[debbugs-tracker] bug#34755: closed ([PATCH] gnu: Remove duplicate r-dnacopy package.)

[GNU bug Tracking System]

Your message dated Tue, 05 Mar 2019 10:25:17 +0100
with message-id <address@hidden>
and subject line Re: [bug#34755] [PATCH] gnu: Remove duplicate r-dnacopy 
package.
has caused the debbugs.gnu.org bug report #34755,
regarding [PATCH] gnu: Remove duplicate r-dnacopy package.
to be marked as done.

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-- 
34755: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=34755
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> --- Begin Message ---
>
>
>
> 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
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> Re: [bug#34755] [PATCH] gnu: Remove duplicate r-dnacopy package.
>
>
>
>
> Date: 
>
> Tue, 05 Mar 2019 10:25:17 +0100
>
>
>
>
> User-agent: 
>
> mu4e 1.0; emacs 26.1
>
>
>
>
> Christopher Baines <address@hidden> 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
>
>
>
> --- End Message ---