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2022-04-14gnu: r-catalyst: Update description.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-catalyst)[description]: Add Texinfo markup and clarify a sentence. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-04-14gnu: r-tcgabiolinks: Update to 2.22.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.22.4.
2022-04-14gnu: r-omnipathr: Update to 3.2.8.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.2.8.
2022-04-14gnu: r-bgeedb: Update to 2.20.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.20.1.
2022-04-14gnu: r-gviz: Update to 1.38.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gviz): Update to 1.38.4.
2022-04-14gnu: r-catalyst: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-catalyst): Update to 1.18.1.
2022-04-14gnu: r-mscoreutils: Update to 1.6.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.6.2.
2022-04-14gnu: r-singler: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-singler): Update to 1.8.1.
2022-04-14gnu: r-s4vectors: Update to 0.32.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.32.4.
2022-04-14gnu: r-experimenthub: Update to 2.2.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-experimenthub): Update to 2.2.1.
2022-04-14gnu: r-universalmotif: Update to 1.12.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.12.4.
2022-04-14gnu: r-variancepartition: Update to 1.24.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.24.1. [propagated-inputs]: Add r-aod, r-rdpack, and r-rhpcblasctl.
2022-04-14gnu: r-cytolib: Update to 2.6.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.6.2.
2022-04-14gnu: r-rsubread: Update to 2.8.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.8.2.
2022-04-14gnu: r-ropls: Update to 1.26.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ropls): Update to 1.26.4.
2022-04-14gnu: r-birewire: Update to 3.26.5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-birewire): Update to 3.26.5. [propagated-inputs]: Remove r-tsne; add r-rtsne.
2022-04-14gnu: r-biocfilecache: Update to 2.2.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocfilecache): Update to 2.2.1.
2022-04-14gnu: r-massspecwavelet: Update to 1.60.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.60.1.
2022-04-14gnu: r-atacseqqc: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.18.1.
2022-04-14gnu: r-genomicscores: Update to 2.6.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomicscores): Update to 2.6.1.
2022-04-14gnu: r-clusterprofiler: Update to 4.2.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.2.2.
2022-04-14gnu: r-enrichplot: Update to 1.14.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.14.2.
2022-04-14gnu: r-geoquery: Update to 2.62.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-geoquery): Update to 2.62.2.
2022-04-14gnu: r-karyoploter: Update to 1.20.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-karyoploter): Update to 1.20.3.
2022-04-14gnu: r-destiny: Update to 3.8.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-destiny): Update to 3.8.1. [native-inputs]: Add r-knitr.
2022-04-14gnu: r-chippeakanno: Update to 3.28.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.28.1.
2022-04-14gnu: r-diffbind: Update to 3.4.11.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.4.11.
2022-04-14gnu: r-systempiper: Update to 2.0.8.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-systempiper): Update to 2.0.8.
2022-04-14gnu: r-stringdb: Update to 2.6.5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-stringdb): Update to 2.6.5.
2022-04-14gnu: r-slingshot: Update to 2.2.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-slingshot): Update to 2.2.1.
2022-04-14gnu: r-rhdf5: Update to 2.38.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.38.1.
2022-04-14gnu: r-regioner: Update to 1.26.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.26.1.
2022-04-14gnu: r-msnbase: Update to 2.20.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-msnbase): Update to 2.20.4.
2022-04-14gnu: r-mutationalpatterns: Update to 3.4.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mutationalpatterns): Update to 3.4.1.
2022-04-14gnu: r-limma: Update to 3.50.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-limma): Update to 3.50.3.
2022-04-14gnu: r-genomicfeatures: Update to 1.46.5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.46.5.
2022-04-14gnu: r-genomeinfodb: Update to 1.30.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.30.1.
2022-04-14gnu: r-ensembldb: Update to 2.18.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.18.4.
2022-04-14gnu: r-biomart: Update to 2.50.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biomart): Update to 2.50.3.
2022-04-14gnu: r-annotationhub: Update to 3.2.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotationhub): Update to 3.2.2.
2022-04-14gnu: Add r-aod.Ricardo Wurmus
* gnu/packages/cran.scm (r-aod): New variable.
2022-04-14gnu: r-tricycle: Move out of annotation packages.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tricycle): Move definition out of the section containing annotation packages.
2022-04-13gnu: gama: Update to 2.18.Efraim Flashner
* gnu/packages/gps.scm (gama): Update to 2.18.
2022-04-13gnu: idris: Fixes test failure.Eric Bavier
* gnu/packages/patches/idris-test-ffi008.patch: New file. * gnu/packages/idris.scm (source): Use it. * gnu/local.mk (dist_patch_DATA): Register it.
2022-04-13gnu: nginx: Update to 1.21.6.Leo Famulari
* gnu/packages/web.scm (nginx): Update to 1.21.6. (nginx-documentation): Update to 1.21.6-2829-1ecf0e0526da.
2022-04-13gnu: Add cl-simple-routes.Foo Chuan Wei
* gnu/packages/lisp-xyz.scm (cl-simple-routes, ecl-simple-routes, sbcl-simple-routes): New variables. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2022-04-13gnu: awscli: Do not propagate inputs.Ricardo Wurmus
* gnu/packages/python-web.scm (awscli)[propagated-inputs]: Move all inputs from here... [inputs]: ...to here.
2022-04-13gnu: awscli: Use PyYAML 6.Ricardo Wurmus
This should be fine because all uses of yaml.load supply the now mandatory loader argument. * gnu/packages/python-web.scm (awscli)[arguments]: Add phase 'use-recent-pyyaml. [propagated-inputs]: Replace python-pyyaml-for-awscli with python-pyyaml.
2022-04-12gnu: wpewebkit: Update to 2.36.0.Maxim Cournoyer
* gnu/packages/webkit.scm (%webkit-version): New variable. (wpewebkit): Update to 2.36.0, rewriting package to inherit from webkitgtk. (webkitgtk)[source]: Use %webkit-version, and adjust definition to match that of wpewebkit.
2022-04-12gnu: webkitgtk: Update to 2.36.0 and enable extra features.Maxim Cournoyer
* gnu/packages/webkit.scm (webkitgtk): Update to 2.36.0. [source]: Remove the webkitgtk-bind-all-fonts.patch and webkitgtk-canonicalize-paths.patch patches. [arguments]: Use gexp. [tests?]: Update comment. [build-type]: Add explanatory comment. [configure-flags]: Enable gamepad support, remove nonexistent USE_SYSTEMD option and enable mini-browser. [phases]{do-not-disable-new-dtags}: New phase. {help-cmake-find-elogind}: Likewise. {patch-gtk-doc-scan}: Simplify to avoid for-each. Locate docbookx.dtd via search-input-file. {embed-absolute-wpebackend-reference}: Use search-input-file. [native-inputs]: Use new style. [inputs]: Likewise. Add elogind and libmanette. [description]: Adjust indentation. (webkitgtk-with-libsoup2): Re-format comment, fixing spacing. [configure-flags]: Use gexp. [propagated-inputs]: Use modify-inputs to replace libsoup with libsoup-minimal-2. * gnu/packages/patches/webkitgtk-bind-all-fonts.patch: Delete file. * gnu/packages/patches/webkitgtk-canonicalize-paths.patch: Likewise. * gnu/local.mk: De-register them.
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