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2023-06-02gnu: python-ipython-documentation: Remove patches.Greg Hogan
* gnu/packages/python-xyz.scm (python-ipython-documentation)[source]: Remove upstreamed patches. * gnu/packages/patches/python-ipython-documentation-chars.patch, gnu/packages/patches/python-ipython-documentation-repro.patch: Delete files. * gnu/local.mk: Remove files. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-06-02gnu: python-docrepr: Fix tests.Greg Hogan
* gnu/packages/patches/python-docrepr-fix-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it here. * gnu/packages/documentation.scm (python-docrepr)[source]<patches>: Use it here. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-06-02gnu: cpp-mustache: Update to 5.0 to fix build.Denis 'GNUtoo' Carikli
* gnu/packages/cpp.scm (cpp-mustache): Update to 5.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-06-02gnu: gcc-boot0: Do not use 'coreutils-boot0' on GNU/Hurd.Ludovic Courtès
Fixes <https://issues.guix.gnu.org/63789>. Reported by Janneke Nieuwenhuizen <janneke@gnu.org>. * gnu/packages/commencement.scm (gcc-boot0)[source]: Use '%bootstrap-coreutils&co' when on GNU/Hurd.
2023-06-02gnu: Add pcsc-cyberjack.Arvid Krein
* gnu/packages/security-token.scm (pcsc-cyberjack): New variable. Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2023-06-02gnu: kicad: Update to 7.0.5.Peter Polidoro
* gnu/packages/engineering.scm (kicad): Update to 7.0.5. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2023-06-02gnu: r-tcgabiolinks: Update to 2.28.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.28.2.
2023-06-02gnu: r-biocthis: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.10.1.
2023-06-02gnu: r-basilisk-utils: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.12.1.
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.
2023-06-02gnu: 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.
2023-06-02gnu: 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>
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