93328f8b89
gnu: r-activedriverwgs: Update to 1.2.0.
...
* gnu/packages/bioconductor.scm (r-activedriverwgs): Update to 1.2.0.
2022-09-20 17:02:09 +02:00
8f3787576c
gnu: r-htscluster: Update to 2.0.10.
...
* gnu/packages/bioconductor.scm (r-htscluster): Update to 2.0.10.
2022-09-20 17:02:09 +02:00
b1dd1f221f
gnu: r-perfmeas: Update to 1.2.5.
...
* gnu/packages/bioconductor.scm (r-perfmeas): Update to 1.2.5.
2022-09-20 17:02:09 +02:00
9c91113ee7
gnu: r-valr: Update to 0.6.5.
...
* gnu/packages/bioconductor.scm (r-valr): Update to 0.6.5.
2022-09-20 17:02:09 +02:00
47fb9d23ea
gnu: Add r-omicade4.
...
* gnu/packages/bioconductor.scm (r-omicade4): New variable.
2022-09-15 15:22:11 +02:00
d3f3968e65
gnu: Add r-made4.
...
* gnu/packages/bioconductor.scm (r-made4): New variable.
2022-09-15 15:22:11 +02:00
ad1d3f98b1
gnu: Add comments to the bottom of a few package modules.
...
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.
2022-09-10 10:45:27 +01:00
9fa3e90789
gnu: r-edger: Update to 3.38.4.
...
* gnu/packages/bioconductor.scm (r-edger): Update to 3.38.4.
[propagated-inputs]: Remove r-statmod.
2022-09-06 08:42:20 +03:00
9626ca8126
gnu: r-genomicalignments: Update to 1.32.1.
...
* gnu/packages/bioconductor.scm (r-genomicalignments): Update to 1.32.1.
2022-09-05 22:58:12 +03:00
3bf7bdccee
gnu: Add r-milor.
...
* gnu/packages/bioconductor.scm (r-milor): New variable.
2022-08-31 23:06:45 +02:00
de66e21580
gnu: r-keggrest: Update to 1.36.3.
...
* gnu/packages/bioconductor.scm (r-keggrest): Update to 1.36.3.
2022-08-29 11:26:56 +03:00
444c300e3e
gnu: r-genomeinfodb: Update to 1.32.3.
...
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.32.3.
2022-08-28 15:47:58 +03:00
10f0d0766c
gnu: r-iranges: Update to 2.30.1.
...
* gnu/packages/bioconductor.scm (r-iranges): Update to 2.30.1.
2022-08-28 13:29:05 +03:00
add211b277
gnu: Add r-scry.
...
* gnu/packages/bioconductor.scm (r-scry): New variable.
2022-08-25 11:55:12 +02:00
4a6c6484df
gnu: Add r-organism-dplyr.
...
* gnu/packages/bioconductor.scm (r-organism-dplyr): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-08-23 12:02:25 +02:00
090663a7a5
gnu: Add r-bladderbatch.
...
* gnu/packages/bioconductor.scm (r-bladderbatch): New variable.
2022-08-23 11:45:59 +02:00
f6bcde85a6
gnu: Add r-pcaexplorer.
...
* gnu/packages/bioconductor.scm (r-pcaexplorer): New variable.
2022-08-23 11:43:20 +02:00
6c21c9fab1
gnu: Add r-parathyroidse.
...
* gnu/packages/bioconductor.scm (r-parathyroidse): New variable.
2022-08-23 11:43:20 +02:00
5a9c2abf9e
gnu: Remove ‘open source’ from package descriptions.
...
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.
2022-08-14 02:00:00 +02:00
593327ef5b
gnu: r-bgx: Build without CPU tuning.
...
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.
2022-08-14 20:43:01 +02:00
8e87bbde13
gnu: r-lpsymphony: Build reproducibly.
...
* gnu/packages/bioconductor.scm (r-lpsymphony)[arguments]: Add build phase
'make-build-order-reproducible.
2022-08-14 20:43:00 +02:00
17d3880de7
gnu: r-activepathways: Update to 1.1.1.
...
* gnu/packages/bioconductor.scm (r-activepathways): Update to 1.1.1.
2022-08-10 15:44:20 +02:00
2efc787811
gnu: Add r-ciara.
...
* gnu/packages/bioconductor.scm (r-ciara): New variable.
2022-08-09 10:49:27 +02:00
3b75131be6
gnu: Add r-biomartr.
...
* gnu/packages/bioconductor.scm (r-biomartr): New variable.
2022-08-05 15:43:09 +02:00
af207dd46d
gnu: Add r-infercnv.
...
* gnu/packages/bioconductor.scm (r-infercnv): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-08-01 23:53:23 +02:00
c6800aa31e
gnu: Add r-muscat.
...
* gnu/packages/bioconductor.scm (r-muscat): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-08-01 16:08:11 +02:00
d1b60cb65b
gnu: Add comma after “i.e.” in descriptions.
