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2022-10-03gnu: r-ggcyto: Update to 1.24.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.24.1.
2022-10-03gnu: r-ncdfflow: Update to 2.42.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.42.1.
2022-10-03gnu: r-rsubread: Update to 2.10.5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.10.5.
2022-10-03gnu: r-rgadem: Update to 2.44.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rgadem): Update to 2.44.1.
2022-10-03gnu: r-enrichplot: Update to 1.16.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.16.2.
2022-10-03gnu: r-dose: Update to 3.22.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dose): Update to 3.22.1.
2022-10-03gnu: r-residualmatrix: Update to 1.6.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-residualmatrix): Update to 1.6.1.
2022-10-03gnu: r-ggtree: Update to 3.4.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ggtree): Update to 3.4.4.
2022-10-03gnu: r-treeio: Update to 1.20.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-treeio): Update to 1.20.2.
2022-10-03gnu: r-scaledmatrix: Update to 1.4.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-scaledmatrix): Update to 1.4.1.
2022-10-03gnu: r-diffbind: Update to 3.6.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.6.4.
2022-10-03gnu: r-zellkonverter: Update to 1.6.5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.6.5.
2022-10-03gnu: r-limma: Update to 3.52.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-limma): Update to 3.52.4.
2022-10-03gnu: r-genomicfeatures: Update to 1.48.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.48.4.
2022-10-03gnu: r-genomeinfodb: Update to 1.32.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.32.4.
2022-10-03gnu: r-gage: Update to 2.46.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gage): Update to 2.46.1.
2022-10-03gnu: r-complexheatmap: Update to 2.12.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-complexheatmap): Update to 2.12.1.
2022-10-03gnu: r-chipseeker: Update to 1.32.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.32.1. [propagated-inputs]: Add r-ggvenndiagram.
2022-10-03gnu: r-biostrings: Update to 2.64.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.64.1.
2022-10-03gnu: r-annotationforge: Update to 1.38.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.38.1.
2022-10-03gnu: r-dearseq: Update to 1.8.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dearseq): Update to 1.8.4.
2022-09-20gnu: r-activedriverwgs: Update to 1.2.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-activedriverwgs): Update to 1.2.0.
2022-09-20gnu: r-htscluster: Update to 2.0.10.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-htscluster): Update to 2.0.10.
2022-09-20gnu: r-perfmeas: Update to 1.2.5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-perfmeas): Update to 1.2.5.
2022-09-20gnu: r-valr: Update to 0.6.5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-valr): Update to 0.6.5.
2022-09-15gnu: Add r-omicade4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-omicade4): New variable.
2022-09-15gnu: Add r-made4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-made4): New variable.
2022-09-10gnu: Add comments to the bottom of a few package modules.Christopher Baines
This will hopefully discourage patches which add new packages to the bottom of files, as this increases the likelihood of conflicts when applying patches. If there are more specific ways that packages should be arranged in specific modules, this message can be updated accordingly. * gnu/packages/bioconductor.scm: Add comment discouraging adding packages to the bottom of the file. * gnu/packages/bioinformatics.scm: ditto. * gnu/packages/cran.scm: ditto. * gnu/packages/crates-io.scm: ditto. * gnu/packages/emacs-xyz.scm: ditto. * gnu/packages/golang.scm: ditto. * gnu/packages/guile-xyz.scm: ditto. * gnu/packages/haskell-xyz.scm: ditto. * gnu/packages/java.scm: ditto. * gnu/packages/julia-xyz.scm: ditto. * gnu/packages/lisp-xyz.scm: ditto. * gnu/packages/ocaml.scm: ditto. * gnu/packages/perl.scm: ditto. * gnu/packages/python-science.scm: ditto. * gnu/packages/python-xyz.scm: ditto. * gnu/packages/ruby.scm: ditto. * gnu/packages/tex.scm: ditto.
2022-09-06gnu: r-edger: Update to 3.38.4.Efraim Flashner
* gnu/packages/bioconductor.scm (r-edger): Update to 3.38.4. [propagated-inputs]: Remove r-statmod.
