I believe they mean as an argument to .Call https://stat.ethz.ch/R-manual/R-devel/library/base/html/CallExternal.html
On Thu, Jul 3, 2025 at 15:41 Sharon Bewick <sbew...@clemson.edu> wrote: > 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 > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
