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2023-03-20gnu: Add r-annotationhubdata.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-annotationhubdata): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-03-20gnu: Add r-affylmgui.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-affylmgui): New variable.
2023-03-20gnu: Add r-tkrplot.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-tkrplot): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
2023-03-20gnu: Add r-affyplm.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-affyplm): New variable.
2023-03-20gnu: Add r-affyilm.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-affyilm): New variable.
2023-03-20gnu: python-google-api-client: Update to 1.12.8.Efraim Flashner
* gnu/packages/python-web.scm (python-google-api-client): Update to 1.12.8. [arguments]: Remove custom phase to adjust setup.py. [native-inputs]: Remove python-oauth2client, python-uritemplate. Move python-httplib2, python-six ... [propagated-inputs]: ... here. Add python-google-api-core-1, python-google-auth-1, python-google-auth-httplib2, python-uritemplate-3.
2023-03-20gnu: python-googleapis-common-protos: Update to 1.56.4.Efraim Flashner
* gnu/packages/python-web.scm (python-googleapis-common-protos): Update to 1.56.4. [arguments]: Enable test suite.
2023-03-20gnu: Add python-google-api-core-1.Efraim Flashner
* gnu/packages/python-web.scm (python-google-api-core-1): New variable.
2023-03-20gnu: Add python-google-auth-1.Efraim Flashner
* gnu/packages/python-web.scm (python-google-auth-1): New variable.
2023-03-20gnu: Add python-google-auth-httplib2.Efraim Flashner
* gnu/packages/python-web.scm (python-google-auth-httplib2): New variable.
2023-03-20gnu: Add python-uritemplate-3.Efraim Flashner
* gnu/packages/python-web.scm (python-uritemplate-3): New variable.
2023-03-20gnu: python-httplib2: Update to 0.15.0.Efraim Flashner
* gnu/packages/python-web.scm (python-httplib2): Update to 0.15.0. [source]: Download using git. [arguments]: Add a phase to adjust the test package version requirements. [native-inputs]: Add python-flake8, python-future, python-mock, python-pytest, python-pytest-cov, python-pytest-forked, python-pytest-randomly, python-pytest-timeout, python-pytest-xdist, python-six. [home-page]: Switch to new upstream homepage.
2023-03-20gnu: zig: Increase max-silent-time.Efraim Flashner
* gnu/packages/zig.scm (zig-0.10)[properties]: Set max-silent-time to 3 hours.
2023-03-20gnu: Add transanno.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (transanno): New variable.
2023-03-20gnu: Add rust-autocompress-0.2.Ricardo Wurmus
* gnu/packages/crates-io.scm (rust-autocompress-0.2): New variable.
2023-03-20gnu: Add rust-temp-testdir-0.2.Ricardo Wurmus
* gnu/packages/crates-io.scm (rust-temp-testdir-0.2): New variable.
2023-03-20gnu: Add rust-bio-0.41.Ricardo Wurmus
* gnu/packages/crates-io.scm (rust-bio-0.41): New variable.
2023-03-20gnu: ruby-rugged: Update to 1.6.2-0.6379f23 and enable tests.Maxim Cournoyer
* gnu/packages/ruby.scm (ruby-rugged): Update to 1.6.2-0.6379f23. [source]: Fetch via git. [arguments]: Enable tests. Add #:phases. [native-inputs]: Add git-minimal/pinned. Remove ruby-minitest and ruby-pry.
2023-03-20gnu: python-django-rq: Update to 2.7.0.Maxim Cournoyer
* gnu/packages/django.scm (python-django-rq): Update to 2.7.0. [arguments]: Replace django-admin.py with django-admin in check phase.
2023-03-20gnu: python-aioredis: Deprecate by python-redis.Maxim Cournoyer
* gnu/packages/databases.scm (python-aioredis): Mark as deprecated by python-redis.
2023-03-20gnu: python-fakeredis: Update to 2.10.1 and enable tests.Maxim Cournoyer
* gnu/packages/databases.scm (python-fakeredis): Update to 2.10.1. [source]: Fetch via git. [build-system]: Use pyproject-build-system. [arguments]: Enable tests. Add #:phases. [native-inputs]: New field. [propagated-inputs]: Remove python-aioredis and python-packaging. [home-page]: Update URL.
2023-03-20gnu: python-redis: Update to 4.5.2 and enable tests.Maxim Cournoyer
* gnu/packages/databases.scm (python-redis): Update to 4.5.2. [source]: Fetch from git. [build-system]: Use pyproject-build-system. [arguments]: Enable tests. Add #:test-flags and #:phases. [native-inputs]: Add field. [propagated-inputs]: Add field. [home-page]: Update URL.
2023-03-20gnu: python-hiredis: Update to 2.2.2 and enable tests.Maxim Cournoyer
* gnu/packages/databases.scm (python-hiredis): Update to 2.2.2. [source]: Fetch via git and apply patches. [build-system]: Use pyproject-build-system. [arguments]: Enable tests. Add #:phases. [native-inputs]: New field. [inputs]: Likewise. * gnu/packages/patches/python-hiredis-fix-header.patch: New file. * gnu/packages/patches/python-hiredis-use-system-hiredis.patch: Likewise. * gnu/local.mk (dist_patch_DATA): Register them.
2023-03-20gnu: hiredis: Update to 1.1.0.Maxim Cournoyer
* gnu/packages/databases.scm (hiredis): Update to 1.1.0.
