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2023-06-02gnu: r-biocviews: Update to 1.68.1.•••* gnu/packages/bioconductor.scm (r-biocviews): Update to 1.68.1. Ricardo Wurmus
2023-06-02gnu: r-rsubread: Update to 2.14.2.•••* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.14.2. Ricardo Wurmus
2023-06-02gnu: r-treeio: Update to 1.24.1.•••* gnu/packages/bioconductor.scm (r-treeio): Update to 1.24.1. Ricardo Wurmus
2023-06-02gnu: r-apeglm: Update to 1.22.1.•••* gnu/packages/bioconductor.scm (r-apeglm): Update to 1.22.1. Ricardo Wurmus
2023-06-02gnu: r-zellkonverter: Update to 1.10.1.•••* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.10.1. Ricardo Wurmus
2023-06-02gnu: r-scmap: Update to 1.22.3.•••* gnu/packages/bioconductor.scm (r-scmap): Update to 1.22.3. Ricardo Wurmus
2023-06-02gnu: r-limma: Update to 3.56.1.•••* gnu/packages/bioconductor.scm (r-limma): Update to 3.56.1. Ricardo Wurmus
2023-06-02gnu: r-edger: Update to 3.42.4.•••* gnu/packages/bioconductor.scm (r-edger): Update to 3.42.4. Ricardo Wurmus
2023-06-02gnu: r-biostrings: Update to 2.68.1.•••* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.68.1. Ricardo Wurmus
2023-06-02gnu: r-biocparallel: Update to 1.34.2.•••* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.34.2. Ricardo Wurmus
2023-06-02gnu: r-densvis: Update to 1.10.2.•••* gnu/packages/bioconductor.scm (r-densvis): Update to 1.10.2. Ricardo Wurmus
2023-06-02gnu: r-delayedarray: Update to 0.26.3.•••* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.26.3. Ricardo Wurmus
2023-06-02gnu: r-dearseq: Update to 1.12.1.•••* gnu/packages/bioconductor.scm (r-dearseq): Update to 1.12.1. Ricardo Wurmus
2023-06-02gnu: r-bambu: Update to 3.2.3.•••* gnu/packages/bioconductor.scm (r-bambu): Update to 3.2.3. Ricardo Wurmus
2023-06-02gnu: r-alpine: Update to 1.26.0.•••* gnu/packages/bioconductor.scm (r-alpine): Update to 1.26.0. Ricardo Wurmus
2023-06-02gnu: r-anvil: Update to 1.12.3.•••* gnu/packages/bioconductor.scm (r-anvil): Update to 1.12.3. Ricardo Wurmus
2023-06-02import/cran: string->license: Add another case for GPLv3+.•••* guix/import/cran.scm (string->license): Translate "GPL (>=3)" to gpl3+. Ricardo Wurmus
2023-06-02gnu: r-biocviews: Sort inputs.•••* gnu/packages/bioconductor.scm (r-biocviews)[propagated-inputs]: Sort them. Ricardo Wurmus
2023-06-02gnu: r-biocparallel: Sort inputs.•••* gnu/packages/bioconductor.scm (r-biocparallel)[propagated-inputs]: Sort them. Ricardo Wurmus
2023-06-02import/cran: Libraries should not use CRAN-GUIX-NAME.•••* guix/import/cran.scm (source-dir->dependencies): Do not use CRAN-GUIX-NAME when processing result of NEEDED-LIBRARIES-IN-DIRECTORY. Ricardo Wurmus
2023-06-02import/cran: Also search Makevars file for libraries.•••* guix/import/cran.scm (needed-libraries-in-directory): Look at Makevars in addition to Makevars.in for libraries. Ricardo Wurmus
2023-06-02gnu: r-dismo: Replace bundled jars.•••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. Ricardo Wurmus
2023-06-02gnu: Add java-maxent.•••* gnu/packages/bioinformatics.scm (java-maxent): New variable. Ricardo Wurmus
2023-06-02gnu: swaylock-effects: Update to 1.6.11.•••* gnu/packages/wm.scm (swaylock-effects): Update to 1.6.11. Andrew Tropin
2023-06-02gnu: xdg-desktop-portal-wlr: Update to 0.7.0.•••* gnu/packages/freedesktop.scm (xdg-desktop-portal-wlr): Update to 0.7.0. [inputs]: Add mesa. Andrew Tropin
2023-06-02gnu: xdg-desktop-portal-gtk: Update to 1.14.1.•••* gnu/packages/freedesktop.scm (xdg-desktop-portal-gtk): Update to 1.14.1. Andrew Tropin
