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2023-06-02gnu: Add r-singlet.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-singlet): New variable.
2023-06-02gnu: Add r-rcppml/devel.Ricardo Wurmus
* gnu/packages/machine-learning.scm (r-rcppml/devel): New variable.
2023-06-02gnu: Add python-cell2cell.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-cell2cell): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-06-02environment: Fix unbound-variable bug with '--symlink'.Ludovic Courtès
Fixes <https://issues.guix.gnu.org/63845>. Reported by Maxim Cournoyer <maxim.cournoyer@gmail.com>. * guix/scripts/environment.scm (launch-environment/container): Reference 'evaluate-populate-directive' before calling 'call-with-container'.
2023-06-02gnu: Add coccinelle.Jean-Pierre De Jesus DIAZ
* gnu/packages/patchutils.scm (coccinelle): New variable. Signed-off-by: Jean-Pierre De Jesus DIAZ <jean@foundationdevices.com> Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-06-02gnu: Add ocaml-pyml.Jean-Pierre De Jesus DIAZ
* gnu/packages/ocaml.ml (ocaml-pyml): New variable. Signed-off-by: Jean-Pierre De Jesus DIAZ <jean@foundationdevices.com> Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-06-02gnu: Add ocaml-stdcompat.Jean-Pierre De Jesus DIAZ
* gnu/packages/ocaml.scm (ocaml-stdcompat): New variable. Signed-off-by: Jean-Pierre De Jesus DIAZ <jean@foundationdevices.com> Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-06-02gnu: Add ocaml-parmap.Jean-Pierre De Jesus DIAZ
* gnu/packages/ocaml.scm (ocaml-parmap): New variable. Signed-off-by: Jean-Pierre De Jesus DIAZ <jean@foundationdevices.com> Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-06-02gnu: Add tmux-plugin-mem-cpu-load.Greg Hogan
* gnu/packages/tmux.scm (tmux-plugin-mem-cpu-load): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-06-02services: Error in MODIFY-SERVICES when services don't existBrian Cully
This patch causes MODIFY-SERVICES to raise an error if a reference is made to a service which isn't in its service list. This it to help users notice if they have an invalid rule, which is currently silently ignored. * gnu/services.scm (%delete-service): new procedure (%apply-clauses): new syntax rule (%modify-service): remove syntax rule Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-06-02tests: Check for service existence in MODIFY-SERVICESBrian Cully
* tests/services.scm ("modify-services: delete non-existing service") ("modify-services: change value for non-existing service"): New tests. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-06-02tests: Add tests for MODIFY-SERVICES procedureBrian Cully
* tests/services.scm ("modify-services: do nothing") ("modify-services: delete service") ("modify-services: change value"): New tests. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-06-02gnu: cuirass: Update to b825967.Ludovic Courtès
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.
2023-06-02gnu: python-ipython-documentation: Update dependencies.Greg Hogan
* gnu/packages/python-xyz.scm (python-ipython-documentation) [native-inputs]: Add python-ipykernel. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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.
2023-06-02read-print: Add 'package/inherit' special form.Ludovic Courtès
* guix/read-print.scm (%special-forms): Add 'package/inherit'.
2023-06-02ci: Reify the timestamps of evaluations.Ludovic Courtès
* guix/ci.scm (<evaluation>)[start-time, checkout-time, completion-time]: New fields.
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.
2023-06-02import/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.
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