bug#36792: closed ([PATCH 03/11] gnu: Add r-all.)

[GNU bug Tracking System]

Your message dated Fri, 21 Feb 2020 18:07:33 +0100
with message-id <CAJ3okZ2GnkOKAPNwz8FwmRbZ+W+pYHiwB=address@hidden>
and subject line patches merged
has caused the debbugs.gnu.org bug report #36797,
regarding [PATCH 03/11] gnu: Add r-all.
to be marked as done.

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-- 
36797: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH 03/11] gnu: Add r-all.
>
>
>
>
> Date: 
>
> Wed, 24 Jul 2019 20:21:56 +0200
>
>
>
>
> * gnu/packages/bioconductor.scm (r-all): New variable.
> ---
>  gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++
>  1 file changed, 30 insertions(+)
>
> diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
> index e5a2d66b2d..18b5711496 100644
> --- a/gnu/packages/bioconductor.scm
> +++ b/gnu/packages/bioconductor.scm
> @@ -865,6 +865,36 @@ which were then sequenced to a depth of ~4 million reads 
> per library,
>  resulting in a complete gene expression profile for each cell.")
>      (license license:artistic2.0)))
>  
> +(define-public r-all
> +  (package
> +    (name "r-all")
> +    (version "1.26.0")
> +    (source (origin
> +              (method url-fetch)
> +              ;; We cannot use bioconductor-uri here because this tarball is
> +              ;; located under "data/experiment/" instead of "bioc/".
> +              (uri (string-append "https://www.bioconductor.org/packages/";
> +                                  "release/data/experiment/src/contrib/"
> +                                  "ALL_" version ".tar.gz"))
> +              (sha256
> +               (base32
> +                "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
> +    (properties
> +      `((upstream-name . "ConsensusClusterPlus")))
> +    (build-system r-build-system)
> +    (propagated-inputs
> +      `(("r-biobase" ,r-biobase)))
> +    (home-page
> +      "https://bioconductor.org/packages/ALL";)
> +    (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
> +    (description
> +      "The data consist of microarrays from 128 different individuals with
> +acute lymphoblastic leukemia (ALL). A number of additional covariates are
> +available. The data have been normalized (using rma) and it is the jointly
> +normalized data that are available here. The data are presented in the form of
> +an exprSet object.")
> +    (license license:artistic2.0)))
> +
>  
>  ;;; Packages
>  
> -- 
> 2.21.0
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> patches merged
>
>
>
>
> Date: 
>
> Fri, 21 Feb 2020 18:07:33 +0100
>
>
>
>
> Dear,
>
> All the patches are merged now; except r-flowpeaks. Because this
> package use Artistic1.0 which is not enough clear to be considered
> "free" [1,2] (GNU's point of view [3]) and upstream are not
> responsive, let clean the bug tracker. :-)
>
> [1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797#16
> [2] https://lists.gnu.org/archive/html/guix-devel/2019-12/msg00286.html
> [3] https://www.gnu.org/licenses/license-list.en.html#ArtisticLicense
>
> All the best,
> simon
>
>
> --- End Message ---