...
* 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>
2022-08-01 14:08:08 +02:00
9238ba5874
gnu: r-affycompatible: Build reproducibly.
...
* gnu/packages/bioconductor.scm (r-affycompatible)[arguments]: Sort XML
elements before generating R code from them.
2022-07-15 00:07:42 +02:00
602cf66c79
gnu: Add r-dittoseq.
...
* gnu/packages/bioconductor.scm (r-dittoseq): New variable.
2022-07-04 13:48:58 +02:00
3bb39fc370
gnu: r-tcgabiolinks: Update to 2.24.3.
...
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.24.3.
2022-07-02 23:56:10 +02:00
af06365a3e
gnu: r-bionetstat: Update to 1.16.1.
...
* gnu/packages/bioconductor.scm (r-bionetstat): Update to 1.16.1.
2022-07-02 23:56:10 +02:00
26981da96b
gnu: r-bgeedb: Update to 2.22.3.
...
* gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.22.3.
2022-07-02 23:56:10 +02:00
5f03154c15
gnu: r-ggbio: Update to 1.44.1.
...
* gnu/packages/bioconductor.scm (r-ggbio): Update to 1.44.1.
2022-07-02 23:56:10 +02:00
11f30bfa3d
gnu: r-rsubread: Update to 2.10.4.
...
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.10.4.
2022-07-02 23:56:10 +02:00
0a5a06ed24
gnu: r-biosigner: Update to 1.24.2.
...
* gnu/packages/bioconductor.scm (r-biosigner): Update to 1.24.2.
[propagated-inputs]: Add r-multiassayexperiment and r-summarizedexperiment.
2022-07-02 23:56:10 +02:00
fbb6489abd
gnu: r-ropls: Update to 1.28.2.
...
* gnu/packages/bioconductor.scm (r-ropls): Update to 1.28.2.
[propagated-inputs]: Add r-multiassayexperiment and r-summarizedexperiment.
2022-07-02 23:56:10 +02:00
4aabb20226
gnu: r-genomicscores: Update to 2.8.2.
...
* gnu/packages/bioconductor.scm (r-genomicscores): Update to 2.8.2.
[propagated-inputs]: Add r-httr.
2022-07-02 23:56:10 +02:00
b7a5534e61
gnu: r-clusterprofiler: Update to 4.4.4.
...
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.4.4.
2022-07-02 23:56:10 +02:00
a17b7aabfd
gnu: r-batchelor: Update to 1.12.3.
...
* gnu/packages/bioconductor.scm (r-batchelor): Update to 1.12.3.
2022-07-02 23:56:10 +02:00
7ff0669cee
gnu: r-matrixgenerics: Update to 1.8.1.
...
* gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.8.1.
2022-07-02 23:56:10 +02:00
605eda07df
gnu: r-zellkonverter: Update to 1.6.3.
...
* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.6.3.
2022-07-02 23:56:09 +02:00
febec55f57
gnu: r-simplifyenrichment: Update to 1.6.1.
...
* gnu/packages/bioconductor.scm (r-simplifyenrichment): Update to 1.6.1.
2022-07-02 23:56:09 +02:00
c4113d3035
gnu: r-rtracklayer: Update to 1.56.1.
...
* gnu/packages/bioconductor.scm (r-rtracklayer): Update to 1.56.1.
2022-07-02 23:56:09 +02:00
5298b57d56
gnu: r-organismdbi: Update to 1.38.1.
...
* gnu/packages/bioconductor.scm (r-organismdbi): Update to 1.38.1.
2022-07-02 23:56:09 +02:00
4e6026031a
gnu: r-limma: Update to 3.52.2.
...
* gnu/packages/bioconductor.scm (r-limma): Update to 3.52.2.
2022-07-02 23:56:09 +02:00
103d4d918f
gnu: r-ensembldb: Update to 2.20.2.
...
* gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.20.2.
2022-07-02 23:56:09 +02:00
01790a6cd6
gnu: r-restfulr: Update to 0.0.15.
...
* gnu/packages/bioconductor.scm (r-restfulr): Update to 0.0.15.
2022-07-02 23:56:04 +02:00
ec23d7caa8
gnu: Add r-antiprofiles.
...
* gnu/packages/bioconductor.scm (r-antiprofiles): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-07-01 10:28:22 +02:00
3109d4a30e
gnu: Add r-annmap.
...
* gnu/packages/bioconductor.scm (r-annmap): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-07-01 10:28:21 +02:00
f004033b47
gnu: Add r-anf.
...
* gnu/packages/bioconductor.scm (r-anf): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-07-01 10:28:21 +02:00
Ricardo Wurmus
Christopher Baines
Efraim Flashner
Mădălin Ionel Patrașcu
Tobias Geerinckx-Rice
Paul A. Patience