2022-09-05gnu: r-genomicalignments: Update to 1.32.1.Efraim Flashner
* gnu/packages/bioconductor.scm (r-genomicalignments): Update to 1.32.1.
2022-08-31gnu: Add r-milor.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-milor): New variable.
2022-08-29gnu: r-keggrest: Update to 1.36.3.Efraim Flashner
* gnu/packages/bioconductor.scm (r-keggrest): Update to 1.36.3.
2022-08-28gnu: r-genomeinfodb: Update to 1.32.3.Efraim Flashner
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.32.3.
2022-08-28gnu: r-iranges: Update to 2.30.1.Efraim Flashner
* gnu/packages/bioconductor.scm (r-iranges): Update to 2.30.1.
2022-08-25gnu: Add r-scry.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-scry): New variable.
2022-08-23gnu: Add r-organism-dplyr.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-organism-dplyr): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-08-23gnu: Add r-bladderbatch.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bladderbatch): New variable.
2022-08-23gnu: Add r-pcaexplorer.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-pcaexplorer): New variable.
2022-08-23gnu: Add r-parathyroidse.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-parathyroidse): New variable.
2022-08-14gnu: Remove ‘open source’ from package descriptions.Tobias Geerinckx-Rice
Also do some (trivial) editing where appropriate. * gnu/packages/bioconductor.scm (r-anaquin, r-rcppnumerical) [description]: Remove superfluous ‘open source’. * gnu/packages/debian.scm (apt-mirror)[description]: Likewise. Add @acronym{}. Drop obscure Ubuntu for famous Trisquel. Reorder. * gnu/packages/documentation.scm (scrollkeeper)[description]: Remove superfluous ‘open systems’. Keep ‘Open Source’ in standard name. * gnu/packages/engineering.scm (freecad, cura-engine)[description]: Remove superfluous ‘open source’ and excessive puffery. * gnu/packages/firmware.scm (make-opensbi-package) [synopsis]: Remove ‘Open Source’. Use @acronym{}. [description]: Fix first sentence to follow guidelines. Use @acronym{}. * gnu/packages/game-development.scm (ioquake3, recastnavigation): [description]: Remove ‘open source’. * gnu/packages/graphics.scm (skia)[description]: Likewise. * gnu/packages/lisp-xyz.scm (sbcl-s-sysdeps)[description]: Likewise. * gnu/packages/machine-learning.scm (onnx)[description]: Likewise. Use @acronym{}. * gnu/packages/ocaml.scm (ocaml-cudf)[description]: Likewise.
2022-08-14gnu: r-bgx: Build without CPU tuning.Ricardo Wurmus
Fixes <https://issues.guix.gnu.org/57210>. * gnu/packages/bioconductor.scm (r-bgx)[arguments]: Add phase 'do-not-tune-cflags-for-reproducibility to patch configure.ac. [inputs]: Add boost. [native-inputs]: Add autoconf and automake.
2022-08-14gnu: r-lpsymphony: Build reproducibly.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-lpsymphony)[arguments]: Add build phase 'make-build-order-reproducible.
2022-08-10gnu: r-activepathways: Update to 1.1.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-activepathways): Update to 1.1.1.
2022-08-09gnu: Add r-ciara.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ciara): New variable.
2022-08-05gnu: Add r-biomartr.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biomartr): New variable.
2022-08-01gnu: Add r-infercnv.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-infercnv): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-08-01gnu: Add r-muscat.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-muscat): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-08-01gnu: Add comma after “i.e.” in descriptions.Paul A. Patience
* gnu/packages/bioconductor.scm (r-anota)[description]: Add comma after “i.e.”. * gnu/packages/code.scm (xenon)[description]: Same. * gnu/packages/cran.scm (r-crosstalk)[description]: Same. * gnu/packages/python-xyz.scm (python-radon)[description]: Same. * gnu/packages/statistics.scm (r-logspline)[description]: Same. * gnu/packages/suckless.scm (tabbed)[description]: Same. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-07-15gnu: r-affycompatible: Build reproducibly.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affycompatible)[arguments]: Sort XML elements before generating R code from them.
2022-07-04gnu: Add r-dittoseq.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dittoseq): New variable.
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