023-10-05refresh: Fix sorting of updates by file and line number....* guix/scripts/refresh.scm (guix-refresh): Add cascade-sort procedure and use it to sort specs by package location. Ricardo Wurmus
2023-10-05doc: contributing: Add alternative setups section....Start with Guile Studio and Vim/NeoVim. * doc/contributing.texi (Alternative Setups): Add section explaining other setups that are similar to the one in The Perfect Setup. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Ekaitz Zarraga
2023-10-05gnu: emacs-telega: Update to 0.8.03-1.17bfa50....* gnu/packages/emacs-xyz.scm (emacs-telega-server): Update to 0.8.03-1.17bfa50. Andrew Tropin
2023-10-05gnu: tdlib: Update to 1.8.16-0.4d1d22d....* gnu/packages/messaging.scm (tdlib): Update to 1.8.16-0.4d1d22d. Andrew Tropin
2023-10-05gnu: r-aplot: Update to 0.2.1....* gnu/packages/cran.scm (r-aplot): Update to 0.2.1. Ricardo Wurmus
2023-10-05gnu: r-tximeta: Update to 1.18.3....* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.18.3. Ricardo Wurmus
2023-10-05gnu: r-biodb: Update to 1.8.1....* gnu/packages/bioconductor.scm (r-biodb): Update to 1.8.1. [propagated-inputs]: Add r-git2r. Ricardo Wurmus
2023-10-05gnu: r-gviz: Update to 1.44.2....* gnu/packages/bioconductor.scm (r-gviz): Update to 1.44.2. Ricardo Wurmus
2023-10-05gnu: r-s4vectors: Update to 0.38.2....* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.38.2. Ricardo Wurmus
2023-10-05gnu: r-biocstyle: Update to 2.28.1....* gnu/packages/bioconductor.scm (r-biocstyle): Update to 2.28.1. Ricardo Wurmus
2023-10-05gnu: r-yapsa: Update to 1.26.8....* gnu/packages/bioconductor.scm (r-yapsa): Update to 1.26.8. Ricardo Wurmus
2023-10-05gnu: r-enrichplot: Update to 1.20.3....* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.20.3. [propagated-inputs]: Add r-ggfun. Ricardo Wurmus
2023-10-05gnu: r-spectra: Update to 1.10.3....* gnu/packages/bioconductor.scm (r-spectra): Update to 1.10.3. Ricardo Wurmus
2023-10-05gnu: r-keggrest: Update to 1.40.1....* gnu/packages/bioconductor.scm (r-keggrest): Update to 1.40.1. Ricardo Wurmus
2023-10-05gnu: r-genomeinfodb: Update to 1.36.4....* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.36.4. Ricardo Wurmus
2023-10-05gnu: r-ensembldb: Update to 2.24.1....* gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.24.1. Ricardo Wurmus
2023-10-05gnu: r-ancombc: Update to 2.2.2....* gnu/packages/bioconductor.scm (r-ancombc): Update to 2.2.2. Ricardo Wurmus
2023-10-05gnu: r-omnipathr: Update to 3.8.2....* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.8.2. Ricardo Wurmus
2023-10-05gnu: curl: Update to 8.3.0....According to upstream, the current version has 19 security issues. See also <https://curl.se/docs/vuln-7.85.0.html>. * gnu/packages/curl.scm (curl/fixed): New variable. (curl): Use it as replacement. Liliana Marie Prikler
2023-10-05gnu: openjdk-10: Fix building on aarch64-linux....* gnu/packages/java.scm (openjdk-10)[arguments]: Replace inherited 'patch-for-aarch64 phase for changes in source code layout. Co-authored-by: Christopher Baines <mail@cbaines.net> Co-authored-by: Tim Johann <t1m@phrogstar.de> Efraim Flashner
2023-10-05gnu: universal-ctags: Update to 6.0.20231001.0....* gnu/packages/code.scm (universal-ctags): Update to 6.0.20231001.0. Efraim Flashner
2023-10-05gnu: tree-sitter-java: Update to 0.20.1....* gnu/packages/tree-sitter.scm (tree-sitter-java): Update to 0.20.1. Signed-off-by: Andrew Tropin <andrew@trop.in> Kjartan Oli Agustsson
2023-10-05gnu: emacs-elpy: Update to 1.35.0-2.7ff8ffa....* gnu/packages/emacs-xyz.scm (emacs-elpy): Update to 1.35.0-2.7ff8ffa. [origin]: Apply patch. [arguments]: Disable a new test in the disable-broken-tests phase. * gnu/packages/patches/emacs-elpy-dup-test-name.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. Maxim Cournoyer
2023-10-04gnu: phoronix-test-suite: Do not propagate gcc-toolchain....* gnu/packages/benchmark.scm (gcc-toolchain*): Replace gcc-toolchain-12 reference with gcc-toolchain. * gnu/packages/benchmark.scm (phoronix-test-suite): Augment wrap-binary phase with GCC variables. [propagated-inputs]: Delete field, moving gcc-toolchain to... [inputs]: ... here. [search-paths]: New field. Maxim Cournoyer
2023-10-04search-paths: Add GCC search paths....* guix/search-paths.scm ($C_INCLUDE_PATH, $CPLUS_INCLUDE_PATH) ($LIBRARY_PATH, %gcc-search-paths): New variables. Maxim Cournoyer
2023-10-04gnu: libxpm: Graft with 3.5.17 [security fixes]....Fixes CVE-2023-43788 and CVE-2023-43789. See the X.Org security advisory <https://lists.x.org/archives/xorg/2023-October/061506.html> for more information. * gnu/packages/xorg.scm (libxpm)[replacement]: New field, set to ... (libxpm/fixed): ... this new variable. John Kehayias
