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2023-06-02gnu: r-biocviews: Sort inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocviews)[propagated-inputs]: Sort them.
2023-06-02gnu: r-biocparallel: Sort inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocparallel)[propagated-inputs]: Sort them.
2023-06-02import/cran: Libraries should not use CRAN-GUIX-NAME.Ricardo Wurmus
* guix/import/cran.scm (source-dir->dependencies): Do not use CRAN-GUIX-NAME when processing result of NEEDED-LIBRARIES-IN-DIRECTORY.
2023-06-02import/cran: Also search Makevars file for libraries.Ricardo Wurmus
* guix/import/cran.scm (needed-libraries-in-directory): Look at Makevars in addition to Makevars.in for libraries.
2023-06-02gnu: r-dismo: Replace bundled jars.Ricardo Wurmus
Fixes <https://issues.guix.gnu.org/63783>. * gnu/packages/cran.scm (r-dismo)[source]: Delete bundled jars. [inputs]: Add java-maxent. [native-inputs]: Add JDK and zip. [arguments]: Add phases 'build-jars and 'strip-jar-timestamps.
2023-06-02gnu: Add java-maxent.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-maxent): New variable.
2023-06-02gnu: swaylock-effects: Update to 1.6.11.Andrew Tropin
* gnu/packages/wm.scm (swaylock-effects): Update to 1.6.11.
2023-06-02gnu: xdg-desktop-portal-wlr: Update to 0.7.0.Andrew Tropin
* gnu/packages/freedesktop.scm (xdg-desktop-portal-wlr): Update to 0.7.0. [inputs]: Add mesa.
2023-06-02gnu: xdg-desktop-portal-gtk: Update to 1.14.1.Andrew Tropin
* gnu/packages/freedesktop.scm (xdg-desktop-portal-gtk): Update to 1.14.1.
2023-06-02gnu: xdg-desktop-portal: Update to 1.16.0.Andrew Tropin
* gnu/packages/freedesktop.scm (xdg-desktop-portal): Update to 1.16.0.
2023-06-02gnu: libportal: Update to 0.6.Andrew Tropin
* gnu/packages/freedesktop.scm (libportal): Update to 0.6. [arguments]: Remove deprecated backends option from #:configure-flags. Add set-qt-environment-variables phase.
2023-06-01gnu: gopls: Update to 0.12.0.Katherine Cox-Buday
* gnu/packages/golang.scm (gopls): Update to 0.12.0.
2023-06-01gnu: Update waybar to 0.9.18.jgart
* gnu/packages/wm.scm (waybar): Update to 0.9.18.
2023-06-01gnu: python-fire: Update to 0.5.0.jgart
* gnu/packages/python-xyz.scm (python-fire): Update to 0.5.0. [inputs]: Remove python-six and python-termcolor. [propagated-inputs]: Add python-six and python-termcolor.
2023-06-01gnu: Add python-colored.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-colored): New variable.
2023-06-01gnu: Add python-plotext.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-plotext): New variable.
2023-06-01gnu: Add python-pyani.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyani): New variable.
2023-06-01gnu: Add python-illumina-utils.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-illumina-utils): New variable.
2023-06-01gnu: libtommath: Honor the #:tests? flag.Efraim Flashner
* gnu/packages/multiprecision.scm (libtommath)[arguments]: Adjust custom 'check phase to honor the #:tests? flag.
2023-06-01gnu: libtommath: Prevent possible integer overflow.Efraim Flashner
* gnu/packages/multiprecision.scm (libtommath)[source]: Add patch. * gnu/packages/patches/libtommath-integer-overflow.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
2023-06-01gnu: bear: Update to 3.1.2.Efraim Flashner
* gnu/packages/build-tools.scm (bear): Update to 3.1.2.
2023-06-01gnu: Add python-ete3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-ete3): New variable.
2023-06-01gnu: parallel: Update to 20230522.Andy Tai
* gnu/packages/parallel.scm (parallel): Update to 20230522. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: zenity: Update to 3.44.1.Greg Hogan
* gnu/packages/gnome.scm (zenity): Update to 3.44.1. [native-inputs]: Add gtk+:bin. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: iperf: Update to 3.13.Greg Hogan
* gnu/packages/networking.scm (iperf): Update to 3.13. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: iotop: Update to 1.23.Greg Hogan
* gnu/packages/linux.scm (iotop): Update to 1.23. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: html-xml-utils: Update to 8.6.Greg Hogan
* gnu/packages/xml.scm (html-xml-utils): Update to 8.6. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: hstr: Update to 3.1.Greg Hogan
* gnu/packages/shellutils.scm (hstr): Update to 3.1. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: glances: Update to 3.4.0.3.Greg Hogan
* gnu/packages/python-xyz.scm (glances): Update to 3.4.0.3. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: fish: Update to 3.6.1.Greg Hogan
* gnu/packages/shells.scm (fish): Update to 3.6.1. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: fio: Update to 3.35.Greg Hogan
* gnu/packages/benchmark.scm (fio): Update to 3.35. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: atop: Update to 2.9.0.Greg Hogan
* gnu/packages/admin.scm (atop): Update to 2.9.0. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: openblas: Update make-flags comments and coding style.Efraim Flashner
* gnu/packages/maths.scm (openblas)[arguments]: In the make-flags use the target-* macros. Adjust the wording describing why the different architectures have the flags they do.
