GNU bug report logs - #34755
[PATCH] gnu: Remove duplicate r-dnacopy package.

Previous Next

To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 34755 in the body.
You can then email your comments to 34755 AT debbugs.gnu.org in the normal way.

Toggle the display of automated, internal messages from the tracker.

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

From: Christopher Baines <mail <at> cbaines.net>
To: guix-patches <at> gnu.org
Subject: [PATCH] gnu: Remove duplicate r-dnacopy package.
Date: Tue,  5 Mar 2019 08:14:08 +0000

This package definition duplicates the earlier definition in the (gnu packages
bioinformatics) module.

This reverts commit c18dccffa20bf09826758210d457d1df477f959c.

* gnu/packages/bioconductor.scm (r-dnacopy): Remove this variable.
---
 gnu/packages/bioconductor.scm | 23 -----------------------
 1 file changed, 23 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ae9d7070c3..dfd3de5901 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -27,7 +27,6 @@
   #:use-module (gnu packages bioinformatics)
   #:use-module (gnu packages cran)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages gcc)
   #:use-module (gnu packages graph)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages statistics)
@@ -1178,28 +1177,6 @@ Viewer (SAV) files, access data, and generate QC plots.")
 sequencing data.")
     (license license:gpl2+)))
 
-(define-public r-dnacopy
-  (package
-    (name "r-dnacopy")
-    (version "1.56.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "DNAcopy" version))
-       (sha256
-        (base32
-         "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
-    (properties `((upstream-name . "DNAcopy")))
-    (build-system r-build-system)
-    (native-inputs `(("gfortran" ,gfortran)))
-    (home-page "https://bioconductor.org/packages/DNAcopy")
-    (synopsis "DNA copy number data analysis")
-    (description
-     "This package implements the @dfn{circular binary segmentation} (CBS)
-algorithm to segment DNA copy number data and identify genomic regions with
-abnormal copy number.")
-    (license license:gpl2+)))
-
 ;; This is a CRAN package, but it uncharacteristically depends on a
 ;; Bioconductor package.
 (define-public r-htscluster
-- 
2.20.1

Message #10 received at 34755-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Christopher Baines <mail <at> cbaines.net>
Cc: 34755-done <at> debbugs.gnu.org
Subject: Re: [bug#34755] [PATCH] gnu: Remove duplicate r-dnacopy package.
Date: Tue, 05 Mar 2019 10:25:17 +0100

Christopher Baines <mail <at> cbaines.net> writes:

> This package definition duplicates the earlier definition in the (gnu packages
> bioinformatics) module.
>
> This reverts commit c18dccffa20bf09826758210d457d1df477f959c.
>
> * gnu/packages/bioconductor.scm (r-dnacopy): Remove this variable.

Thanks for noticing this.

I’d rather remove the packgae from (gnu packages bioinformatics).  I’ll
take care of this today.

-- 
Ricardo

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.