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2023-06-02gnu: r-megadepth: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-megadepth): Update to 1.10.0.
2023-06-02gnu: r-s4arrays: Update to 1.0.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-s4arrays): Update to 1.0.4.
2023-06-02gnu: r-biocviews: Update to 1.68.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocviews): Update to 1.68.1.
2023-06-02gnu: r-rsubread: Update to 2.14.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.14.2.
2023-06-02gnu: r-treeio: Update to 1.24.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-treeio): Update to 1.24.1.
2023-06-02gnu: r-apeglm: Update to 1.22.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-apeglm): Update to 1.22.1.
2023-06-02gnu: r-zellkonverter: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.10.1.
2023-06-02gnu: r-scmap: Update to 1.22.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-scmap): Update to 1.22.3.
2023-06-02gnu: r-limma: Update to 3.56.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-limma): Update to 3.56.1.
2023-06-02gnu: r-edger: Update to 3.42.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-edger): Update to 3.42.4.
2023-06-02gnu: r-biostrings: Update to 2.68.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.68.1.
2023-06-02gnu: r-biocparallel: Update to 1.34.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.34.2.
2023-06-02gnu: r-densvis: Update to 1.10.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-densvis): Update to 1.10.2.
2023-06-02gnu: r-delayedarray: Update to 0.26.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.26.3.
2023-06-02gnu: r-dearseq: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dearseq): Update to 1.12.1.
2023-06-02gnu: r-bambu: Update to 3.2.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bambu): Update to 3.2.3.
2023-06-02gnu: r-alpine: Update to 1.26.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-alpine): Update to 1.26.0.
2023-06-02gnu: r-anvil: Update to 1.12.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-anvil): Update to 1.12.3.
2023-06-02import/cran: string->license: Add another case for GPLv3+.Ricardo Wurmus
* guix/import/cran.scm (string->license): Translate "GPL (>=3)" to gpl3+.
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>
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