Re: [Rd] S3 generic/method consistency issue with R CMD check

From: Drew Schmidt <schmidt_at_math.utk.edu>
Date: Wed, 28 Nov 2012 17:12:24 -0500 (EST)

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

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Received on Thu 29 Nov 2012 - 03:20:18 GMT

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