Good catch. This should have been fixed in r-devel, revision 60192. If
nothing bad results in other tests, we'll port it to the current patched
version.
Thanks,
John
On 8/5/12 4:31 PM, Martin Morgan wrote:
after this
setClass("A")
setGeneric("bar", function(x, y) standardGeneric("bar"))
setMethod(bar, signature(x="A", y="A"), function(x, y) {})
setMethod(bar, signature(x="A", y="ANY"), function(x, y) {})
the method for signature c("A", "A") contains package information
> str(getMethod(bar, c("A", "A")))
Formal class 'MethodDefinition' [package "methods"] with 4 slots
..@ .Data :function (x, y)
..@ target :Formal class 'signature' [package "methods"] with 3 slots
.. .. ..@ .Data : chr [1:2] "A" "A"
.. .. ..@ names : chr [1:2] "x" "y"
.. .. ..@ package: chr [1:2] ".GlobalEnv" ".GlobalEnv"
..@ defined:Formal class 'signature' [package "methods"] with 3 slots
.. .. ..@ .Data : chr [1:2] "A" "A"
.. .. ..@ names : chr [1:2] "x" "y"
.. .. ..@ package: chr [1:2] ".GlobalEnv" ".GlobalEnv"
..@ generic: atomic [1:1] bar
.. ..- attr(*, "package")= chr ".GlobalEnv"
but the method for signature c("A", "ANY") does not
> str(getMethod(bar, c("A", "ANY")))
Formal class 'MethodDefinition' [package "methods"] with 4 slots
..@ .Data :function (x, y)
..@ target :Formal class 'signature' [package "methods"] with 3 slots
.. .. ..@ .Data : chr [1:2] "A" "ANY"
.. .. ..@ names : chr [1:2] "x" "y"
.. .. ..@ package: chr [1:2] "" ""
..@ defined:Formal class 'signature' [package "methods"] with 3 slots
.. .. ..@ .Data : chr [1:2] "A" "ANY"
.. .. ..@ names : chr [1:2] "x" "y"
.. .. ..@ package: chr [1:2] "" ""
..@ generic: atomic [1:1] bar
.. ..- attr(*, "package")= chr ".GlobalEnv"
This does not occur when the order of setMethod calls is reversed. The
reason is that the package information added when
methods/R/Methods.R:552 calls matchSignature are stripped (because
matchSignature returns a vector with trailing 'ANY' classes removed)
by the call to .matchSigLength at line 603.
The context for this is the thread starting at
https://stat.ethz.ch/pipermail/bioconductor/2012-August/047241.html
where a complicated package dependency and attempt to redefine an
existing method leads to
Error : package slot missing from signature for generic 'sampleNames<-'
and classes LumiBatch, ANY
cannot use with duplicate class names (the package may need to be
re-installed)
Martin
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