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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