GNU bug report logs -
#42126
[PATCH] gnu: Add r-transphylo
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Reported by: Antoine Côté <antoine.cote <at> posteo.net>
Date: Mon, 29 Jun 2020 15:15:02 UTC
Severity: normal
Tags: patch
Done: Ricardo Wurmus <rekado <at> elephly.net>
Bug is archived. No further changes may be made.
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:
bug#42126
; Package
guix-patches
.
(Mon, 29 Jun 2020 15:15:02 GMT)
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Acknowledgement sent
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Antoine Côté <antoine.cote <at> posteo.net>
:
New bug report received and forwarded. Copy sent to
guix-patches <at> gnu.org
.
(Mon, 29 Jun 2020 15:15:02 GMT)
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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
---
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
Reply sent
to
Ricardo Wurmus <rekado <at> elephly.net>
:
You have taken responsibility.
(Fri, 11 Sep 2020 08:53:02 GMT)
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Antoine Côté <antoine.cote <at> posteo.net>
:
bug acknowledged by developer.
(Fri, 11 Sep 2020 08:53:02 GMT)
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Message #10 received at 42126-done <at> debbugs.gnu.org (full text, mbox):
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
bug archived.
Request was from
Debbugs Internal Request <help-debbugs <at> gnu.org>
to
internal_control <at> debbugs.gnu.org
.
(Fri, 09 Oct 2020 11:24:07 GMT)
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This bug report was last modified 3 years and 199 days ago.
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