[R-pkg-devel] [External] Re: Two errors

[iuke-tier@ey m@iii@g oii uiow@@edu]

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…

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.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
> This Message Is From An External Sender: Use caution when opening links or attachments if you do not recognize the sender.
>
> 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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>>
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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
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