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.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 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 > > [[alternative HTML version deleted]] > > > ______________________________________________ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel<https://stat.ethz.ch/mailman/listinfo/r-package-devel> [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
