Re: [R-pkg-devel] Two errors

Jiří Moravec Sat, 05 Jul 2025 18:08:19 -0700

I would like to add that copy pasting is also a valid way to includedependencies.


Just make sure to get contributions right.


-- Jirka

On 5/07/25 11:19, Michael Chirico wrote:

Sharon, Luke noted that (somewhat strangely [1]) {ape} is exporting the
registered entry point for that routine, so you should just be able to do:

importFrom(ape,seq_root2tip)

and be on your way.

[1] ?ape::seq_root2tip notes that "other packages" use it, but none of
those are on CRAN, could be a Bioconductor thing:
https://github.com/search?q=org%3Acran+%2Fseq_root2tip%5Cb%2F+lang%3AR+-repo%3Acran%2Fape&type=code

Mike C

On Fri, Jul 4, 2025 at 4:03 PM Sharon Bewick <sbew...@clemson.edu> wrote:

So I think the only solution that CRAN will accept is linking against
headers. I can download an ape.h header file, but for the life of me, I’m
having trouble figuring out how to link it in my R package. I’ve read what
I can find online, but haven’t been successful. Right now, I have the ape.h
file in an src folder. I also have

LinkingTo: Rcpp, ape

In my DESCRIPTION file



But I’m getting all sorts of errors. Does anyone have an example of how I
can do this that I might be able to work from?



Thanks in advance!!!!

Sharon





*From: *Iris Simmons <ikwsi...@gmail.com>
*Date: *Thursday, July 3, 2025 at 5:11 PM
*To: *Sharon Bewick <sbew...@clemson.edu>
*Cc: *Michael Chirico <michaelchiri...@gmail.com>, R Package Development <
r-package-devel@r-project.org>
*Subject: *Re: [R-pkg-devel] Two errors

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attachments if you do not recognize the sender.

I believe the suggestion was that you should alternatively write:

.Call("seq_root2tip", nt$edge, length(nt$tip.label), nt$Nnode, PACKAGE =
"ape")

however, that generates the following note that CRAN is very unlikely to
accept:

* checking foreign function calls ... NOTE
Foreign function call to a different package:
   .Call("seq_root2tip", ..., PACKAGE = "ape")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.

The other possibility is adding:

importFrom(ape, seq_root2tip)

to your NAMESPACE and not modifying your code, but that generates a
different note:

* checking foreign function calls ... NOTE
Registration problem:
   symbol 'seq_root2tip' not in namespace:
    .Call(seq_root2tip, ...)
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.

Your best bet is to ask the maintainers of package:ape to add and
export an R function like this:

idk <- function (...)
.Call(seq_root2tip, ...)

There are also ways to do it in C using R_RegisterCCallable and
R_GetCCallable but that might be too complicated for something like
this.

On Thu, Jul 3, 2025 at 6:33 PM 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

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Re: [R-pkg-devel] Two errors

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