There seems to be a bug arising when using multiple S4 generics with "..." as the signature. The following code works as expected: ##############################################################> setGeneric("rbind", function(..., deparse.level=1)standardGeneric("rbind"), + signature = "...") Creating a generic for "rbind" in package ".GlobalEnv" (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ: (...), (deparse.level)) [1] "rbind"> rbind(1)[,1] [1,] 1> rbindstandardGeneric for "rbind" defined from package ".GlobalEnv" function (..., deparse.level = 1) standardGeneric("rbind") <environment: 0x83862f4> Methods may be defined for arguments: ... Use showMethods("rbind") for currently available ones.> removeGeneric("rbind")[1] TRUE> rbindfunction (..., deparse.level = 1) .Internal(rbind(deparse.level, ...)) <environment: namespace:base>> setGeneric("order", signature="...",+ function (..., na.last=TRUE, decreasing=FALSE) + standardGeneric("order")) Creating a generic for "order" in package ".GlobalEnv" (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ: (...), (na.last, decreasing)) [1] "order"> rbind(1)[,1] [1,] 1> setGeneric("rbind", function(..., deparse.level=1)standardGeneric("rbind"), + signature = "...") Creating a generic for "rbind" in package ".GlobalEnv" (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ: (...), (deparse.level)) [1] "rbind"> rbind(1)[,1] [1,] 1 ########################################################## That is, rbind(1) always returns the expected result. The rbind() generic is set, then removed, the order() generic is set, and the rbind() generic is set again. No problems. But in a new session, this code breaks, where the rbind() generic is not set before the order() generic: ########################################################> setGeneric("order", signature="...",+ function (..., na.last=TRUE, decreasing=FALSE) + standardGeneric("order")) Creating a generic for "order" in package ".GlobalEnv" (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ: (...), (na.last, decreasing)) [1] "order"> rbind(1)[,1] [1,] 1> setGeneric("rbind", function(..., deparse.level=1)standardGeneric("rbind"), + signature = "...") Creating a generic for "rbind" in package ".GlobalEnv" (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ: (...), (deparse.level)) [1] "rbind"> rbind(1)Error in .Method(..., na.last = na.last, decreasing = decreasing, deparse.level = deparse.level) : object "na.last" not found ############################################################## It looks like something is trying to send the parameters of order() to an rbind() method. Weird.. Thanks, Michael> sessionInfo()R version 2.9.0 Under development (unstable) (--) i686-pc-linux-gnu locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base [[alternative HTML version deleted]]
As an extra curiosity, courtesy of Herve, selectMethod() does not seem to be confused:> rbind(1)Error in .Method(..., na.last = na.last, decreasing = decreasing, deparse.level = deparse.level) : object "na.last" not found> foo <- selectMethod("rbind", "numeric") > fooMethod Definition (Class "derivedDefaultMethod"): function (..., deparse.level = 1) .Internal(rbind(deparse.level, ...)) <environment: namespace:base> Signatures: ... target "numeric" defined "numeric"> foo(1)[,1] [1,] 1>On Tue, Nov 25, 2008 at 2:38 PM, Michael Lawrence <mflawren@fhcrc.org>wrote:> There seems to be a bug arising when using multiple S4 generics with "..." > as the signature. > > The following code works as expected: > > ############################################################## > > > setGeneric("rbind", function(..., deparse.level=1) > standardGeneric("rbind"), > + signature = "...") > Creating a generic for "rbind" in package ".GlobalEnv" > (the supplied definition differs from and overrides the implicit > generic in package "base": Signatures differ: (...), (deparse.level)) > [1] "rbind" > > rbind(1) > [,1] > [1,] 1 > > rbind > standardGeneric for "rbind" defined from package ".GlobalEnv" > > function (..., deparse.level = 1) > standardGeneric("rbind") > <environment: 0x83862f4> > Methods may be defined for arguments: ... > Use showMethods("rbind") for currently available ones. > > removeGeneric("rbind") > [1] TRUE > > rbind > function (..., deparse.level = 1) > .Internal(rbind(deparse.level, ...)) > <environment: namespace:base> > > setGeneric("order", signature="...", > + function (..., na.last=TRUE, decreasing=FALSE) > + standardGeneric("order")) > Creating a generic for "order" in package ".GlobalEnv" > (the supplied definition differs from and overrides the implicit > generic in package "base": Signatures differ: (...), (na.last, decreasing)) > [1] "order" > > rbind(1) > [,1] > [1,] 1 > > setGeneric("rbind", function(..., deparse.level=1) > standardGeneric("rbind"), > + signature = "...") > Creating a generic for "rbind" in package ".GlobalEnv" > (the supplied definition differs from and overrides the implicit > generic in package "base": Signatures differ: (...), (deparse.level)) > [1] "rbind" > > rbind(1) > [,1] > [1,] 1 > > ########################################################## > > That is, rbind(1) always returns the expected result. The rbind() generic > is set, then removed, the order() generic is set, and the rbind() generic is > set again. No problems. > > But in a new session, this code breaks, where the rbind() generic is not > set before the order() generic: > > ######################################################## > > > setGeneric("order", signature="...", > + function (..., na.last=TRUE, decreasing=FALSE) > + standardGeneric("order")) > Creating a generic for "order" in package ".GlobalEnv" > (the supplied definition differs from and overrides the implicit > generic in package "base": Signatures differ: (...), (na.last, decreasing)) > [1] "order" > > rbind(1) > [,1] > [1,] 1 > > setGeneric("rbind", function(..., deparse.level=1) > standardGeneric("rbind"), > + signature = "...") > Creating a generic for "rbind" in package ".GlobalEnv" > (the supplied definition differs from and overrides the implicit > generic in package "base": Signatures differ: (...), (deparse.level)) > [1] "rbind" > > rbind(1) > Error in .Method(..., na.last = na.last, decreasing = decreasing, > deparse.level = deparse.level) : > object "na.last" not found > > ############################################################## > > It looks like something is trying to send the parameters of order() to an > rbind() method. Weird.. > > Thanks, > Michael > > > sessionInfo() > R version 2.9.0 Under development (unstable) (--) > i686-pc-linux-gnu > > locale: > C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > >[[alternative HTML version deleted]]
There were a bunch of red herrings in your example, but the end result
is at least as weird.
