GNU bug report logs - #75750
[PATCH] gnu: Add r-phytools.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
Subject: bug#75750: closed (Re: [bug#75750] [PATCH] gnu: Add r-phytools.)
Date: Wed, 22 Jan 2025 12:00:02 +0000

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Your bug report

#75750: [PATCH] gnu: Add r-phytools.

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to 75750 <at> debbugs.gnu.org.

-- 
75750: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=75750
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
Cc: 75750-done <at> debbugs.gnu.org, Laurent Gatto <laurent.gatto <at> gmail.com>,
 Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: Re: [bug#75750] [PATCH] gnu: Add r-phytools.
Date: Wed, 22 Jan 2025 12:58:50 +0100

Navid Afkhami <navid.afkhami <at> mdc-berlin.de> writes:

> * gnu/packages/cran.scm (r-phytools): New variable.

Applied, thank you!

-- 
Ricardo

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From: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add r-phytools.
Date: Wed, 22 Jan 2025 09:09:14 +0000

* gnu/packages/cran.scm (r-phytools): New variable.

Change-Id: Ie4fa9f40febf3b114a3da38b9cdf668e8ac415ca
---
 gnu/packages/cran.scm | 45 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 936f3cf593..7f822be32a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -38153,6 +38153,51 @@ (define-public r-phylogram
 across a wide array of bioinformatic R packages.")
     (license license:gpl3)))
 
+(define-public r-phytools
+  (package
+    (name "r-phytools")
+    (version "2.4-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "phytools" version))
+       (sha256
+        (base32 "1i25dlikdx9av5653ra2709sjm9fc3fsis1yfsb7zagivi408ph9"))))
+    (properties `((upstream-name . "phytools")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-ape
+                             r-clustergeneration
+                             r-coda
+                             r-combinat
+                             r-deoptim
+                             r-doparallel
+                             r-expm
+                             r-foreach
+                             r-maps
+                             r-mass
+                             r-mnormt
+                             r-nlme
+                             r-numderiv
+                             r-optimparallel
+                             r-phangorn
+                             r-scatterplot3d))
+    (home-page "https://github.com/liamrevell/phytools")
+    (synopsis "Phylogenetic tools for comparative biology")
+    (description
+     "This package offers extensive tools for phylogenetic analysis.
+It focuses on phylogenetic comparative biology but also includes methods for
+visualizing, analyzing, manipulating, reading, writing, and inferring phylogenetic
+trees.  Functions for comparative biology include ancestral state reconstruction,
+model fitting, and phylogeny and trait data simulation.  A broad range of plotting
+methods includes mapping trait evolution on trees, projecting trees into phenotype
+space or geographic maps, and visualizing correlated speciation between trees.
+Additional functions allow for reading, writing, analyzing, inferring, simulating,
+and manipulating phylogenetic trees and comparative data.  Examples include computing
+consensus trees, simulating trees and data under various models, and attaching species
+or clades to a tree either randomly or non-randomly.  This package provides numerous tools
+for tree manipulations and analyses that are valuable for phylogenetic research.")
+    (license license:gpl2+)))
+
 (define-public r-kmer
   (package
     (name "r-kmer")

base-commit: 309ad9fcdacf732691f0220c4122757d9940b97d
-- 
2.43.0

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