2023-10-04gnu: libx11: Update replacement to 1.8.7 [security fixes]....Fixes CVE-2023-43785, CVE-2023-43786, and CVE-2023-43787. See the X.Org security advisory <https://lists.x.org/archives/xorg/2023-October/061506.html> for more information. * gnu/packages/xorg.scm (libx11-fixed): Update to 1.8.7. John Kehayias
2023-10-04gnu: emacs-debbugs: Preserve subject when replying to patch threads....* gnu/packages/patches/emacs-debbugs-keep-patch-subject.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/emacs-xyz.scm (emacs-debbugs) [origin]: Use it. Maxim Cournoyer
2023-10-04gnu: Remove suitesparse-3....* gnu/packages/maths.scm (suitesparse-3): Delete variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> David Elsing
2023-10-04gnu: scilab: Update to 2023.1.0....* gnu/packages/maths.scm (scilab): Update to 2023.1.0. [source] Use git-fetch. <modules>: Add (guix build utils) and (ice-9 ftw). <patches>: Add patch for hdf5 >= 1.10. <snippet>: Move contents of the "scilab" directory to its parents. Remove the other files and autogenerated files. [native-inputs]: Add autoconf, autoconf-archive, automake, bison, eigen, flex, libtool, ocaml and ocaml-findlib. [inputs]: Add ocaml-num, replace hdf5-1.8 by hdf5-1.14 and suitesparse-3 by suitesparse. [arguments]: Remove quasiquote. Add --enable-build-parser, --with-eigen-include=..., OCAMLC=... and OCAMLOPT=... to #:configure-flags. <#:phases>: Add fix-ocaml-num, remove-desktop-files, bootstrap-dynamic_link-scripts and build-parsers phases. Remove fixes for compilation and linker errors from the pre-build phase. [home-page]: Update URL. [description]: Add two spaces between sentences. [license]: Update to gpl2 and bsd-3. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> David Elsing
2023-10-04gnu: parallel: Update to 20230922....* gnu/packages/parallel.scm (parallel): Update to 20230922. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Andy Tai
2023-10-04gnu: freerdp: Update to 2.11.2....* gnu/packages/rdesktop.scm (freerdp): Update to 2.11.2. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Timotej Lazar
2023-10-04gnu: guile-mastodon: Update to 0.0.1-0a94ae6b...Message-ID: <0064c4ff9262c4906131909ae1276667033f8811.1696343806.git.ekaitz@elenq.tech> From: Ekaitz Zarraga <ekaitz@elenq.tech> Date: Tue, 3 Oct 2023 16:28:58 +0200 Subject: [PATCH] gnu: guile-mastodon: Update to 0.0.1-0a94ae6b * gnu/packages/guile-xyz.scm (guile-mastodon): Update to 0.0.1-0a94ae6b Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Ekaitz Zarraga
2023-10-04gnu: kicad: Update to 7.0.8....* gnu/packages/engineering.scm (kicad): Update to 7.0.8. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Peter Polidoro
2023-10-04guix: meson-configuration: Fix boolean assigment....* guix/build/meson-configuration.scm (write-assigment): Print true for #t and false for #f. Previously it was inverting the values. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Jean-Pierre De Jesus DIAZ
2023-10-04gnu: ultrastar-deluxe: Update to 2023.9.0....* gnu/packages/games.scm (ultrastar-deluxe): Update to 2023.9.0. [source]: Use tagged version again. Tested-by: Jonathan Brielmaier <jonathan.brielmaier@web.de> Jonathan Brielmaier
2023-10-04gnu: r-dofuture: Add r-markdown....* gnu/packages/cran.scm (r-dofuture)[native-inputs]: Add r-markdown. Mădălin Ionel Patrașcu
2023-10-04gnu: Add r-arrayquality....* gnu/packages/bioconductor.scm (r-arrayquality): New variable. Mădălin Ionel Patrașcu
2023-10-04gnu: Add r-arraymvout....* gnu/packages/bioconductor.scm (r-arraymvout): New variable. Mădălin Ionel Patrașcu
2023-10-04gnu: Add r-parody....* gnu/packages/bioconductor.scm (r-parody): New variable. Mădălin Ionel Patrașcu
2023-10-04gnu: Add r-mdqc....* gnu/packages/bioconductor.scm (r-mdqc): New variable. Mădălin Ionel Patrașcu
2023-10-04gnu: Add r-apcomplex....* gnu/packages/bioconductor.scm (r-apcomplex): New variable. Mădălin Ionel Patrașcu
2023-10-04gnu: Add r-org-sc-sgd-db....* gnu/packages/bioconductor.scm (r-org-sc-sgd-db): New variable. Mădălin Ionel Patrașcu
2023-10-04gnu: Add r-hybridmtest....* gnu/packages/bioconductor.scm (r-hybridmtest): New variable. Mădălin Ionel Patrașcu
2023-10-04gnu: Add r-repmis....* gnu/packages/cran.scm (r-repmis): New variable. Mădălin Ionel Patrașcu
2023-10-04gnu: Add r-anota2seq....* gnu/packages/bioconductor.scm (r-anota2seq): New variable. Mădălin Ionel Patrașcu
2023-10-04gnu: emacs-yeetube: Update to 2.0.5....* gnu/packages/emacs-xyz.scm (emacs-yeetube): Update to 2.0.5. [arguments]<#:phases>: Update variable names holding executable locations. Nicolas Goaziou
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