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2023-03-15gnu: r-rsubread: Update to 2.12.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.12.3.
2023-03-15gnu: r-iclusterplus: Update to 1.34.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-iclusterplus): Update to 1.34.3.
2023-03-15gnu: r-rbowtie2: Update to 2.4.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rbowtie2): Update to 2.4.2.
2023-03-15gnu: r-motifbreakr: Update to 2.12.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-motifbreakr): Update to 2.12.3.
2023-03-15gnu: r-clusterexperiment: Update to 2.18.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-clusterexperiment): Update to 2.18.2.
2023-03-15gnu: r-clusterprofiler: Update to 4.6.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.6.2.
2023-03-15gnu: r-sigpathway: Update to 1.66.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-sigpathway): Update to 1.66.2.
2023-03-15gnu: r-linnorm: Update to 2.22.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-linnorm): Update to 2.22.2.
2023-03-15gnu: r-glmgampoi: Update to 1.10.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-glmgampoi): Update to 1.10.2.
2023-03-15gnu: r-diffbind: Update to 3.8.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.8.4.
2023-03-15gnu: r-scmap: Update to 1.20.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-scmap): Update to 1.20.2.
2023-03-15gnu: r-mutationalpatterns: Update to 3.8.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mutationalpatterns): Update to 3.8.1.
2023-03-15gnu: r-muscat: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-muscat): Update to 1.12.1.
2023-03-15gnu: r-limma: Update to 3.54.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-limma): Update to 3.54.2.
2023-03-15gnu: r-lfa: Update to 1.28.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-lfa): Update to 1.28.2.
2023-03-15gnu: r-genomicalignments: Update to 1.34.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomicalignments): Update to 1.34.1.
2023-03-15gnu: r-annotationdbi: Update to 1.60.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.60.2.
2023-03-15gnu: r-infercnv: Update to 1.14.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-infercnv): Update to 1.14.2.
2023-03-15gnu: r-bandits: Update to 1.14.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bandits): Update to 1.14.2.
2023-03-15gnu: r-bambu: Update to 3.0.8.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bambu): Update to 3.0.8.
2023-03-15gnu: r-atena: Update to 1.4.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-atena): Update to 1.4.1. [propagated-inputs]: Add r-matrixstats.
2023-03-15gnu: r-alpsnmr: Update to 4.0.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-alpsnmr): Update to 4.0.4. [propagated-inputs]: Add r-cli.
2023-03-15gnu: r-biocpkgtools: Update to 1.16.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.16.1. [source]: Add snippet to remove bundled minified JavaScript files. [native-inputs]: Add esbuild, js-bootstrap, js-d3, js-jquery, and js-underscore. [arguments]: Add build phase 'process-javascript.
2023-03-15gnu: r-mast: Update to 1.24.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mast): Update to 1.24.1. [source]: Delete minified JavaScript. [arguments]: Add build phase 'process-javascript. [native-inputs]: Add esbuild and js-jquery-sticky-kit.
2023-03-15gnu: sbcl-nclasses: Update to 0.3.0.Pierre Neidhardt
* gnu/packages/lisp-xyz.scm (sbcl-nclasses): Update to 0.3.0.
2023-03-15gnu: Add sbcl-stumpwm-hostname.jgart
* gnu/packages/wm.scm (sbcl-stumpwm-hostname): New variable. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2023-03-15gnu: sbcl-mcclim: Update project urls.jgart
* gnu/packages/lisp-xyz.scm (sbcl-mcclim)[source]: Update source url. [home-page]: Update project home page. Signed-off-by: Andreas Enge <andreas@enge.fr>
2023-03-15gnu: reprotest: Update to 0.7.23.Vagrant Cascadian
* gnu/packages/diffoscope.scm (reprotest): Update to 0.7.23. [phases] Update adjust-locales.
2023-03-15gnu: diffoscope: Update to 238.Vagrant Cascadian
* gnu/packages/diffoscope.scm (diffoscope): Update to 238. [native-inputs]: Switch from poppler to poppler-next.
2023-03-15gnu: emacs-org-modern: Update to 0.9.Andrew Tropin
* gnu/packages/emacs-xyz.scm (emacs-org-modern): Update to 0.9.
2023-03-14gnu: r-rhandsontable: Move to (gnu packages cran).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhandsontable): Move this variable from here... * gnu/packages/cran.scm (r-rhandsontable): ...to here.
