bug#71476: closed ([PATCH] gnu: Add r-rphyloxml.)

[GNU bug Tracking System]

Your message dated Fri, 28 Jun 2024 22:49:52 +0200
with message-id <87zfr4vllb.fsf@elephly.net>
and subject line [PATCH] gnu: Add r-rphyloxml.
has caused the debbugs.gnu.org bug report #71476,
regarding [PATCH] gnu: Add r-rphyloxml.
to be marked as done.

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-- 
71476: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=71476
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-rphyloxml.
>
>
>
>
> Date: 
>
> Mon, 10 Jun 2024 15:41:37 +0000
>
>
>
>
> * gnu/packages/bioinformatics.scm (r-rphyloxml): New variable.
>
> Change-Id: I5b799986064f2af5fe74454f2e78fea7d9947260
> ---
>  gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++
>  1 file changed, 43 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index cecd94bbb7..3282258b48 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -14096,6 +14096,49 @@ (define-public sambamba
>  sort, markdup, and depth.")
>      (license license:gpl2+)))
>  
> +(define-public r-rphyloxml
> +  (let ((commit "a30e39249239b2de01d6964ae2a2205a6c48b475")
> +        (revision "1"))
> +    (package
> +      (name "r-rphyloxml")
> +      (version (git-version "0.0-9000" revision commit))
> +      (source
> +       (origin
> +         (method git-fetch)
> +         (uri (git-reference
> +               (url "https://github.com/USCbiostats/rphyloxml";)
> +               (commit commit)))
> +         (file-name (git-file-name name version))
> +         (sha256
> +          (base32 "15ijzqvjxx6vqyqlg5asdbqlhw1g0ix6palf1rism3si0qapddgw"))))
> +      (properties `((upstream-name . "rphyloxml")))
> +      (build-system r-build-system)
> +      (arguments
> +       (list
> +        #:modules '((guix build r-build-system)
> +                    (guix build minify-build-system)
> +                    (guix build utils)
> +                    (ice-9 match))
> +        #:imported-modules `(,@%r-build-system-modules (guix build
> +                                                        minify-build-system))
> +        #:phases '(modify-phases %standard-phases
> +                    (add-after 'unpack 'process-javascript
> +                      (lambda* (#:key inputs #:allow-other-keys)
> +                        (with-directory-excursion "inst/"
> +                          (for-each (match-lambda
> +                                      ((source . target) (minify source
> +                                                                 #:target
> +                                                                 target)))
> +                                    '())))))))
> +      (propagated-inputs (list r-ape r-xml2))
> +      (native-inputs (list esbuild))
> +      (home-page "https://github.com/USCbiostats/rphyloxml";)
> +      (synopsis "Read and write phyloXML files in R")
> +      (description
> +       "The package reads phylogenetic data in the @code{phyloXML} format.
> +It also includes functions for writing data in this format.")
> +      (license license:expat))))
> +
>  (define-public ritornello
>    (package
>      (name "ritornello")
>
> base-commit: 2b2337f275a6421a0d0964c54987df4ac74162e6
> -- 
> 2.34.1
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-rphyloxml.
>
>
>
>
> Date: 
>
> Fri, 28 Jun 2024 22:49:52 +0200
>
>
>
>
> Thanks for the patch.  This one was incomplete: the importer only
> generates a skeleton to replace minified JavaScript files.  I fleshed it
> out and added the missing inputs.
>
> -- 
> Ricardo
>
>
> --- End Message ---