[R-pkg-devel] "apparent S3 methods" note in R CMD check

[Martin Maechler]

>>>>> John Fox <jfox at 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