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2023-05-10gnu: cuirass: Update to 4a8a4bc.Ludovic Courtès
Fixes <https://issues.guix.gnu.org/63389>. * gnu/packages/ci.scm (cuirass): Update to 4a8a4bc. [arguments]: Remove 'set-PATH-for-tests' and 'disable-remote-tests' phases, which are unnecessary. In 'wrap-program' phase, check for "guile-gnutls". [inputs]: Replace GUILE-FIBERS with GUILE-FIBERS-1.1 and GNUTLS with GUILE-GNUTLS.
2023-05-10gnu: emacs-gerbil-mode: Move to scheme.scm.Ludovic Courtès
This fixes a bug due to a top-level circular reference: $ guix show scheme48 [...] ice-9/boot-9.scm:1685:16: In procedure raise-exception: error: gerbil: unbound variable * gnu/packages/emacs-xyz.scm (emacs-gerbil-mode): Move to... * gnu/packages/scheme.scm (emacs-gerbil-mode): ... here.
2023-05-10tests: docker-system: Add missing import.Ludovic Courtès
This is a followup to f51888272558d98cf5c196b93fb6c499056fbf6c. * gnu/tests/docker.scm (run-docker-system-test)["load system image and run it"]: Use (guix build utils).
2023-05-10system: Fix reference to Hurd bug in comment.Ludovic Courtès
* gnu/system.scm (hurd-multiboot-modules): Fix bug reference in comment.
2023-05-09gnu: icecat: Update to 102.11.0-guix0-preview1 [security fixes].Mark H Weaver
Includes fixes for CVE-2023-32205, CVE-2023-32206, CVE-2023-32207, CVE-2023-32211, CVE-2023-32212, CVE-2023-32213, CVE-2023-32214, and CVE-2023-32215. * gnu/packages/gnuzilla.scm (%icecat-base-version, %icecat-build-id): Update. (icecat-source): Update gnuzilla commit, base version, and hashes.
2023-05-09gnu: Add python-clinguin.Liliana Marie Prikler
* gnu/packages/potassco.scm (python-clinguin): New variable.
2023-05-09gnu: python-fastapi: Do not delete tests, and add orjson.Ricardo Wurmus
* gnu/packages/python-web.scm (python-fastapi)[arguments]: Remove all custom phases; ignore two test files. [propagated-inputs]: Add python-orjson.
2023-05-09gnu: Add python-fastapi.Liliana Marie Prikler
* gnu/packages/python-web.scm (python-fastapi): New variable.
2023-05-09gnu: python-databases: Revise description.Liliana Marie Prikler
* gnu/packages/databases.scm (python-databases)[synopsis]: Spell out “Asynchronous”. [description]: Mention that it's a wrapper around other libraries using SQLAlchemy.
2023-05-09gnu: python-databases: Update to 0.7.0.Liliana Marie Prikler
* gnu/packages/databases.scm (python-databases): Update to 0.7.0.
2023-05-09gnu: python-aiosqlite: Update to 0.18.0.Liliana Marie Prikler
* gnu/packages/databases.scm (python-aiosqlite): Update to 0.18.0. [source]: Use git-fetch and git-reference. [build-system]: Use pyproject-build-system. [arguments]: Adjust accordingly. [propagated-inputs]: Remove. [native-inputs]: Remove python-aiounittest. Add python-flit-core, python-coverage and python-mypy.
2023-05-09gnu: python-aiomysql: Update to 0.1.1.Liliana Marie Prikler
* gnu/packages/databases.scm (python-aiomysql): Update to 0.1.1. [build-system]: Change to pyproject-build-system.
2023-05-09gnu: python-pymysql: Update to 1.0.2.Liliana Marie Prikler
* gnu/packages/databases.scm (python-pymysql): Update to 1.0.2.
2023-05-09gnu: python-sqlalchemy: Use pyproject-build-system.Ricardo Wurmus
* gnu/packages/databases.scm (python-sqlalchemy)[arguments]: Replace custom 'check phase with #:test-flags. [build-system]: Use pyproject-build-system.
2023-05-09gnu: python-sqlalchemy: Update to 1.4.42.Liliana Marie Prikler
* gnu/packages/databases.scm (python-sqlalchemy): Update to 1.4.42.
