Thanks so much for the tips! I think I’ve fixed #2. But I’m not sure what you mean by #1. Where should the "seq_root2tip" with PACKAGE="ape" go? In the NAMESPACE file? In the Description file? Somewhere in the code?
So sorry for not understanding! Thanks! Sharon From: Michael Chirico <michaelchiri...@gmail.com> Date: Thursday, July 3, 2025 at 4:13 PM To: Sharon Bewick <sbew...@clemson.edu> Cc: R Package Development <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. 1. all functions in R are variables. You can "trick" code tools by writing seq_root2tip=NULL in the same scope but consider (a) C routines are typically part of a package's private interface (b) it might be preferable to use the string "seq_root2tip" with PACKAGE="ape" 2. phytree is not the same as phytree<- : importFrom(phyloseq, "phytree<-") is what you want assuming it's exported) (c.f. `x = phyteee(...)` vs. `phytree(x) <- ...`) Mike C On Thu, Jul 3, 2025, 2:57 PM Sharon Bewick <sbew...@clemson.edu<mailto:sbew...@clemson.edu>> 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’ but seq_root2tip is a function, not a global variable. 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… Thanks! Sharon [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org<mailto:R-package-devel@r-project.org> mailing list 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
