bug#42126: closed ([PATCH] gnu: Add r-transphylo)

[GNU bug Tracking System]

Your message dated Fri, 11 Sep 2020 10:53:14 +0200
with message-id <87blic3dad.fsf@elephly.net>
and subject line Re: [bug#42126] [PATCH] gnu: Add r-transphylo
has caused the debbugs.gnu.org bug report #42126,
regarding [PATCH] gnu: Add r-transphylo
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs@gnu.org.)


-- 
42126: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=42126
GNU Bug Tracking System
Contact help-debbugs@gnu.org with problems
> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-transphylo
>
>
>
>
> Date: 
>
> Mon, 29 Jun 2020 11:05:18 -0400
>
>
>
>
> ---
>  gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
>  1 file changed, 25 insertions(+)
>
> diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
> index 70af2d30f0..749eee7856 100644
> --- a/gnu/packages/cran.scm
> +++ b/gnu/packages/cran.scm
> @@ -21,6 +21,7 @@
>  ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
>  ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
>  ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
> +;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
>  ;;;
>  ;;; This file is part of GNU Guix.
>  ;;;
> @@ -22372,3 +22373,27 @@ using @dfn{SHAP} (Shapley additive explanation) 
> visualization plots for
>  and force plot.  It relies on the @code{XGBoost} package to produce SHAP
>  values.")
>      (license license:expat)))
> +
> +(define-public r-transphylo
> +  (package
> +  (name "r-transphylo")
> +  (version "1.4.4")
> +  (source
> +    (origin
> +      (method url-fetch)
> +      (uri (cran-uri "TransPhylo" version))
> +      (sha256
> +        (base32
> +          "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9"))))
> +  (properties `((upstream-name . "TransPhylo")))
> +  (build-system r-build-system)
> +  (propagated-inputs
> +    `(("r-ape" ,r-ape) ("r-rcpp" ,r-rcpp)))
> +  (native-inputs `(("r-knitr" ,r-knitr)))
> +  (home-page
> +    "https://cran.r-project.org/web/packages/TransPhylo/";)
> +  (synopsis
> +    "Inference of Transmission Tree from a Dated Phylogeny")
> +  (description
> +    "Inference of transmission tree from a dated phylogeny.  Includes methods 
> to simulate and analyse outbreaks.  The methodology is described in Didelot et 
> al. (2014) <doi:10.1093/molbev/msu121>, Didelot et al. (2017) 
> <doi:10.1093/molbev/msw275>.")
> +  (license license:gpl2+)))
> -- 
> 2.27.0
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> Re: [bug#42126] [PATCH] gnu: Add r-transphylo
>
>
>
>
> Date: 
>
> Fri, 11 Sep 2020 10:53:14 +0200
>
>
>
>
> User-agent: 
>
> mu4e 1.4.13; emacs 27.1
>
>
>
>
> Hi Antoine,
>
> thank you for your patch!
>
> I have updated the description and synopsis, fixed the indentation, and
> pushed the patch to the “master” branch with commit 5412b14ba6.
>
> My apologies for the delay!
>
> -- 
> Ricardo
>
>
> --- End Message ---