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* gnu: Add r-omicade4.Ricardo Wurmus2022-09-15
| | | | * gnu/packages/bioconductor.scm (r-omicade4): New variable.
* gnu: Add r-made4.Ricardo Wurmus2022-09-15
| | | | * gnu/packages/bioconductor.scm (r-made4): New variable.
* gnu: Add comments to the bottom of a few package modules.Christopher Baines2022-09-10
| | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* gnu: r-edger: Update to 3.38.4.Efraim Flashner2022-09-06
| | | | | * gnu/packages/bioconductor.scm (r-edger): Update to 3.38.4. [propagated-inputs]: Remove r-statmod.
* gnu: r-genomicalignments: Update to 1.32.1.Efraim Flashner2022-09-05
| | | | * gnu/packages/bioconductor.scm (r-genomicalignments): Update to 1.32.1.
* gnu: Add r-milor.Ricardo Wurmus2022-08-31
| | | | * gnu/packages/bioconductor.scm (r-milor): New variable.
* gnu: r-keggrest: Update to 1.36.3.Efraim Flashner2022-08-29
| | | | * gnu/packages/bioconductor.scm (r-keggrest): Update to 1.36.3.
* gnu: r-genomeinfodb: Update to 1.32.3.Efraim Flashner2022-08-28
| | | | * gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.32.3.
* gnu: r-iranges: Update to 2.30.1.Efraim Flashner2022-08-28
| | | | * gnu/packages/bioconductor.scm (r-iranges): Update to 2.30.1.
* gnu: Add r-scry.Ricardo Wurmus2022-08-25
| | | | * gnu/packages/bioconductor.scm (r-scry): New variable.
* gnu: Add r-organism-dplyr.Mădălin Ionel Patrașcu2022-08-23
| | | | | | * gnu/packages/bioconductor.scm (r-organism-dplyr): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add r-bladderbatch.Ricardo Wurmus2022-08-23
| | | | * gnu/packages/bioconductor.scm (r-bladderbatch): New variable.
* gnu: Add r-pcaexplorer.Mădălin Ionel Patrașcu2022-08-23
| | | | * gnu/packages/bioconductor.scm (r-pcaexplorer): New variable.
* gnu: Add r-parathyroidse.Mădălin Ionel Patrașcu2022-08-23
| | | | * gnu/packages/bioconductor.scm (r-parathyroidse): New variable.
* gnu: Remove ‘open source’ from package descriptions.Tobias Geerinckx-Rice2022-08-14
| | | | | | | | | | | | | | | | | | | | | | | 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.
* gnu: r-bgx: Build without CPU tuning.Ricardo Wurmus2022-08-14
| | | | | | | | | 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.
* gnu: r-lpsymphony: Build reproducibly.Ricardo Wurmus2022-08-14
| | | | | * gnu/packages/bioconductor.scm (r-lpsymphony)[arguments]: Add build phase 'make-build-order-reproducible.
* gnu: r-activepathways: Update to 1.1.1.Ricardo Wurmus2022-08-10
| | | | * gnu/packages/bioconductor.scm (r-activepathways): Update to 1.1.1.
* gnu: Add r-ciara.Ricardo Wurmus2022-08-09
| | | | * gnu/packages/bioconductor.scm (r-ciara): New variable.
* gnu: Add r-biomartr.Ricardo Wurmus2022-08-05
| | | | * gnu/packages/bioconductor.scm (r-biomartr): New variable.
* gnu: Add r-infercnv.Mădălin Ionel Patrașcu2022-08-01
| | | | | | * gnu/packages/bioconductor.scm (r-infercnv): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add r-muscat.Mădălin Ionel Patrașcu2022-08-01
| | | | | | * gnu/packages/bioconductor.scm (r-muscat): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add comma after “i.e.” in descriptions.Paul A. Patience2022-08-01
| | | | | | | | | | | | * 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>
* gnu: r-affycompatible: Build reproducibly.Ricardo Wurmus2022-07-15
| | | | | * gnu/packages/bioconductor.scm (r-affycompatible)[arguments]: Sort XML elements before generating R code from them.
* gnu: Add r-dittoseq.Ricardo Wurmus2022-07-04
| | | | * gnu/packages/bioconductor.scm (r-dittoseq): New variable.
* gnu: r-tcgabiolinks: Update to 2.24.3.Ricardo Wurmus2022-07-02
| | | | * gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.24.3.
