[R-pkg-devel] Two errors

[Duncan Murdoch]

On 2025-07-03 6:32 p.m., Sharon Bewick wrote:
> 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…

You need to be collaborating with the ape maintainer to fix that package 
so it works for your problem.  Most package maintainers are happy to 
accept suggested improvements.

Duncan Murdoch

> 
> *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
>>
>>       [[alternative HTML version deleted]]
>>
>>
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