R devel - Nov 2012 - S3 generic/method consistency issue with R CMD check

Hi,

I'm having some trouble setting methods for the qr family of functions.  I
believe I have distilled my misunderstanding in the code snippet below:


foo <- function(x, ...) UseMethod("foo")

foo.default <- function(x) { }

# foo

setGeneric(name = "foo", useAsDefault = foo)

setMethod("foo", signature(x="bar"),
  function(x, ...) { }
)

setGeneric(name="foo.Q",
  function(y, ...)
    standardGeneric("foo.Q")
)

setMethod("foo.Q", signature(y="bar"),
  function(y, ...) { }
)

# QR

setGeneric(name = "qr", useAsDefault = qr)

setMethod("qr", signature(x="bar"),
  function(x, ...) { }
)

setGeneric(name="qr.Q",
  function(y, ...)
    standardGeneric("qr.Q")
)

setMethod("qr.Q", signature(y="bar"),
  function(y, ...) { }
)


If you send this to R CMD check, then it gives exactly one WARNING about
S3 consistency:


* checking S3 generic/method consistency ... WARNING
qr:
  function(x, ...)
qr.Q:
  function(y, ...)


This seems to be complaining about the fact that qr.Q dispatches on 'y'
instead of 'x'.  But there is no complaint about foo/foo.Q even though,
I
believe, the only difference is a mechanical substitution of
generic/method names.

Ultimately I would like to be able to set methods for the qr family in a
way that maximally mimics R in both syntax and return.  I'm clearly doing
something wrong, but I'm not really sure how else to proceed.  Any help in
clearing up my misunderstanding here would be greatly appreciated.

Thanks.

-- 
Drew Schmidt
National Institute for Computational Sciences
University of Tennessee

More on this.  It looks to me like there is some kind of issue
specifically with the qr and qr.* functions in R CMD check, as my last
email suggests.  Additionally, by changing the dispatch of the qr.*
functions from y to x (in this example), such as:


setGeneric(name="qr.Q",
  function(x, ...)
    standardGeneric("qr.Q"),
)

setMethod("qr.Q", signature(x="bar"),
  function(x, ...) { }
)


we avoid the WARNING.  So too does:


setGeneric(name="qr_Q",
  function(y, ...)
    standardGeneric("qr_Q")
)

setMethod("qr_Q", signature(y="bar"),
  function(y, ...) { }
)


avoid the WARNING.

This suggests to me that R CMD check is incorrectly using "qr"'s
dispatch
for "qr.Q", even when we specify "qr.Q" as S4 generic with
dispatch y.
More to the point, it looks to me like R CMD check is applying S3 rules to
S4 methods for this specific set of base:: functions.

Not sure how else to interpret what I'm seeing here, but I still have
doubts as to my understanding of this issue.  Would very much appreciate
some insight.

Apologies in advance if I botch the reply threading; I am using a very
limited webmail client and I'm not sure if this will work properly.

--
Drew Schmidt
National Institute for Computational Sciences
University of Tennessee