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

Previous Next

To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 75750 in the body.
You can then email your comments to 75750 AT debbugs.gnu.org in the normal way.

Toggle the display of automated, internal messages from the tracker.

Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

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

Message #10 received at 75750-done <at> debbugs.gnu.org (full text, mbox):

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

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.