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2023-06-02gnu: cuirass: Update to b825967.•••Fixes a regression introduced with the guile-squee update in 63e5975cac15102e35032d15fcd90e43d5610fa4 (which brings non-blocking/asynchronous 'exec-query') whereby Cuirass would call 'exec-query' whereby another command was being processed. * gnu/packages/ci.scm (cuirass): Update to b825967. Ludovic Courtès
2023-06-02gnu: python-ipython-documentation: Update dependencies.•••* gnu/packages/python-xyz.scm (python-ipython-documentation) [native-inputs]: Add python-ipykernel. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Greg Hogan
2023-06-02gnu: python-ipython-documentation: Remove patches.•••* 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> Greg Hogan
2023-06-02gnu: python-docrepr: Fix tests.•••* 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> Greg Hogan
2023-06-02gnu: cpp-mustache: Update to 5.0 to fix build.•••* gnu/packages/cpp.scm (cpp-mustache): Update to 5.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Denis 'GNUtoo' Carikli
2023-06-02gnu: gcc-boot0: Do not use 'coreutils-boot0' on GNU/Hurd.•••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. Ludovic Courtès
2023-06-02gnu: Add pcsc-cyberjack.•••* gnu/packages/security-token.scm (pcsc-cyberjack): New variable. Signed-off-by: 宋文武 <iyzsong@member.fsf.org> Arvid Krein
2023-06-02gnu: kicad: Update to 7.0.5.•••* gnu/packages/engineering.scm (kicad): Update to 7.0.5. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net> Peter Polidoro
2023-06-02gnu: r-tcgabiolinks: Update to 2.28.2.•••* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.28.2. Ricardo Wurmus
2023-06-02gnu: r-biocthis: Update to 1.10.1.•••* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.10.1. Ricardo Wurmus
2023-06-02gnu: r-basilisk-utils: Update to 1.12.1.•••* gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.12.1. Ricardo Wurmus
2023-06-02gnu: r-megadepth: Update to 1.10.0.•••* gnu/packages/bioconductor.scm (r-megadepth): Update to 1.10.0. Ricardo Wurmus
2023-06-02gnu: r-s4arrays: Update to 1.0.4.•••* gnu/packages/bioconductor.scm (r-s4arrays): Update to 1.0.4. Ricardo Wurmus
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
2023-06-02gnu: 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
2023-06-02gnu: 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
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