[R-pkg-devel] Two errors

[Sharon Bewick]

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…



From: Duncan Murdoch <murdoch.duncan using gmail.com>
Date: Thursday, July 3, 2025 at 4:13 PM
To: Sharon Bewick <sbewick using clemson.edu>, r-package-devel using r-project.org <r-package-devel using 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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