On Thu, 3 Jul 2025, Sharon Bewick wrote:
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The problem is that the function that ape exports is way too slow. Using C
directly really sped up my program, which is a bit slow even at that…
[Just replying to the list since reply-all seems to be bouncing for me]
The ideal approach would be to try to understand why the exported
function is slow and see if that can be improved. Profiling might help.
ape does actually export the variable seq_root2tip for use with
.Call() (see the info in ape::seq_root2tip). So you can import it and
use is as seq_root2tip or use it as ape::seq_root2tip.
Best,
luke
From: Duncan Murdoch <murdoch.dun...@gmail.com>
Date: Thursday, July 3, 2025 at 4:13 PM
To: Sharon Bewick <sbew...@clemson.edu>, r-package-devel@r-project.org
<r-package-devel@r-project.org>
Subject: Re: [R-pkg-devel] Two errors
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On 2025-07-03 5:57 p.m., Sharon Bewick wrote:
1. I�m trying to upload my R package. However, I use the ape function
seq_root2tip but for the sake of speed am calling it using .Call:
toroot<-.Call(seq_root2tip, nt$edge, length(nt$tip.label), nt$Nnode)
How do I get R to recognize the seq_root2tip function from ape in this C call?
It is throwing up a NOTE that is getting my package rejected:
shade_branch: no visible binding for global variable �seq_root2tip�
If ape doesn't export seq_root2tip, then you shouldn't use it. Use
whatever function ape exported.
but seq_root2tip is a function, not a global variable.
In R, most functions are objects, there isn't really a distinction
between variables and functions.
2. I�m also getting a NOTE about: no visible global function definition for
�phy_tree<-�
I have declared phy_tree in the NAMESPACE file: importFrom(phyloseq,phy_tree)
I don�t know what the problem is�
"phy_tree" and "phy_tree<-" are two different functions. Import both of
them (if both are exported).
Duncan Murdoch
Thanks!
Sharon
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--
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics and Fax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: luke-tier...@uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu/
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