GNU bug report logs - #42126
[PATCH] gnu: Add r-transphylo

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#42126: closed ([PATCH] gnu: Add r-transphylo)
Date: Fri, 11 Sep 2020 08:53:02 +0000

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Your message dated Fri, 11 Sep 2020 10:53:14 +0200
with message-id <87blic3dad.fsf <at> 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 <at> gnu.org.)


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From: Antoine Côté <antoine.cote <at> posteo.net>
To: guix-patches <at> gnu.org
Cc: Antoine Côté <antoine.cote <at> posteo.net>
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 <at> gmail.com>
 ;;; Copyright © 2020 Naga Malleswari <nagamalli <at> riseup.net>
 ;;; Copyright © 2020 Eric Brown <ecbrown <at> ericcbrown.com>
+;;; Copyright © 2020 Antoine Côté <antoine.cote <at> 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

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: Antoine Côté <antoine.cote <at> posteo.net>
Cc: 42126-done <at> debbugs.gnu.org
Subject: Re: [bug#42126] [PATCH] gnu: Add r-transphylo
Date: Fri, 11 Sep 2020 10:53:14 +0200

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

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