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$Nnode)
How do I get R to recognize the seq_root2tip function from ape in this C call?
It is throw
The problem is that the function that ape exports is way too slow. Using C
directly really sped up my program, which is a bit slow even at that…
From: Duncan Murdoch
Date: Thursday, July 3, 2025 at 4:13 PM
To: Sharon Bewick , r-package-devel@r-project.org
Subject: Re: [R-pkg-devel] Two error
Ah, ok great, thanks.
So I added:
toroot<-.Call(seq_root2tip, nt$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_root2t
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 a
On Thu, 3 Jul 2025, Sharon Bewick wrote:
[You don't often get email from sbew...@clemson.edu. Learn why this is
important at https://aka.ms/LearnAboutSenderIdentification ]
The problem is that the function that ape exports is way too slow. Using C
directly really sped up my program, which is
I believe the suggestion was that you should alternatively write:
.Call("seq_root2tip", nt$edge, length(nt$tip.label), nt$Nnode, PACKAGE = "ape")
however, that generates the following note that CRAN is very unlikely to accept:
* checking foreign function calls ... NOTE
Foreign function call to a
I think you can put it in quotes so then it won’t be an issue. Other wise
you can use the global variables function:
https://www.r-bloggers.com/2019/08/no-visible-binding-for-global-variable/amp/
On Thu, Jul 3, 2025 at 15:52 Sharon Bewick wrote:
> Ah, ok great, thanks.
>
>
>
> So I added:
>
> to
On 2025-07-03 6:32 p.m., Sharon Bewick wrote:
The problem is that the function that ape exports is way too slow. Using
C directly really sped up my program, which is a bit slow even at that…
You need to be collaborating with the ape maintainer to fix that package
so it works for your problem.
I believe they mean as an argument to .Call
https://stat.ethz.ch/R-manual/R-devel/library/base/html/CallExternal.html
On Thu, Jul 3, 2025 at 15:41 Sharon Bewick wrote:
> Thanks so much for the tips!
>
> I think I’ve fixed #2. But I’m not sure what you mean by #1. Where should
> the "seq_root2tip
Thanks so much for the tips!
I think I’ve fixed #2. But I’m not sure what you mean by #1. Where should the
"seq_root2tip" with PACKAGE="ape" go? In the NAMESPACE file? In the Description
file? Somewhere in the code?
So sorry for not understanding!
Thanks!
Sharon
From: Michael Chirico
Date: T
On 2025-07-03 5:57 p.m., Sharon Bewick wrote:
1. I�m trying to upload my R package. However, I use the ape function
seq_root2tip but for the sake of speed am calling it using .Call:
toroot<-.Call(seq_root2tip, nt$edge, length(nt$tip.label), nt$Nnode)
How do I get R to recognize the seq_root2ti
On Thu, 3 Jul 2025, Sharon Bewick wrote:
[You don't often get email from sbew...@clemson.edu. Learn why this is
important at https://aka.ms/LearnAboutSenderIdentification ]
The problem is that the function that ape exports is way too slow. Using C
directly really sped up my program, which is
On Thu, 5 Jun 2025 19:49:48 -0400
Duncan Murdoch wrote:
> I'm pretty sure CRAN doesn't care what is in the title, as long as
>
> - The new one follows their rules (re capitalization etc.)
> - The change doesn't follow the last package change too rapidly.
>
> It would be best if you change
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