2023-05-09gnu: python-starlette: Update to 0.25.0.Liliana Marie Prikler
* gnu/packages/python-web.scm (python-starlette): Update to 0.25.0. [source]: Switch to git-fetch and git-reference. [build-system]: Use pyproject-build-system. [native-inputs]: Add python-hatchling, python-httpx, python-pytest, and python-typing-extensions-next.
2023-05-09services: guix-build-coordinator: Support extra environment vars.Christopher Baines
I'm looking at this because I need to do some debugging of Guile's GC, and there are some useful environment variables for that, but it should be generally useful. * gnu/services/guix.scm (guix-build-coordinator-configuration-extra-environment-variables): New procedure. (guix-build-coordinator-shepherd-services): Pass the environment variables to the shepherd. * doc/guix.texi (Guix Services): Document it.
2023-05-09service: qemu-binfmt: Remove broken qemu targets.Efraim Flashner
* gnu/services.virtualization.scm (%qemu-platforms): Remove %i486, %aarch64be.
2023-05-09Revert "gnu: rust-bootstrap: Remove aarch64 as a supported architecture."Efraim Flashner
This reverts commit c56d57110de1412d3529940d4f856611d123da66. rust-bootstrap *IS* supported on aarch64-linux, and the build farm will catch up eventually.
2023-05-09gnu: r-scran: Update to 1.28.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-scran): Update to 1.28.1.
2023-05-09gnu: r-scuttle: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-scuttle): Update to 1.10.1.
2023-05-09gnu: r-chromvar: Update to 1.22.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chromvar): Update to 1.22.1.
2023-05-09gnu: r-hdf5array: Update to 1.28.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.28.1. [propagated-inputs]: Add r-s4arrays.
2023-05-09gnu: r-s4vectors: Update to 0.38.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.38.1.
2023-05-09gnu: r-preprocesscore: Update to 1.62.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.62.1.
2023-05-09gnu: r-iclusterplus: Update to 1.36.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-iclusterplus): Update to 1.36.1.
2023-05-09gnu: r-clusterprofiler: Update to 4.8.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.8.1.
2023-05-09gnu: r-dose: Update to 3.26.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dose): Update to 3.26.1.
2023-05-09gnu: r-linnorm: Update to 2.24.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-linnorm): Update to 2.24.1.
2023-05-09gnu: r-dnacopy: Update to 1.74.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.74.1.
2023-05-09gnu: r-scaledmatrix: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-scaledmatrix): Update to 1.8.1.
2023-05-09gnu: r-glmgampoi: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-glmgampoi): Update to 1.12.1.
2023-05-09gnu: r-oligo: Update to 1.64.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-oligo): Update to 1.64.1.
2023-05-09gnu: r-summarizedexperiment: Update to 1.30.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-summarizedexperiment): Update to 1.30.1. [propagated-inputs]: Add r-s4arrays.
2023-05-09gnu: r-scmap: Update to 1.22.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-scmap): Update to 1.22.1.
2023-05-09gnu: r-rhdf5filters: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rhdf5filters): Update to 1.12.1.
2023-05-09gnu: r-pcaexplorer: Update to 2.26.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-pcaexplorer): Update to 2.26.1.
2023-05-09gnu: r-impute: Update to 1.74.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-impute): Update to 1.74.1.
2023-05-09gnu: r-genefilter: Update to 1.82.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genefilter): Update to 1.82.1.
2023-05-09gnu: r-edger: Update to 3.42.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-edger): Update to 3.42.2.
2023-05-09gnu: r-deseq2: Update to 1.40.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.40.1.
2023-05-09gnu: r-biocparallel: Update to 1.34.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.34.1.
2023-05-09gnu: r-annotationdbi: Update to 1.62.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.62.1.
2023-05-09gnu: r-densvis: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-densvis): Update to 1.10.1.
2023-05-09gnu: r-delayedarray: Update to 0.26.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.26.2. [propagated-inputs]: Add r-s4arrays.
2023-05-09gnu: r-bandits: Update to 1.16.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bandits): Update to 1.16.1.
2023-05-09gnu: r-bambu: Update to 3.2.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bambu): Update to 3.2.2.
2023-05-09gnu: r-amplican: Update to 1.22.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-amplican): Update to 1.22.1. [propagated-inputs]: Remove r-clustercrit; add r-cluster.
2023-05-09gnu: r-affyplm: Update to 1.76.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affyplm): Update to 1.76.1.
2023-05-09gnu: Add r-s4arrays.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-s4arrays): New variable.
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