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2023-10-05gnu: r-learnr: Update to 0.11.5.Ricardo Wurmus
* gnu/packages/cran.scm (r-learnr): Update to 0.11.5. [native-inputs]: Add esbuild.
2023-10-05gnu: r-renv: Update to 1.0.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-renv): Update to 1.0.3.
2023-10-05gnu: r-rio: Update to 1.0.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-rio): Update to 1.0.1. [propagated-inputs]: Remove r-openxlsx; add r-lifecycle, r-r-utils, r-stringi, and r-writexl.
2023-10-05gnu: r-import: Update to 1.3.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-import): Update to 1.3.1.
2023-10-05gnu: r-tinytex: Update to 0.47.Ricardo Wurmus
* gnu/packages/cran.scm (r-tinytex): Update to 0.47.
2023-10-05gnu: r-psych: Update to 2.3.9.Ricardo Wurmus
* gnu/packages/cran.scm (r-psych): Update to 2.3.9.
2023-10-05gnu: r-rmysql: Update to 0.10.26.Ricardo Wurmus
* gnu/packages/cran.scm (r-rmysql): Update to 0.10.26.
2023-10-05gnu: r-limsolve: Update to 1.5.7.Ricardo Wurmus
* gnu/packages/cran.scm (r-limsolve): Update to 1.5.7.
2023-10-05gnu: r-lamw: Update to 2.2.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-lamw): Update to 2.2.1.
2023-10-05gnu: r-sp: Update to 2.1-0.Ricardo Wurmus
* gnu/packages/cran.scm (r-sp): Update to 2.1-0.
2023-10-05gnu: r-prettyunits: Update to 1.2.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-prettyunits): Update to 1.2.0.
2023-10-05gnu: r-ctrdata: Update to 1.15.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-ctrdata): Update to 1.15.2.
2023-10-05gnu: r-pkgload: Update to 1.3.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-pkgload): Update to 1.3.3. [propagated-inputs]: Add r-pkgbuild.
2023-10-05gnu: r-gensa: Update to 1.1.10.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-gensa): Update to 1.1.10.1.
2023-10-05gnu: r-d3r: Update to 1.1.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-d3r): Update to 1.1.0. [propagated-inputs]: Remove r-rlang.
2023-10-05gnu: r-jqr: Update to 1.3.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-jqr): Update to 1.3.0.
2023-10-05gnu: r-curl: Update to 5.1.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-curl): Update to 5.1.0.
2023-10-05gnu: r-jade: Update to 2.0-4.Ricardo Wurmus
* gnu/packages/cran.scm (r-jade): Update to 2.0-4.
2023-10-05gnu: r-gunifrac: Update to 1.8.Ricardo Wurmus
* gnu/packages/cran.scm (r-gunifrac): Update to 1.8. [propagated-inputs]: Add r-inline.
2023-10-05gnu: r-ggstatsplot: Update to 0.12.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggstatsplot): Update to 0.12.1.
2023-10-05gnu: r-datawizard: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-datawizard): Update to 0.9.0.
2023-10-05gnu: r-activepathways: Update to 2.0.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-activepathways): Update to 2.0.2.
2023-10-05gnu: r-valr: Update to 0.7.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-valr): Update to 0.7.0. [propagated-inputs]: Add r-lifecycle.
2023-10-05gnu: r-biomartr: Update to 1.0.5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biomartr): Update to 1.0.5.
2023-10-05refresh: Fix sorting of updates by file and line number.Ricardo Wurmus
* guix/scripts/refresh.scm (guix-refresh): Add cascade-sort procedure and use it to sort specs by package location.
2023-10-05doc: contributing: Add alternative setups section.Ekaitz Zarraga
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>
2023-10-05gnu: emacs-telega: Update to 0.8.03-1.17bfa50.Andrew Tropin
* gnu/packages/emacs-xyz.scm (emacs-telega-server): Update to 0.8.03-1.17bfa50.
2023-10-05gnu: tdlib: Update to 1.8.16-0.4d1d22d.Andrew Tropin
* gnu/packages/messaging.scm (tdlib): Update to 1.8.16-0.4d1d22d.
2023-10-05gnu: r-aplot: Update to 0.2.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-aplot): Update to 0.2.1.
2023-10-05gnu: r-tximeta: Update to 1.18.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.18.3.
2023-10-05gnu: r-biodb: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biodb): Update to 1.8.1. [propagated-inputs]: Add r-git2r.
2023-10-05gnu: r-gviz: Update to 1.44.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gviz): Update to 1.44.2.
2023-10-05gnu: r-s4vectors: Update to 0.38.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.38.2.
2023-10-05gnu: r-biocstyle: Update to 2.28.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocstyle): Update to 2.28.1.
2023-10-05gnu: r-yapsa: Update to 1.26.8.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-yapsa): Update to 1.26.8.
2023-10-05gnu: r-enrichplot: Update to 1.20.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.20.3. [propagated-inputs]: Add r-ggfun.
2023-10-05gnu: r-spectra: Update to 1.10.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-spectra): Update to 1.10.3.
2023-10-05gnu: r-keggrest: Update to 1.40.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-keggrest): Update to 1.40.1.
2023-10-05gnu: r-genomeinfodb: Update to 1.36.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.36.4.
2023-10-05gnu: r-ensembldb: Update to 2.24.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.24.1.
2023-10-05gnu: r-ancombc: Update to 2.2.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ancombc): Update to 2.2.2.
2023-10-05gnu: r-omnipathr: Update to 3.8.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.8.2.
2023-10-05gnu: curl: Update to 8.3.0.Liliana Marie Prikler
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.
2023-10-05gnu: openjdk-10: Fix building on aarch64-linux.Efraim Flashner
* 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>
2023-10-05gnu: universal-ctags: Update to 6.0.20231001.0.Efraim Flashner
* gnu/packages/code.scm (universal-ctags): Update to 6.0.20231001.0.
2023-10-05gnu: tree-sitter-java: Update to 0.20.1.Kjartan Oli Agustsson
* gnu/packages/tree-sitter.scm (tree-sitter-java): Update to 0.20.1. Signed-off-by: Andrew Tropin <andrew@trop.in>
2023-10-05gnu: emacs-elpy: Update to 1.35.0-2.7ff8ffa.Maxim Cournoyer
* 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.
2023-10-04gnu: phoronix-test-suite: Do not propagate gcc-toolchain.Maxim Cournoyer
* 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.
2023-10-04search-paths: Add GCC search paths.Maxim Cournoyer
* guix/search-paths.scm ($C_INCLUDE_PATH, $CPLUS_INCLUDE_PATH) ($LIBRARY_PATH, %gcc-search-paths): New variables.
2023-10-04gnu: libxpm: Graft with 3.5.17 [security fixes].John Kehayias
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.
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