bug#44311: closed ([PATCH] gnu: Add r-deconstructsigs.)

[GNU bug Tracking System]

Your message dated Tue, 22 Dec 2020 23:38:30 +0100
with message-id <87wnx9mpp5.fsf@elephly.net>
and subject line Re: [bug#44311] [PATCH] gnu: Add r-deconstructsigs.
has caused the debbugs.gnu.org bug report #44311,
regarding [PATCH] gnu: Add r-deconstructsigs.
to be marked as done.

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44311: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=44311
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-deconstructsigs.
>
>
>
>
> Date: 
>
> Thu, 29 Oct 2020 22:39:49 +0530
>
>
>
>
> * gnu/packages/cran.scm (r-deconstructsigs): New variable.
> ---
>  gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
>  1 file changed, 30 insertions(+)
>
> diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
> index 82caaf54f6..75d9ae7de2 100644
> --- a/gnu/packages/cran.scm
> +++ b/gnu/packages/cran.scm
> @@ -24715,3 +24715,33 @@ modal regression and conditional density estimation in 
> the
>  presence/absence of measurement error. Bandwidth selection is 
>  also provided for each method.")
>      (license license:gpl2+)))
> +
> +(define-public r-deconstructsigs
> +  (package
> +    (name "r-deconstructsigs")
> +    (version "1.8.0")
> +    (source
> +      (origin
> +        (method url-fetch)
> +        (uri (cran-uri "deconstructSigs" version))
> +        (sha256
> +          (base32
> +            "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
> +    (properties
> +      `((upstream-name . "deconstructSigs")))
> +    (build-system r-build-system)
> +    (propagated-inputs
> +      `(("r-bsgenome" ,r-bsgenome)
> +        ("r-bsgenome-hsapiens-ucsc-hg19"
> +         ,r-bsgenome-hsapiens-ucsc-hg19)
> +        ("r-genomeinfodb" ,r-genomeinfodb)
> +        ("r-reshape2" ,r-reshape2)))
> +    (home-page
> +      "https://github.com/raerose01/deconstructSigs";)
> +    (synopsis "Identifies Signatures Present in a Tumor Sample")
> +    (description
> +      "Takes sample information in the form of the fraction of 
> +mutations in each of 96 trinucleotide contexts and identifies 
> +the weighted combination of published signatures that, when summed, 
> +most closely reconstructs the mutational profile.")
> +    (license license:gpl2+)))
> -- 
> 2.28.0
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> Re: [bug#44311] [PATCH] gnu: Add r-deconstructsigs.
>
>
>
>
> Date: 
>
> Tue, 22 Dec 2020 23:38:30 +0100
>
>
>
>
> User-agent: 
>
> mu4e 1.4.13; emacs 27.1
>
>
>
>
> Hi Aniket,
>
> > * gnu/packages/cran.scm (r-deconstructsigs): New variable.
>
> I’m sorry, but we need to drop this patch because
> gnu/packages/bioconductor.scm already contains this definition.
>
> “Already” really isn’t quite the right word, because you submitted your
> patch before I added the definition to the bioconductor module when
> Simon and I upgraded our CRAN and Bioconductor packages.
>
> This package is in the bioconductor module because it depends on the
> Bioconductor package r-bsgenome-hsapiens-ucsc-hg19.
>
> -- 
> Ricardo
>
>
> --- End Message ---