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Author SHA1 Message Date
Ricardo Wurmus
eed76ad91a
gnu: r-flowviz: Update to 1.60.2. 
* gnu/packages/bioconductor.scm (r-flowviz): Update to 1.60.2.
 2022-10-03 19:08:08 +02:00
Ricardo Wurmus
f82d20caae
gnu: r-ggcyto: Update to 1.24.1. 
* gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.24.1.
 2022-10-03 19:08:08 +02:00
Ricardo Wurmus
1c3750c9ea
gnu: r-ncdfflow: Update to 2.42.1. 
* gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.42.1.
 2022-10-03 19:08:08 +02:00
Ricardo Wurmus
23e42e77d4
gnu: r-rsubread: Update to 2.10.5. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.10.5.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
597106f234
gnu: r-rgadem: Update to 2.44.1. 
* gnu/packages/bioconductor.scm (r-rgadem): Update to 2.44.1.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
83f0c1a39d
gnu: r-enrichplot: Update to 1.16.2. 
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.16.2.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
842431a036
gnu: r-dose: Update to 3.22.1. 
* gnu/packages/bioconductor.scm (r-dose): Update to 3.22.1.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
2b4a7fa22e
gnu: r-residualmatrix: Update to 1.6.1. 
* gnu/packages/bioconductor.scm (r-residualmatrix): Update to 1.6.1.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
1cb30ba714
gnu: r-ggtree: Update to 3.4.4. 
* gnu/packages/bioconductor.scm (r-ggtree): Update to 3.4.4.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
a047448aad
gnu: r-treeio: Update to 1.20.2. 
* gnu/packages/bioconductor.scm (r-treeio): Update to 1.20.2.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
41f029c12a
gnu: r-scaledmatrix: Update to 1.4.1. 
* gnu/packages/bioconductor.scm (r-scaledmatrix): Update to 1.4.1.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
e581479be8
gnu: r-diffbind: Update to 3.6.4. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.6.4.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
309cfcedca
gnu: r-zellkonverter: Update to 1.6.5. 
* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.6.5.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
039d894b9d
gnu: r-limma: Update to 3.52.4. 
* gnu/packages/bioconductor.scm (r-limma): Update to 3.52.4.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
a16c87fae1
gnu: r-genomicfeatures: Update to 1.48.4. 
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.48.4.
 2022-10-03 19:08:06 +02:00
Ricardo Wurmus
a15ad5ebe3
gnu: r-genomeinfodb: Update to 1.32.4. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.32.4.
 2022-10-03 19:08:06 +02:00
Ricardo Wurmus
ba6a3e7d39
gnu: r-gage: Update to 2.46.1. 
* gnu/packages/bioconductor.scm (r-gage): Update to 2.46.1.
 2022-10-03 19:08:06 +02:00
Ricardo Wurmus
c82320aa21
gnu: r-complexheatmap: Update to 2.12.1. 
* gnu/packages/bioconductor.scm (r-complexheatmap): Update to 2.12.1.
 2022-10-03 19:08:06 +02:00
Ricardo Wurmus
038eeeaf2a
gnu: r-chipseeker: Update to 1.32.1. 
* gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.32.1.
[propagated-inputs]: Add r-ggvenndiagram.
 2022-10-03 19:08:06 +02:00
Ricardo Wurmus
15243c2f84
gnu: r-biostrings: Update to 2.64.1. 
* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.64.1.
 2022-10-03 19:08:06 +02:00
Ricardo Wurmus
29a947216c
gnu: r-annotationforge: Update to 1.38.1. 
* gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.38.1.
 2022-10-03 19:08:06 +02:00
Ricardo Wurmus
96b560ac8b
gnu: r-dearseq: Update to 1.8.4. 
* gnu/packages/bioconductor.scm (r-dearseq): Update to 1.8.4.
 2022-10-03 19:08:03 +02:00
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