[R-pkg-devel] Two errors

[Sharon Bewick]

Ah, ok great, thanks.

So I added:
toroot<-.Call(seq_root2tip, nt$edge, length(nt$tip.label), nt$Nnode, PACKAGE = 'ape')

But check() is still throwing up a note:

basic_branch: no visible binding for global variable ‘seq_root2tip’
  shade_branch: no visible binding for global variable ‘seq_root2tip’
  Undefined global functions or variables:
    seq_root2tip

Any thoughts?
Sharon

From: Josiah Parry <josiah.parry using gmail.com>
Date: Thursday, July 3, 2025 at 4:46 PM
To: Sharon Bewick <sbewick using clemson.edu>
Cc: Michael Chirico <michaelchirico4 using gmail.com>, R Package Development <r-package-devel using r-project.org>
Subject: Re: [R-pkg-devel] Two errors

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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 <sbewick using clemson.edu<mailto:sbewick using 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 <michaelchirico4 using gmail.com<mailto:michaelchirico4 using gmail.com>>
Date: Thursday, July 3, 2025 at 4:13 PM
To: Sharon Bewick <sbewick using clemson.edu<mailto:sbewick using clemson.edu>>
Cc: R Package Development <r-package-devel using r-project.org<mailto: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.
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 <sbewick using clemson.edu<mailto:sbewick using clemson.edu><mailto:sbewick using clemson.edu<mailto:sbewick using 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

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