2023-06-02gnu: xdg-desktop-portal: Update to 1.16.0.•••* gnu/packages/freedesktop.scm (xdg-desktop-portal): Update to 1.16.0. Andrew Tropin
2023-06-02gnu: libportal: Update to 0.6.•••* gnu/packages/freedesktop.scm (libportal): Update to 0.6. [arguments]: Remove deprecated backends option from #:configure-flags. Add set-qt-environment-variables phase. Andrew Tropin
2023-06-01gnu: gopls: Update to 0.12.0.•••* gnu/packages/golang.scm (gopls): Update to 0.12.0. Katherine Cox-Buday
2023-06-01gnu: Update waybar to 0.9.18.•••* gnu/packages/wm.scm (waybar): Update to 0.9.18. jgart
2023-06-01gnu: python-fire: Update to 0.5.0.•••* 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. jgart
2023-06-01gnu: Add python-colored.•••* gnu/packages/python-xyz.scm (python-colored): New variable. Ricardo Wurmus
2023-06-01gnu: Add python-plotext.•••* gnu/packages/python-xyz.scm (python-plotext): New variable. Ricardo Wurmus
2023-06-01gnu: Add python-pyani.•••* gnu/packages/bioinformatics.scm (python-pyani): New variable. Ricardo Wurmus
2023-06-01gnu: Add python-illumina-utils.•••* gnu/packages/bioinformatics.scm (python-illumina-utils): New variable. Ricardo Wurmus
2023-06-01gnu: libtommath: Honor the #:tests? flag.•••* gnu/packages/multiprecision.scm (libtommath)[arguments]: Adjust custom 'check phase to honor the #:tests? flag. Efraim Flashner
2023-06-01gnu: libtommath: Prevent possible integer overflow.•••* 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. Efraim Flashner
2023-06-01gnu: bear: Update to 3.1.2.•••* gnu/packages/build-tools.scm (bear): Update to 3.1.2. Efraim Flashner
2023-06-01gnu: Add python-ete3.•••* gnu/packages/bioinformatics.scm (python-ete3): New variable. Ricardo Wurmus
2023-06-01gnu: parallel: Update to 20230522.•••* gnu/packages/parallel.scm (parallel): Update to 20230522. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Andy Tai
2023-06-01gnu: zenity: Update to 3.44.1.•••* gnu/packages/gnome.scm (zenity): Update to 3.44.1. [native-inputs]: Add gtk+:bin. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Greg Hogan
2023-06-01gnu: iperf: Update to 3.13.•••* gnu/packages/networking.scm (iperf): Update to 3.13. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Greg Hogan
2023-06-01gnu: iotop: Update to 1.23.•••* gnu/packages/linux.scm (iotop): Update to 1.23. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Greg Hogan
2023-06-01gnu: html-xml-utils: Update to 8.6.•••* gnu/packages/xml.scm (html-xml-utils): Update to 8.6. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Greg Hogan
2023-06-01gnu: hstr: Update to 3.1.•••* gnu/packages/shellutils.scm (hstr): Update to 3.1. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Greg Hogan
2023-06-01gnu: glances: Update to 3.4.0.3.•••* gnu/packages/python-xyz.scm (glances): Update to 3.4.0.3. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Greg Hogan
2023-06-01gnu: fish: Update to 3.6.1.•••* gnu/packages/shells.scm (fish): Update to 3.6.1. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Greg Hogan
2023-06-01gnu: fio: Update to 3.35.•••* gnu/packages/benchmark.scm (fio): Update to 3.35. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Greg Hogan
2023-06-01gnu: atop: Update to 2.9.0.•••* gnu/packages/admin.scm (atop): Update to 2.9.0. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Greg Hogan
2023-06-01gnu: openblas: Update make-flags comments and coding style.•••* 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. Efraim Flashner
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