Subject: bug#30984: closed (Re: [bug#30984] [PATCH] gnu: Add r-regioner.)

From: [email-masked] (GNU bug Tracking System)
Date: Fri, 30 Mar 2018 14:50:02 +0000

Your bug report

#30984: [PATCH] gnu: Add r-regioner.

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to [email-masked].

-- 
30984: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=30984
GNU Bug Tracking System
Contact [email-masked] with problems

Subject: Re: [bug#30984] [PATCH] gnu: Add r-regioner.
From: Leo Famulari <[email-masked]>
To: Roel Janssen <[email-masked]>
Cc: [email-masked]
Date: Fri, 30 Mar 2018 10:49:24 -0400
List-Id: <debbugs-submit.debbugs.gnu.org>

On Thu, Mar 29, 2018 at 02:23:15PM +0200, Roel Janssen wrote:
> From b6b0a7900a3d8b87efe798ff65387838b7e2487c Mon Sep 17 00:00:00 2001
> From: Roel Janssen <[email-masked]>
> Date: Thu, 29 Mar 2018 14:20:20 +0200
> Subject: [PATCH] gnu: Add r-regioner.
> 
> * gnu/packages/bioconductor.scm (r-regioner): New variable.

Thanks! Pushed as 183ce9884924794677eefca78cf445ada5551260

Subject: [PATCH] gnu: Add r-regioner.
From: Roel Janssen <[email-masked]>
To: guix-patches <[email-masked]>
Date: Thu, 29 Mar 2018 14:23:15 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

>From b6b0a7900a3d8b87efe798ff65387838b7e2487c Mon Sep 17 00:00:00 2001
From: Roel Janssen <[email-masked]>
Date: Thu, 29 Mar 2018 14:20:20 +0200
Subject: [PATCH] gnu: Add r-regioner.

* gnu/packages/bioconductor.scm (r-regioner): New variable.
---
 gnu/packages/bioconductor.scm | 32 +++++++++++++++++++++++++++++++-
 1 file changed, 31 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f557dce8e..09581d9fd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Ricardo Wurmus <[email-masked]>
+;;; Copyright © 2018 Roel Janssen <[email-masked]>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -21,7 +22,9 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix build-system r)
-  #:use-module (gnu packages))
+  #:use-module (gnu packages)
+  #:use-module (gnu packages statistics)
+  #:use-module (gnu packages bioinformatics))
 
 (define-public r-hpar
   (package
@@ -40,3 +43,30 @@
     (description "This package provides a simple interface to and data from
 the Human Protein Atlas project.")
     (license license:artistic2.0)))
+
+(define-public r-regioner
+  (package
+    (name "r-regioner")
+    (version "1.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "regioneR" version))
+       (sha256
+        (base32
+         "1vprp3l929hwzmvgskbhawfgnrymwc9n2rxd16rgagnv1dxnjxfp"))))
+    (properties `((upstream-name . "regioneR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-memoise" ,r-memoise)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-iranges" ,r-iranges)))
+    (home-page "https://bioconductor.org/packages/regioneR/")
+    (synopsis "Association analysis of genomic regions")
+    (description "This package offers a statistical framework based on
+customizable permutation tests to assess the association between genomic
+region sets and other genomic features.")
+    (license license:artistic2.0)))
-- 
2.16.2

Dear Guix,

I'd like to add “r-regioner”, which is a Bioconductor package.  I
noticed there is a “bioconductor.scm” module.  Should I add it there, or
should I add it to “bioinformatics.scm” instead?

Kind regards,
Roel Janssen