R devel - Dec 2012 - namespace S3 and S4 generic imports cannot both be satisfied:

PkgA wishes to write a method for 'unique' on S4 class 'A'.
?Methods indicates
that one should

   setGeneric("unique")

   setClass("A")
   unique.A <- function(x, incomparables=FALSE, ...) {}
   setMethod(unique, "A", unique.A)

Both S3 and S4 methods need to be exported in the NAMESPACE

   import(methods)
   S3method(unique, A)
   exportMethods(unique)

PkgB introduces a new class and method

   setClass("B")
   unique.B <- function(x, incomparables=FALSE, ...) {}
   setMethod(unique, "B", unique.B)

and in the NAMESPACE has

   import(methods)
   importFrom(PkgA, unique)
   S3method(unique, B)
   exportMethods(unique)

Unfortuantely, R CMD check says that

* checking whether package 'PkgB' can be installed ... WARNING
Found the following significant warnings:
   Warning: found an S4 version of 'unique' so it has not been imported
correctly
See '/home/mtmorgan/tmp/PkgB.Rcheck/00install.out' for details.

This is from (svn r61253) R-devel/src/library/base/R/namespace.R:1339, where the
code finds the S4 generic, but not the S3 generic. Obviously the namespace 
cannot have both the S3 and S4 symbols defined, but this seems to be required? A
workaround might extend the check to include getGeneric(genname)@default.

This scenario is reproducible in the attached tarball

   tar xzf PkgAB.tar.gz
   R CMD INSTALL PkgA
   R CMD check PkgB

Martin Morgan
-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793
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Yes, you are right.

Mixing S3 and S4 methods for a generic is fine, although in subtle cases 
one is safer promoting the S3 method to an S4 method, as you did in your 
example.

Usually, the default method for the S4 generic is the S3 generic.  But, 
in general, it's not possible to check algorithmically whether the S3 
methods will be dispatched.  For example, an S4 method on "vector"
could
dispatch S3 methods on subclasses "numeric", etc. (don't ask why
...),
for a generic that had no default method.

That the trouble with this check isn't found right away is likely 
because one is typically working with a primitive where no generic 
function is created.

Should be fixed in rev. 61263.  Please check on your real example; it 
seems fine on the test you submitted.

Thanks for the catch.

John

On 12/8/12 3:05 PM, Martin Morgan wrote:
> PkgA wishes to write a method for 'unique' on S4 class 'A'.
?Methods
> indicates that one should
>
>    setGeneric("unique")
>
>    setClass("A")
>    unique.A <- function(x, incomparables=FALSE, ...) {}
>    setMethod(unique, "A", unique.A)
>
> Both S3 and S4 methods need to be exported in the NAMESPACE
>
>    import(methods)
>    S3method(unique, A)
>    exportMethods(unique)
>
> PkgB introduces a new class and method
>
>    setClass("B")
>    unique.B <- function(x, incomparables=FALSE, ...) {}
>    setMethod(unique, "B", unique.B)
>
> and in the NAMESPACE has
>
>    import(methods)
>    importFrom(PkgA, unique)
>    S3method(unique, B)
>    exportMethods(unique)
>
> Unfortuantely, R CMD check says that
>
> * checking whether package 'PkgB' can be installed ... WARNING
> Found the following significant warnings:
>    Warning: found an S4 version of 'unique' so it has not been
imported
> correctly
> See '/home/mtmorgan/tmp/PkgB.Rcheck/00install.out' for details.
>
> This is from (svn r61253) R-devel/src/library/base/R/namespace.R:1339,
> where the code finds the S4 generic, but not the S3 generic. Obviously
> the namespace cannot have both the S3 and S4 symbols defined, but this
> seems to be required? A workaround might extend the check to include
> getGeneric(genname)@default.
>
> This scenario is reproducible in the attached tarball
>
>    tar xzf PkgAB.tar.gz
>    R CMD INSTALL PkgA
>    R CMD check PkgB
>
> Martin Morgan
>
>
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>