[R-pkg-devel] S3 generic/method consistency false positive when dplyr imported

[Aaron A. King]

Thanks for the fast reply!

When I follow your suggestion above, I get

library(pomp)
dplyr::filter(structure(list(), class = 'traj'))

Error in UseMethod("filter") :
  no applicable method for 'filter' applied to an object of class "traj"

Which is not what would happen if my filter.traj function were called.  So
the S3 dispatch system is not confused.  Thus this really is a false
positive.

It still leaves open the question, why does this suddenly appear when dplyr
is loaded?  If I understand you correctly, it would be triggered by the
inclusion of the generic 'filter' in dplyr, which was previously not
present. However, since the S3 dispatch system is not itself confused, I
suppose it must be the case that the S3 generic/method consistency checker
itself is confused.  I wonder, how does the checker decide when to throw a
NOTE?  Is it a simple pattern-matching system, something like "If X.Y is
exported, where X is a generic and Y is any string and X.Y is not declared
as an S3 method, then throw NOTE"?

Dr. Aaron A. King
University of Michigan


On Wed, Jan 4, 2023 at 4:22 PM Ivan Krylov <krylov.r00t using gmail.com> wrote:

> On Wed, 4 Jan 2023 15:54:52 -0500
> "Aaron A. King" <kingaa using umich.edu> wrote:
>
> > Why does inclusion of *dplyr* in the import list appear to trigger
> > these warnings when they were not there before?
>
> I think that's because dplyr itself contains an S3 generic named
> "filter", and having a package namespace loaded (not even attached) is
> enough to take its registered S3 methods into consideration for method
> dispatch. Here we have an opposite situation, though, and your
> functions aren't registered as S3 methods. Will your function still be
> called if you artificially construct a wrong object and feed it to
> dplyr::filter while your package namespace is attached?
>
> library(YOURPACKAGE)
> dplyr::filter(structure(list(), class = 'traj'))
>
> Additionally, stats::filter doesn't seem to be an S3 generic, so that's
> one thing that the check gets confused about.
>
> --
> Best regards,
> Ivan
>

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