bug#55615: closed ([PATCH] gnu: Add r-pscbs.)

[GNU bug Tracking System]

Your message dated Tue, 24 May 2022 23:29:36 +0200
with message-id <87wneahb5b.fsf@elephly.net>
and subject line Re: [bug#55615] [PATCH] gnu: Add r-pscbs.
has caused the debbugs.gnu.org bug report #55615,
regarding [PATCH] gnu: Add r-pscbs.
to be marked as done.

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-- 
55615: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=55615
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-pscbs.
>
>
>
>
> Date: 
>
> Tue, 24 May 2022 20:08:50 +0200
>
>
>
>
> * gnu/packages/bioconductor.scm (r-pscbs): New variable.
> ---
>  gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++
>  1 file changed, 42 insertions(+)
>
> diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
> index 80cf28c954..7fed1aa18b 100644
> --- a/gnu/packages/bioconductor.scm
> +++ b/gnu/packages/bioconductor.scm
> @@ -4560,6 +4560,48 @@ (define-public r-pcamethods
>  structure (pcaRes) to provide a common interface to the PCA results.")
>      (license license:gpl3+)))
>  
> +;; This is a CRAN package, but it depends on a Bioconductor package:
> +;; r-aroma-light, r-dnacopy..
> +(define-public r-pscbs
> +  (package
> +    (name "r-pscbs")
> +    (version "0.66.0")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (cran-uri "PSCBS" version))
> +       (sha256
> +        (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q"))))
> +    (properties `((upstream-name . "PSCBS")))
> +    (build-system r-build-system)
> +    (arguments
> +     `(#:phases
> +      (modify-phases %standard-phases
> +          (add-before 'install 'change-home-dir
> +            (lambda _
> +              ;; Change from /homeless-shelter to /tmp for write permission.
> +              (setenv "HOME" "/tmp"))))))
> +    (propagated-inputs
> +     (list r-aroma-light
> +           r-dnacopy
> +           r-future
> +           r-listenv
> +           r-matrixstats
> +           r-r-cache
> +           r-r-methodss3
> +           r-r-oo
> +           r-r-utils))
> +    (native-inputs
> +     (list r-r-rsp       ;used to build vignettes
> +           r-r-devices))
> +    (home-page "https://github.com/HenrikBengtsson/PSCBS";)
> +    (synopsis "Analysis of Parent-Specific DNA Copy Numbers")
> +    (description
> +     "Segmentation of allele-specific DNA copy number data and detection of
> +regions with abnormal copy number within each parental chromosome.  Both
> +tumor-normal paired and tumor-only analyses are supported.")
> +    (license license:gpl2+)))
> +
>  (define-public r-protgenerics
>    (package
>      (name "r-protgenerics")
>
> base-commit: 01793ed03e8aa0960bff7adc21fd270e1527e68e
> -- 
> 2.36.0
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> Re: [bug#55615] [PATCH] gnu: Add r-pscbs.
>
>
>
>
> Date: 
>
> Tue, 24 May 2022 23:29:36 +0200
>
>
>
>
> User-agent: 
>
> mu4e 1.6.10; emacs 28.0.50
>
>
>
>
> zimoun <zimon.toutoune@gmail.com> writes:
>
> > * gnu/packages/bioconductor.scm (r-pscbs): New variable.
>
> Applied with formatting changes.  Thanks!
>
> -- 
> Ricardo
>
>
> --- End Message ---