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2023-03-21gnu: r-intervals: Update to 0.15.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-intervals): Update to 0.15.3.
2023-03-21gnu: r-maldiquant: Update to 1.22.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-maldiquant): Update to 1.22.1.
2023-03-21gnu: r-metafor: Update to 4.0-0.Ricardo Wurmus
* gnu/packages/cran.scm (r-metafor): Update to 4.0-0. [propagated-inputs]: Add r-numderiv. [native-inputs]: Add r-r-rsp.
2023-03-21gnu: r-qgraph: Update to 1.9.4.Ricardo Wurmus
* gnu/packages/cran.scm (r-qgraph): Update to 1.9.4.
2023-03-21gnu: r-ggfortify: Update to 0.4.16.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggfortify): Update to 0.4.16.
2023-03-21gnu: r-sf: Update to 1.0-12.Ricardo Wurmus
* gnu/packages/cran.scm (r-sf): Update to 1.0-12.
2023-03-21gnu: r-glmmtmb: Update to 1.1.6.Ricardo Wurmus
* gnu/packages/cran.scm (r-glmmtmb): Update to 1.1.6.
2023-03-21gnu: r-fnn: Update to 1.1.3.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-fnn): Update to 1.1.3.2.
2023-03-21gnu: r-truncnorm: Update to 1.0-9.Ricardo Wurmus
* gnu/packages/cran.scm (r-truncnorm): Update to 1.0-9.
2023-03-21gnu: r-partykit: Update to 1.2-19.Ricardo Wurmus
* gnu/packages/cran.scm (r-partykit): Update to 1.2-19.
2023-03-21gnu: r-nmf: Update to 0.26.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-nmf): Update to 0.26.
2023-03-21gnu: sbcl-history-tree: Update to 0.1.1.Pierre Neidhardt
* gnu/packages/lisp-xyz.scm (sbcl-history-tree): Update to 0.1.1.
2023-03-21gnu: r-singlecellexperiment: Update to 1.20.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-singlecellexperiment): Update to 1.20.1.
2023-03-21gnu: r-variancepartition: Update to 1.28.9.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.28.9.
2023-03-21gnu: r-biocparallel: Update to 1.32.6.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.32.6.
2023-03-20gnu: Add mygnuhealth.Petr Hodina
* gnu/packages/medical.scm (mygnuhealth): New variable. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Co-authored-by: Morgan Smith <Morgan.J.Smith@outlook.com> Modified-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2023-03-20gnu: zabbix-agentd: Update to 6.0.14.Kaelyn Takata
* gnu/packages/monitoring.scm (zabbix-agentd): Update to 6.0.14. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2023-03-20gnu: tesseract-ocr: Use standard TESSDATA_PREFIX.Simon South
* gnu/packages/ocr.scm (tesseract-ocr-tessdata-fast): Install data to 'share/tessdata' prefix rather than 'share/tesseract-ocr/tessdata'. (tesseract-ocr) [arguments]: Delete adjust-TESSDATA_PREFIX-macro. Adjust installation prefix in install-minimal-tessdata phase. [native-search-paths]: Search for files under share/tessdata directly. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2023-03-20gnu: emacs-magit-gerrit: Update to 0.4-1.a975215.Maxim Cournoyer
* gnu/packages/emacs-xyz.scm (emacs-magit-gerrit): Update to 0.4-1.a975215.
2023-03-20gnu: emacs-magit: Update to 3.3.0-4.a760dd1.Maxim Cournoyer
This update resolves a problem where configuring a remote would result in the error "Symbol’s function definition is void: transient--with-suspended-override". * gnu/packages/emacs-xyz.scm (emacs-magit): Update to 3.3.0-4.a760dd1.
2023-03-20gnu: emacs-transient: Update to 0.3.7-1.0ae0de4.Maxim Cournoyer
* gnu/packages/emacs-xyz.scm (emacs-transient): Update to 0.3.7-1.0ae0de4. [propagated-inputs]: Remove emacs-dash; add emacs-compat.
2023-03-21gnu: lepton-eda: Update to 1.9.18-20220529.Ricardo Wurmus
* gnu/packages/engineering.scm (lepton-eda): Update to 1.9.18-20220529. [inputs]: Add guile-readline. [arguments]: Adjust build phase 'fix-dynamic-link; add build phase 'fix-tests.
2023-03-21gnu: Add ctrlr.Ricardo Wurmus
* gnu/packages/music.scm (ctrlr): New variable.
2023-03-20gnu: openjdk10: Apply patch again.Andreas Enge
This partially reverts commit 7636c49b45adb9870cf416c64bde032ec858a820 where the patch was dropped. * gnu/packages/java.scm (openjdk10)[source]: Apply patch.
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.
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