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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