* gnu: r-bionetstat: Update to 1.16.1.Ricardo Wurmus2022-07-02
| | | | * gnu/packages/bioconductor.scm (r-bionetstat): Update to 1.16.1.
* gnu: r-bgeedb: Update to 2.22.3.Ricardo Wurmus2022-07-02
| | | | * gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.22.3.
* gnu: r-ggbio: Update to 1.44.1.Ricardo Wurmus2022-07-02
| | | | * gnu/packages/bioconductor.scm (r-ggbio): Update to 1.44.1.
* gnu: r-rsubread: Update to 2.10.4.Ricardo Wurmus2022-07-02
| | | | * gnu/packages/bioconductor.scm (r-rsubread): Update to 2.10.4.
* gnu: r-biosigner: Update to 1.24.2.Ricardo Wurmus2022-07-02
| | | | | * gnu/packages/bioconductor.scm (r-biosigner): Update to 1.24.2. [propagated-inputs]: Add r-multiassayexperiment and r-summarizedexperiment.
* gnu: r-ropls: Update to 1.28.2.Ricardo Wurmus2022-07-02
| | | | | * gnu/packages/bioconductor.scm (r-ropls): Update to 1.28.2. [propagated-inputs]: Add r-multiassayexperiment and r-summarizedexperiment.
* gnu: r-genomicscores: Update to 2.8.2.Ricardo Wurmus2022-07-02
| | | | | * gnu/packages/bioconductor.scm (r-genomicscores): Update to 2.8.2. [propagated-inputs]: Add r-httr.
* gnu: r-clusterprofiler: Update to 4.4.4.Ricardo Wurmus2022-07-02
| | | | * gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.4.4.
* gnu: r-batchelor: Update to 1.12.3.Ricardo Wurmus2022-07-02
| | | | * gnu/packages/bioconductor.scm (r-batchelor): Update to 1.12.3.
* gnu: r-matrixgenerics: Update to 1.8.1.Ricardo Wurmus2022-07-02
| | | | * gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.8.1.
* gnu: r-zellkonverter: Update to 1.6.3.Ricardo Wurmus2022-07-02
| | | | * gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.6.3.
* gnu: r-simplifyenrichment: Update to 1.6.1.Ricardo Wurmus2022-07-02
| | | | * gnu/packages/bioconductor.scm (r-simplifyenrichment): Update to 1.6.1.
* gnu: r-rtracklayer: Update to 1.56.1.Ricardo Wurmus2022-07-02
| | | | * gnu/packages/bioconductor.scm (r-rtracklayer): Update to 1.56.1.
* gnu: r-organismdbi: Update to 1.38.1.Ricardo Wurmus2022-07-02
| | | | * gnu/packages/bioconductor.scm (r-organismdbi): Update to 1.38.1.
* gnu: r-limma: Update to 3.52.2.Ricardo Wurmus2022-07-02
| | | | * gnu/packages/bioconductor.scm (r-limma): Update to 3.52.2.
* gnu: r-ensembldb: Update to 2.20.2.Ricardo Wurmus2022-07-02
| | | | * gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.20.2.
* gnu: r-restfulr: Update to 0.0.15.Ricardo Wurmus2022-07-02
| | | | * gnu/packages/bioconductor.scm (r-restfulr): Update to 0.0.15.
* gnu: Add r-antiprofiles.Mădălin Ionel Patrașcu2022-07-01
| | | | | | * gnu/packages/bioconductor.scm (r-antiprofiles): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add r-annmap.Mădălin Ionel Patrașcu2022-07-01
| | | | | | * gnu/packages/bioconductor.scm (r-annmap): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add r-anf.Mădălin Ionel Patrașcu2022-07-01
| | | | | | * gnu/packages/bioconductor.scm (r-anf): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add r-anaquin.Mădălin Ionel Patrașcu2022-07-01
| | | | | | * gnu/packages/bioconductor.scm (r-anaquin): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add r-amaretto.Mădălin Ionel Patrașcu2022-06-30
| | | | * gnu/packages/bioconductor.scm (r-amaretto): New variable.
* gnu: Add r-amountain.Mădălin Ionel Patrașcu2022-06-30
| | | | * gnu/packages/bioconductor.scm (r-amountain): New variable.
* gnu: r-metap: Update to 1.8.Ricardo Wurmus2022-06-30
| | | | | * gnu/packages/bioconductor.scm (r-metap): Update to 1.8. [propagated-inputs]: Add r-mathjaxr and r-qqconf.
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