GNU bug report logs - #50570
[PATCH 0/2] R packages

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 0/2] R packages
Date: Mon, 13 Sep 2021 16:18:12 +0200

Hi,

Trivial addition.  The package r-presto does not have a tag version, hence the
commit; they say in README about CRAN but the archive does not contain it, or
I miss it.

All the best,
simon


zimoun (2):
  gnu: Add r-simplifyenrichment.
  gnu: Add r-presto.

 gnu/packages/bioconductor.scm   | 40 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++
 2 files changed, 74 insertions(+)


base-commit: 53f54d4aa252fed425180641f27094600522c4f1
-- 
2.32.0

Message #8 received at 50570 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 50570 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 1/2] gnu: Add r-simplifyenrichment.
Date: Mon, 13 Sep 2021 16:20:27 +0200

* gnu/packages/bioconductor.scm (r-simplifyenrichment): New variable.
---
 gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 25202410e5..e59ba07d23 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4236,6 +4236,46 @@ purposes.  The package also contains legacy support for early single-end,
 ungapped alignment formats.")
     (license license:artistic2.0)))
 
+(define-public r-simplifyenrichment
+  (package
+    (name "r-simplifyenrichment")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "simplifyEnrichment" version))
+       (sha256
+        (base32
+         "0rqa414kvyjjmj4932zk39rqa14z13b57rkrxdrf16jmq2r437vh"))))
+    (properties
+     `((upstream-name . "simplifyEnrichment")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-circlize" ,r-circlize)
+       ("r-clue" ,r-clue)
+       ("r-cluster" ,r-cluster)
+       ("r-complexheatmap" ,r-complexheatmap)
+       ("r-digest" ,r-digest)
+       ("r-getoptlong" ,r-getoptlong)
+       ("r-go-db" ,r-go-db)
+       ("r-gosemsim" ,r-gosemsim)
+       ("r-matrix" ,r-matrix)
+       ("r-org-hs-eg-db" ,r-org-hs-eg-db)
+       ("r-proxyc" ,r-proxyc)
+       ("r-slam" ,r-slam)
+       ("r-tm" ,r-tm)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/jokergoo/simplifyEnrichment")
+    (synopsis "Simplify Functional Enrichment Results")
+    (description "This package provides a new clustering algorithm, binary
+cut, for clustering similarity matrices of functional terms is implemeted in
+this package.  It also provideds functionalities for visualizing, summarizing
+and comparing the clusterings.")
+    (license license:expat)))
+
+
 (define-public r-trajectoryutils
   (package
     (name "r-trajectoryutils")
-- 
2.32.0

Message #11 received at 50570 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 50570 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 2/2] gnu: Add r-presto.
Date: Mon, 13 Sep 2021 16:20:28 +0200

* gnu/packages/bioinformatics.scm (r-presto): New variable.
---
 gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c3ab0ce354..647feff9ec 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -21,6 +21,7 @@
 ;;; Copyright © 2020 Bonface Munyoki Kilyungi <bonfacemunyoki <at> gmail.com>
 ;;; Copyright © 2021 Tim Howes <timhowes <at> lavabit.com>
 ;;; Copyright © 2021 Hong Li <hli <at> mdc-berlin.de>
+;;; Copyright © 2021 Simon Tournier <zimon.toutoune <at> gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -7417,6 +7418,39 @@ sequence.")
     (supported-systems '("i686-linux" "x86_64-linux"))
     (license license:bsd-3)))
 
+(define-public r-presto
+  (let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad")
+        (revision "0"))
+    (package
+      (name "r-presto")
+      (version (git-version "1.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/immunogenomics/presto")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1c3fmag4r4p2lvbvxlxyck9dvfw1prbwcl9665mmlx4a35750hk8"))))
+      (properties `((upstream . "presto")))
+      (build-system r-build-system)
+      (propagated-inputs
+       `(("r-data-table" ,r-data-table)
+         ("r-deseq2" ,r-deseq2)
+         ("r-dplyr" ,r-dplyr)
+         ("r-matrix" ,r-matrix)
+         ("r-rcpp" ,r-rcpp)
+         ("r-rcpparmadillo" ,r-rcpparmadillo)
+         ("r-reshape2" ,r-reshape2)
+         ("r-rlang" ,r-rlang)
+         ("r-tidyr" ,r-tidyr)))
+      (home-page "https://github.com/immunogenomics/presto")
+      (synopsis "Fast Functions for Differential Expression using Wilcox and AUC")
+      (description "This package performs a fast Wilcoxon rank sum test and
+auROC analysis.")
+      (license license:gpl3))))
+
 (define-public r-snapatac
   (package
     (name "r-snapatac")
-- 
2.32.0

Message #16 received at 50570-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: 50570-done <at> debbugs.gnu.org
Subject: Re: [bug#50570] [PATCH 0/2] R packages
Date: Mon, 20 Sep 2021 22:13:45 +0200

Thank you for the patches.  Pushed to the “master” branch with 
commit f80824fe0997f3e5d73ef16b8d42d248ce31cc69.

-- 
Ricardo

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