It was decided that should not be an error to omit documentation for a generic function defined in a package (whose sole purpose is to extend a current function to be generic). It appears that the implementation of that decision was to treat all generic functions in packages as non-entities. That is probably not the best and one can argue that there should be no warning if a generic is documented (nor one if it isn't and there is already documentation for it somewhere).
Actually methods are also treated as non-entities, unless they are actually assigned into a function name, which the setMethod function does not do in itself nor require. This seems wrong - it should definitely be considered a mistake to define a new method using setMethod and not document it. Such documentation cannot occur in the .Rd file belonging to the class that it operates on if that class is defined in a different package.
Classes defined using setClass are similarly treated an non-entities. It seems that rcmd check is largely "unaware" of formal methods and classes.
Regards Gordon
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