2023-06-01gnu: openblas: Update architectures we provide substitutes for.Efraim Flashner
* gnu/packages/maths.scm (openblas)[arguments]: Adjust the substitutable? flag to only not provide substitutes when building for powerpc-linux. Adjust the comment accordingly.
2023-06-01gnu: openblas-ilp64: Add powerpc64le-linux as a supported system.Efraim Flashner
* gnu/packages/maths.scm (openblas-ilp64)[supported-systems]: Add powerpc64le-linux.
2023-06-01gnu: r-mbecs: Fix indentation.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mbecs)[arguments]: Adjust indentation and spelling of comment.
2023-06-01gnu: Add squashfuse.Ricardo Wurmus
* gnu/packages/file-systems.scm (squashfuse): New variable.
2023-06-01gnu: Add r-mbecs.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-mbecs): New variable.
2023-05-31gnu: Remove linux-libre 6.2.Leo Famulari
This kernel series is no longer supported upstream. * gnu/packages/linux.scm (linux-libre-6.2-version, linux-libre-6.2-gnu-revision, deblob-scripts-6.2, linux-libre-6.2-pristine-source, linux-libre-6.2-source, linux-libre-headers-6.2, linux-libre-6.2): Remove variables. * gnu/packages/aux-files/linux-libre/6.2-arm.conf, gnu/packages/aux-files/linux-libre/6.2-arm64.conf, gnu/packages/aux-files/linux-libre/6.2-i686.conf, gnu/packages/aux-files/linux-libre/6.2-x86_64.conf: Delete files. * Makefile.am (AUX_FILES): Remove them.
2023-05-31gnu: linux-libre 4.14: Update to 4.14.316.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.316. (linux-libre-4.14-pristine-source): Update hash.
2023-05-31gnu: linux-libre 4.19: Update to 4.19.284.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.284. (linux-libre-4.19-pristine-source): Update hash.
2023-05-31gnu: linux-libre 5.4: Update to 5.4.244.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.244. (linux-libre-5.4-pristine-source): Update hash.
2023-05-31gnu: linux-libre 5.10: Update to 5.10.181.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.181. (linux-libre-5.10-pristine-source): Update hash.
2023-05-31gnu: linux-libre 5.15: Update to 5.15.114.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.114. (linux-libre-5.15-pristine-source): Update hash.
2023-05-31gnu: linux-libre 6.1: Update to 6.1.31.Leo Famulari
* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.31. (linux-libre-6.1-pristine-source): Update hash.
2023-05-31gnu: linux-libre: Update to 6.3.5.Leo Famulari
* gnu/packages/linux.scm (linux-libre-6.3-version): Update to 6.3.5. (linux-libre-6.3-pristine-source): Update hash.
2023-05-31tests: Use quasiquoted 'match' patterns for package sexps.Ludovic Courtès
Turns out it's easier to read. * tests/cpan.scm ("cpan->guix-package"): Use a quasiquoted pattern. * tests/elpa.scm (eval-test-with-elpa): Likewise. * tests/gem.scm ("gem->guix-package") ("gem->guix-package with a specific version") ("gem-recursive-import") ("gem-recursive-import with a specific version"): Likewise. * tests/hexpm.scm ("hexpm-recursive-import"): Likewise. * tests/opam.scm ("opam->guix-package"): Likewise. * tests/pypi.scm ("pypi->guix-package, no wheel") ("pypi->guix-package, wheels") ("pypi->guix-package, no usable requirement file.") ("pypi->guix-package, package name contains \"-\" followed by digits"): Likewise. * tests/texlive.scm ("texlive->guix-package"): Likewise.
2023-05-31gnu: Add updater input properties for R and Python packages.Ludovic Courtès
* gnu/packages/cran.scm (r-glue, r-xfun, r-vctrs) (r-lifecycle): Turn comment about r-knitr into 'properties' field. * gnu/packages/mpi.scm (python-mpi4py)[properties]: New field.
2023-05-31upstream: Honor package properties for ignored and extra inputs.Ludovic Courtès
* guix/upstream.scm (update-package-inputs)[filtered-inputs] [regular-inputs, native-inputs, propagated-inputs]: New procedures. Use them in 'update-field' calls. * tests/guix-refresh.sh (GUIX_TEST_UPDATER_TARGETS): Add "libreoffice" to the dependencies of "the-test-package". Add 'updater-ignored-inputs' property to "the-test-package". * doc/guix.texi (Invoking guix refresh): Document it.
2023-05-31import: gem: Updater provides input list.Ludovic Courtès
* guix/import/gem.scm (import-release): Add 'inputs' field. * tests/gem.scm ("package-latest-release"): New test.
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