GNU bug report logs - #47171
[PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).

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From: zimoun <zimon.toutoune <at> gmail.com>
To: 47171 <at> debbugs.gnu.org
Cc: rekado <at> elephly.net, zimoun <zimon.toutoune <at> gmail.com>
Subject: [bug#47171] [PATCH v2 2/3] gnu: r-absfiltergsea: Move to (gnu packages bioconductor).
Date: Wed, 17 Mar 2021 21:14:13 +0100

* gnu/packages/cran.scm (r-absfiltergsea): Move this variable from here...
* gnu/packages/bioconductor.scm (r-absfiltergsea): ...to here.
---
 gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++
 gnu/packages/cran.scm         | 27 ---------------------------
 2 files changed, 28 insertions(+), 27 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b5ac2750f3..6530a31fb5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1294,6 +1294,34 @@ naming and share the same rich and consistent \"Vector API\" as much as
 possible.")
     (license license:artistic2.0)))
 
+;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
+(define-public r-absfiltergsea
+  (package
+    (name "r-absfiltergsea")
+    (version "1.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "AbsFilterGSEA" version))
+       (sha256
+        (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
+    (properties `((upstream-name . "AbsFilterGSEA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-deseq" ,r-deseq)
+       ("r-limma" ,r-limma)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
+    (synopsis "Improved false positive control of gene-permuting with absolute filtering")
+    (description
+     "This package provides a function that performs gene-permuting of a gene-set
+enrichment analysis (GSEA) calculation with or without the absolute filtering.
+  Without filtering, users can perform (original) two-tailed or one-tailed
+absolute GSEA.")
+    (license license:gpl2)))
+
 ;; This is a CRAN package, but it depends on r-biobase from Bioconductor.
 (define-public r-bisquerna
   (package
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 93fe44c25c..54d895e9fe 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -26591,33 +26591,6 @@ include Markov models of discrete and continuous trait evolution and constant
 rate speciation and extinction.")
     (license license:gpl2+)))
 
-(define-public r-absfiltergsea
-  (package
-    (name "r-absfiltergsea")
-    (version "1.5.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "AbsFilterGSEA" version))
-       (sha256
-        (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
-    (properties `((upstream-name . "AbsFilterGSEA")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-deseq" ,r-deseq)
-       ("r-limma" ,r-limma)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)))
-    (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
-    (synopsis "Improved false positive control of gene-permuting with absolute filtering")
-    (description
-     "This package provides a function that performs gene-permuting of a gene-set
-enrichment analysis (GSEA) calculation with or without the absolute filtering.
-  Without filtering, users can perform (original) two-tailed or one-tailed
-absolute GSEA.")
-    (license license:gpl2)))
-
 (define-public r-calculus
   (package
     (name "r-calculus")
-- 
2.30.1

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