2023-03-14gnu: Add r-premessa.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-premessa): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
2023-03-14gnu: icecat: Update to 102.9.0-guix0-preview1 [security fixes].Mark H Weaver
Includes fixes for CVE-2023-25751, CVE-2023-25752, CVE-2023-28162, CVE-2023-28163, CVE-2023-28164, and CVE-2023-28176. * gnu/packages/gnuzilla.scm (%icecat-base-version, %icecat-build-id): Update. (icecat-source): Update gnuzilla commit, base version, and hashes.
2023-03-14gnu: Add r-rhandsontable.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhandsontable): New variable. Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
2023-03-14gnu: r-tidyverse: Update to 2.0.0.Navid Afkhami
* gnu/packages/cran.scm (r-tidyverse): Update to 2.0.0. [propagated-inputs]: Remove r-crayon; add r-conflicted and r-ragg.
2023-03-14gnu: pcb-rnd: Update to 3.1.0.Ricardo Wurmus
* gnu/packages/engineering.scm (pcb-rnd): Update to 3.1.0. [inputs]: Add librnd. [arguments]: Use gexp; set LIBRND_PREFIX.
2023-03-14gnu: Add librnd.Ricardo Wurmus
* gnu/packages/engineering.scm (librnd): New variable.
2023-03-14gnu: pcb: Remove eudev.Ricardo Wurmus
* gnu/packages/engineering.scm (pcb)[inputs]: Remove eudev as it is no longer necessary to add it for mesa.
2023-03-14gnu: pcb: Drop input labels.Ricardo Wurmus
* gnu/packages/engineering.scm (pcb)[inputs, native-inputs]: Remove package labels.
2023-03-14gnu: pcb: Update to 4.3.0.Ricardo Wurmus
* gnu/packages/engineering.scm (pcb): Update to 4.3.0. [arguments]: Remove obsolete build phases.
2023-03-14gnu: pcb: Use gexp.Ricardo Wurmus
* gnu/packages/engineering.scm (pcb)[arguments]: Use gexp and drop trailing #T from build phases.
2023-03-14gnu: lepton-eda: Adjust format.Ricardo Wurmus
* gnu/packages/engineering.scm (lepton-eda): Move arguments above inputs, and reformat source field.
2023-03-14gnu: lepton-eda: Use gexp for arguments.Ricardo Wurmus
* gnu/packages/engineering.scm (lepton-eda)[arguments]: Use gexp.
2023-03-14gnu: lepton-eda: Drop input labels.Ricardo Wurmus
* gnu/packages/engineering.scm (lepton-eda)[native-inputs, inputs]: Do not use redundant package labels.
2023-03-14gnu: guix-build-coordinator: Update to 0-73.7c1eedf.Christopher Baines
* gnu/packages/package-management.scm (guix-build-coordinator): Update to 0-73.7c1eedf.
2023-03-14gnu: mruby: Update to 3.2.0.Yovan Naumovski
* gnu/packages/ruby.scm (mruby): Update to 3.2.0. [arguments]: Remove unnecessary substitutions in the 'disable-broken-tests phase. [description]: Update. Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-03-14gnu: autokey: Update to 0.96.0.Bruno Victal
* gnu/packages/python-xyz.scm (autokey): Update to 0.96.0. [source]: Patch tests. [arguments]: Enable tests. Prefer PATH over substitute* in phase 'fix-paths. Add phase 'setup-env-vars. Rename 'wrap-autokey-gi to 'wrap-autokey and set PATH. [build-system]: Switch to pyproject-build-system. [native-inputs]: Add python-pytest, python-pytest-cov and python-pyhamcrest. Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-03-14gnu: tesseract-ocr: Update to 5.3.0.kiasoc5
* gnu/packages/ocr.scm (tesseract-ocr): Update to 5.3.0. Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-03-14gnu: gimagereader: Update to 3.4.1.kiasoc5
* gnu/packages/ocr.scm (gimagereader): Update to 3.4.1. [inputs]: Remove quazip-0; add quazip. Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-03-14gnu: phantomsocks: Update to 0.0.0-20230223180716-34d21f24a9eb.Hilton Chain
* gnu/packages/networking.scm (phantomsocks): Update to 0.0.0-20230223180716-34d21f24a9eb. Signed-off-by: Christopher Baines <mail@cbaines.net>
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