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2848 Commits

Author SHA1 Message Date
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
47fb9d23ea
gnu: Add r-omicade4. 
* gnu/packages/bioconductor.scm (r-omicade4): New variable.
 2022-09-15 15:22:11 +02:00
Ricardo Wurmus
d3f3968e65
gnu: Add r-made4. 
* gnu/packages/bioconductor.scm (r-made4): New variable.
 2022-09-15 15:22:11 +02:00
Christopher Baines
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
Efraim Flashner
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
Efraim Flashner
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
Ricardo Wurmus
3bf7bdccee
gnu: Add r-milor. 
* gnu/packages/bioconductor.scm (r-milor): New variable.
 2022-08-31 23:06:45 +02:00
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Ricardo Wurmus
add211b277
gnu: Add r-scry. 
* gnu/packages/bioconductor.scm (r-scry): New variable.
 2022-08-25 11:55:12 +02:00
Mădălin Ionel Patrașcu
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
Ricardo Wurmus
090663a7a5
gnu: Add r-bladderbatch. 
* gnu/packages/bioconductor.scm (r-bladderbatch): New variable.
 2022-08-23 11:45:59 +02:00
Mădălin Ionel Patrașcu
f6bcde85a6
gnu: Add r-pcaexplorer. 
* gnu/packages/bioconductor.scm (r-pcaexplorer): New variable.
 2022-08-23 11:43:20 +02:00
Mădălin Ionel Patrașcu
6c21c9fab1
gnu: Add r-parathyroidse. 
* gnu/packages/bioconductor.scm (r-parathyroidse): New variable.
 2022-08-23 11:43:20 +02:00
Tobias Geerinckx-Rice
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
2efc787811
gnu: Add r-ciara. 
* gnu/packages/bioconductor.scm (r-ciara): New variable.
 2022-08-09 10:49:27 +02:00
Ricardo Wurmus
3b75131be6
gnu: Add r-biomartr. 
* gnu/packages/bioconductor.scm (r-biomartr): New variable.
 2022-08-05 15:43:09 +02:00
Mădălin Ionel Patrașcu
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
Mădălin Ionel Patrașcu
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
Paul A. Patience
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
Ricardo Wurmus
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
Ricardo Wurmus
602cf66c79
gnu: Add r-dittoseq. 
* gnu/packages/bioconductor.scm (r-dittoseq): New variable.
 2022-07-04 13:48:58 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Mădălin Ionel Patrașcu
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
Mădălin Ionel Patrașcu
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
Mădălin Ionel Patrașcu
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