| Commit message (Collapse) | Author | Age |
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* gnu/packages/bioconductor.scm (r-omicade4): New variable.
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* gnu/packages/bioconductor.scm (r-made4): New variable.
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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.
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* gnu/packages/bioconductor.scm (r-edger): Update to 3.38.4.
[propagated-inputs]: Remove r-statmod.
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* gnu/packages/bioconductor.scm (r-genomicalignments): Update to 1.32.1.
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* gnu/packages/bioconductor.scm (r-milor): New variable.
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* gnu/packages/bioconductor.scm (r-keggrest): Update to 1.36.3.
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* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.32.3.
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* gnu/packages/bioconductor.scm (r-iranges): Update to 2.30.1.
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* gnu/packages/bioconductor.scm (r-scry): New variable.
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* gnu/packages/bioconductor.scm (r-organism-dplyr): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/bioconductor.scm (r-bladderbatch): New variable.
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* gnu/packages/bioconductor.scm (r-pcaexplorer): New variable.
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* gnu/packages/bioconductor.scm (r-parathyroidse): New variable.
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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.
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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.
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* gnu/packages/bioconductor.scm (r-lpsymphony)[arguments]: Add build phase
'make-build-order-reproducible.
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* gnu/packages/bioconductor.scm (r-activepathways): Update to 1.1.1.
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* gnu/packages/bioconductor.scm (r-ciara): New variable.
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* gnu/packages/bioconductor.scm (r-biomartr): New variable.
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* gnu/packages/bioconductor.scm (r-infercnv): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/bioconductor.scm (r-muscat): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* 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>
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* gnu/packages/bioconductor.scm (r-affycompatible)[arguments]: Sort XML
elements before generating R code from them.
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* gnu/packages/bioconductor.scm (r-dittoseq): New variable.
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* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.24.3.
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* gnu/packages/bioconductor.scm (r-bionetstat): Update to 1.16.1.
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* gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.22.3.
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* gnu/packages/bioconductor.scm (r-ggbio): Update to 1.44.1.
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* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.10.4.
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* gnu/packages/bioconductor.scm (r-biosigner): Update to 1.24.2.
[propagated-inputs]: Add r-multiassayexperiment and r-summarizedexperiment.
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* gnu/packages/bioconductor.scm (r-ropls): Update to 1.28.2.
[propagated-inputs]: Add r-multiassayexperiment and r-summarizedexperiment.
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* gnu/packages/bioconductor.scm (r-genomicscores): Update to 2.8.2.
[propagated-inputs]: Add r-httr.
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* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.4.4.
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* gnu/packages/bioconductor.scm (r-batchelor): Update to 1.12.3.
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* gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.8.1.
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* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.6.3.
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* gnu/packages/bioconductor.scm (r-simplifyenrichment): Update to 1.6.1.
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* gnu/packages/bioconductor.scm (r-rtracklayer): Update to 1.56.1.
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* gnu/packages/bioconductor.scm (r-organismdbi): Update to 1.38.1.
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* gnu/packages/bioconductor.scm (r-limma): Update to 3.52.2.
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* gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.20.2.
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* gnu/packages/bioconductor.scm (r-restfulr): Update to 0.0.15.
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* gnu/packages/bioconductor.scm (r-antiprofiles): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/bioconductor.scm (r-annmap): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/bioconductor.scm (r-anf): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/bioconductor.scm (r-anaquin): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/bioconductor.scm (r-amaretto): New variable.
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* gnu/packages/bioconductor.scm (r-amountain): New variable.
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* gnu/packages/bioconductor.scm (r-metap): Update to 1.8.
[propagated-inputs]: Add r-mathjaxr and r-qqconf.
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