2023-03-20gnu: redis: Use gexps and streamline.Maxim Cournoyer
* gnu/packages/databases.scm (redis) [arguments]: Merge the use-correct-tclsh into the patch-paths phase. Use 'which' instead of assoc-ref. Move the #:make-flags argument before the #:phases one. Use cc-for-target as the value of the CC make flag. [native-inputs]: Move field below arguments.
2023-03-20gnu: redis: Update to 7.0.9 [security fixes].Maxim Cournoyer
Fixes CVE-2023-25155, CVE-2022-36021 and more; see https://raw.githubusercontent.com/redis/redis/7.0/00-RELEASENOTES. * gnu/packages/databases.scm (redis): Update to 7.0.9. [native-inputs]: Add pkg-config and which. [arguments]: Add a patch-paths phase. Skip the AOF-related tests. [properties]: Add a lint-hidden-cve property.
2023-03-20services: network-manager: Add missing shadowing of 'iwd?' field.Andrew Tropin
* gnu/services/networking.scm (network-manager-shepherd-service): Add missing shadowing of 'iwd?' field by using let* instead of let.
2023-03-20home: 'home-environment-with-provenance' uses the HE location info.Sergey Trofimov
* gnu/home.scm (home-environment-with-provenance): Make `config-file` optional, with the default taken from the HE location info. Signed-off-by: Andrew Tropin <andrew@trop.in>
2023-03-20gnu: emacs-eshell-syntax-highlighting: Update to 0.3-0.1ba39a9.conses
* gnu/packages/emacs-xyz.scm (emacs-eshell-syntax-highlighting): Update to 0.3-0.1ba39a9. Signed-off-by: Andrew Tropin <andrew@trop.in>
2023-03-20gnu: Add emacs-geiser-eros.Andrew Tropin
* gnu/packages/emacs-xyz.scm (emacs-geiser-eros): New variable.
2023-03-19gnu: linux-libre: Update kernel configs for 6.2.7.Leo Famulari
* gnu/packages/aux-files/linux-libre/6.2-arm.conf, gnu/packages/aux-files/linux-libre/6.2-arm64.conf, gnu/packages/aux-files/linux-libre/6.2-i686.conf, gnu/packages/aux-files/linux-libre/6.2-x86_64.conf: Set some new configuration options.
2023-03-19gnu: linux-libre 4.14: Update to 4.14.310.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.310. (linux-libre-4.14-pristine-source, deblob-scripts-4.14): Update hashes.
2023-03-19gnu: linux-libre 4.19: Update to 4.19.278.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.278. (linux-libre-4.19-pristine-source, deblob-scripts-4.19): Update hashes.
2023-03-19gnu: linux-libre 5.4: Update to 5.4.237.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.237. (linux-libre-5.4-pristine-source, deblob-scripts-5.4): Update hashes.
2023-03-19gnu: linux-libre 5.10: Update to 5.10.175.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.175. (linux-libre-5.10-pristine-source, deblob-scripts-5.10): Update hashes.
2023-03-19gnu: linux-libre 5.15: Update to 5.15.103.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.103. (linux-libre-5.15-pristine-source, deblob-scripts-5.15): Update hashes.
2023-03-19gnu: linux-libre 6.1: Update to 6.1.20.Leo Famulari
* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.20. (linux-libre-6.1-pristine-source, deblob-scripts-6.1): Update hashes.
2023-03-19gnu: linux-libre: Update to 6.2.7.Leo Famulari
* gnu/packages/linux.scm (linux-libre-6.2-version): Update to 6.2.7. (linux-libre-6.2-pristine-source, deblob-scripts-6.2): Update hashes.
2023-03-19gnu: atop: Update to 2.8.1.Yovan Naumovski
* gnu/packages/admin.scm (atop): Update to 2.8.1. Signed-off-by: Leo Famulari <leo@famulari.name>
2023-03-19gnu: r-flexmix: Update to 2.3-19.Ricardo Wurmus
* gnu/packages/statistics.scm (r-flexmix): Update to 2.3-19.
2023-03-19gnu: r-xml: Update to 3.99-0.14.Ricardo Wurmus
* gnu/packages/statistics.scm (r-xml): Update to 3.99-0.14.
2023-03-19gnu: r-blob: Update to 1.2.4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-blob): Update to 1.2.4.
2023-03-19gnu: r-gtable: Update to 0.3.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-gtable): Update to 0.3.2. [propagated-inputs]: Add r-cli, r-glue, r-lifecycle, and r-rlang.
2023-03-19gnu: r-commonmark: Update to 1.9.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-commonmark): Update to 1.9.0.
2023-03-19gnu: r-qpdf: Update to 1.3.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-qpdf): Update to 1.3.2.
2023-03-19gnu: r-mlr3: Update to 0.15.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-mlr3): Update to 0.15.0.
2023-03-19gnu: r-paradox: Update to 0.11.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-paradox): Update to 0.11.1.
2023-03-19gnu: r-anndata: Update to 0.7.5.6.Ricardo Wurmus
* gnu/packages/cran.scm (r-anndata): Update to 0.7.5.6.
2023-03-19gnu: r-wk: Update to 0.7.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-wk): Update to 0.7.2.
2023-03-19gnu: r-insight: Update to 0.19.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-insight): Update to 0.19.1.
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