Dear Martin,
Thank you for addressing this issue. Introducing a nonS3method() directive in
NAMESPACE seems a reasonable solution. It could replace export() for functions
with "."s in their names.
Best,
John
On Fri, 12 Jun 2015 09:55:18 +0200
Martin Maechler <maech...@stat.math.ethz.ch> wrote:
> >>>>> John Fox <j...@mcmaster.ca>
> >>>>> on Wed, 10 Jun 2015 10:12:46 -0400 writes:
>
> > Dear list members,
> > One of the packages I maintain, effects, generates the following note
> in R
> > CMD check:
>
> > * checking S3 generic/method consistency ... NOTE
> > Found the following apparent S3 methods exported but not registered:
> > all.effects
>
> > The offending function, all.effects(), is deprecated in favour of
> > allEffects(), but I'd rather not get rid of it for backwards
> compatibility.
> > Is there any way to suppress the note without removing all.effects()?
>
> > To be clear, all.effects() is *not* a method of all(), and is defined as
>
> >> effects::all.effects
> > function (...)
> > {
> > .Deprecated("allEffects")
> > allEffects(...)
> > }
>
> Dear John,
> this is a good question without an obvious answer for the
> moment.
>
> The check producing it is relatively new *and* has helped to
> detect problems in many packages and places, but I would agree
> is a "False Positive" in this case.
>
> One reason for such a check is the following output {in R >= 3.2.0},
>
> > require("effects")
> Loading required package: effects
> > methods(all)
> [1] all,ddiMatrix-method all,ldiMatrix-method
> all,lsparseMatrix-method
> [4] all,Matrix-method all,nsparseMatrix-method all.effects
>
> see '?methods' for accessing help and source code
> >
>
> which wrongly does list your all.effects() among the all
> methods.... and indeed (even worse), it *is* taken as S3 method
> for all():
>
> > ex <- structure(FALSE, class="effects")
> > all(ex)
> Error: $ operator is invalid for atomic vectors
> In addition: Warning message:
> 'all.effects' is deprecated.
> Use 'allEffects' instead.
> See help("Deprecated")
> >
>
> ---
>
> Now I agree .. and have e-talked about this with another R core
> member .. that it would be desirable for the package author to
> effectively declare the fact that such a function is not an S3
> method even though it "looks like it" at least if looked from far.
>
> So, ideally, you could have something like
>
> nonS3method("all.effects")
>
> somewhere in your package source ( in NAMESPACE or R/*.R )
> which would tell the package-checking code -- but *ALSO* all the other S3
> method code that all.effects should be treated as a regular R
> function.
>
> I would very much like such a feature in R, and for that reason,
> I'm cross posting this (as one of the famous exceptions that
> accompany real-life rules!!) to R-devel.
>
> There is one current work-around -- some would say "hack" -- in the R sources
> for exceptions on a per package basis, and I will now activate
> that workaround for you.
>
> Martin
>
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