bug#51422: closed ([PATCH] gnu: Add r-phyloseq)

[GNU bug Tracking System]

Your message dated Wed, 01 Dec 2021 09:34:05 +0100
with message-id <87wnkosoy4.fsf@elephly.net>
and subject line [PATCH] gnu: Add r-phyloseq
has caused the debbugs.gnu.org bug report #51422,
regarding [PATCH] gnu: Add r-phyloseq
to be marked as done.

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51422: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=51422
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> --- Begin Message ---
>
>
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> Subject: 
>
> [PATCH] gnu: Add r-phyloseq
>
>
>
>
> Date: 
>
> Tue, 26 Oct 2021 23:27:52 +0200
>
>
>
>
> From: Nicolas Vallet <nicolas.vallet@inserm.fr>
>
> * gnu/packages/cran.scm (r-phyloseq): New variable
> ---
>  gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++
>  1 file changed, 40 insertions(+)
>
> diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
> index 90a0e1f288..8dc875de69 100644
> --- a/gnu/packages/bioconductor.scm
> +++ b/gnu/packages/bioconductor.scm
> @@ -11,6 +11,7 @@
>  ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
>  ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
>  ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
> +;;; Copyright © 2021 Nicolas Vallet <nls.vallet@gmail.com>
>  ;;;
>  ;;; This file is part of GNU Guix.
>  ;;;
> @@ -14813,3 +14814,42 @@ and other associated metadata.  De novo transcriptomes 
> can be linked to the
>  appropriate sources with linkedTxomes and shared for computational
>  reproducibility.")
>      (license license:gpl2)))
> +
> +
> +(define-public r-phyloseq
> +  (package
> +   (name "r-phyloseq")
> +   (version "1.36.0")
> +   (source
> +    (origin
> +     (method url-fetch)
> +     (uri (bioconductor-uri "phyloseq" version))
> +     (sha256
> +      (base32 "192gv00xfnv9ljkgb0iw8sqzsay4f3vllyyc1slzsn15713fc4pi"))))
> +   (properties `((upstream-name . "phyloseq")))
> +   (build-system r-build-system)
> +   (propagated-inputs
> +    `(("r-ade4" ,r-ade4)
> +      ("r-ape" ,r-ape)
> +      ("r-biobase" ,r-biobase)
> +      ("r-biocgenerics" ,r-biocgenerics)
> +      ("r-biomformat" ,r-biomformat)
> +      ("r-biostrings" ,r-biostrings)
> +      ("r-cluster" ,r-cluster)
> +      ("r-data-table" ,r-data-table)
> +      ("r-foreach" ,r-foreach)
> +      ("r-ggplot2" ,r-ggplot2)
> +      ("r-igraph" ,r-igraph)
> +      ("r-multtest" ,r-multtest)
> +      ("r-plyr" ,r-plyr)
> +      ("r-reshape2" ,r-reshape2)
> +      ("r-scales" ,r-scales)
> +      ("r-vegan" ,r-vegan)))
> +   (native-inputs `(("r-knitr" ,r-knitr)))
> +   (home-page "https://github.com/joey711/phyloseq";)
> +   (synopsis "Handling and analysis of high-throughput microbiome census data")
> +   (description
> +    "Phyloseq provides a set of classes and
> +tools to facilitate the import, storage, analysis,
> +and graphical display of microbiome census data.")
> +   (license license:agpl3+)))
>
> base-commit: c6adc0947396daa6d85ab08837f9cbc86f4d8722
> -- 
> 2.25.1
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-phyloseq
>
>
>
>
> Date: 
>
> Wed, 01 Dec 2021 09:34:05 +0100
>
>
>
>
> User-agent: 
>
> mu4e 1.6.10; emacs 28.0.50
>
>
>
>
> Hi,
>
> thank you for the patch!  I applied it to the “master” branch with 
> trivial changes.  I also upgraded it to 1.38.0.
>
> My apologies for the delay!
>
> --
> Ricardo
>
>
> --- End Message ---