Near as I can figure, it's a bug in the evaluator when assigning a local
function call object that is then modified. I'll look a bit at the
code, but someone more expert in the innards of the evaluator might be
needed.
All you need is to do one of the setGeneric() calls. The clue is to
look at a utility function in the methods package that constructs a
function call to .Method.
The bug is that after the first call, the definition of the utility
function has been modified to contain the results of the call. So all
the arguments from successive calls accumulate!
The minimal example is below. Look at the "call <-" line the
second
time the function .makeDotsCall is printed: it has the arguments from
order() in the expression on the right hand side.
At a guess, for some reason object "call" isn't marked correctly
in the
NAMED() field, so the evaluation of, e.g., call$na.last <-
as.name("na.last") overwrites the expression in the definition of
.makeDotsCall.
John
> methods:::.makeDotsCall
function (formals)
{
call <- quote(.Method(...))
if (length(formals) > 1) {
idots <- match("...", formals)
for (what in formals[-idots]) {
eval(substitute(call$NAME <- as.name(WHAT), list(NAME =
as.name(what),
WHAT = what)))
}
}
call
}
<environment: namespace:methods>
> setGeneric("order", signature="...",
+ function (..., na.last=TRUE, decreasing=FALSE)
+ standardGeneric("order"))
Creating a generic for "order" in package ".GlobalEnv"
(the supplied definition differs from and overrides the implicit
generic in package "base": Signatures differ: (...), (na.last,
decreasing))
[1] "order"
> methods:::.makeDotsCall
function (formals)
{
call <- quote(.Method(..., na.last = na.last, decreasing = decreasing))
Michael Lawrence wrote:> There seems to be a bug arising when using multiple S4 generics with
"..."
> as the signature.
>
> The following code works as expected:
>
> ##############################################################
>
>
>> setGeneric("rbind", function(..., deparse.level=1)
>>
> standardGeneric("rbind"),
> + signature = "...")
> Creating a generic for "rbind" in package ".GlobalEnv"
> (the supplied definition differs from and overrides the implicit
generic
> in package "base": Signatures differ: (...), (deparse.level))
> [1] "rbind"
>
>> rbind(1)
>>
> [,1]
> [1,] 1
>
>> rbind
>>
> standardGeneric for "rbind" defined from package
".GlobalEnv"
>
> function (..., deparse.level = 1)
> standardGeneric("rbind")
> <environment: 0x83862f4>
> Methods may be defined for arguments: ...
> Use showMethods("rbind") for currently available ones.
>
>> removeGeneric("rbind")
>>
> [1] TRUE
>
>> rbind
>>
> function (..., deparse.level = 1)
> .Internal(rbind(deparse.level, ...))
> <environment: namespace:base>
>
>> setGeneric("order", signature="...",
>>
> + function (..., na.last=TRUE, decreasing=FALSE)
> + standardGeneric("order"))
> Creating a generic for "order" in package ".GlobalEnv"
> (the supplied definition differs from and overrides the implicit
generic
> in package "base": Signatures differ: (...), (na.last,
decreasing))
> [1] "order"
>
>> rbind(1)
>>
> [,1]
> [1,] 1
>
>> setGeneric("rbind", function(..., deparse.level=1)
>>
> standardGeneric("rbind"),
> + signature = "...")
> Creating a generic for "rbind" in package ".GlobalEnv"
> (the supplied definition differs from and overrides the implicit
generic
> in package "base": Signatures differ: (...), (deparse.level))
> [1] "rbind"
>
>> rbind(1)
>>
> [,1]
> [1,] 1
>
> ##########################################################
>
> That is, rbind(1) always returns the expected result. The rbind() generic
is
> set, then removed, the order() generic is set, and the rbind() generic is
> set again. No problems.
>
> But in a new session, this code breaks, where the rbind() generic is not
set
> before the order() generic:
>
> ########################################################
>
>
>> setGeneric("order", signature="...",
>>
> + function (..., na.last=TRUE, decreasing=FALSE)
> + standardGeneric("order"))
> Creating a generic for "order" in package ".GlobalEnv"
> (the supplied definition differs from and overrides the implicit
generic
> in package "base": Signatures differ: (...), (na.last,
decreasing))
> [1] "order"
>
>> rbind(1)
>>
> [,1]
> [1,] 1
>
>> setGeneric("rbind", function(..., deparse.level=1)
>>
> standardGeneric("rbind"),
> + signature = "...")
> Creating a generic for "rbind" in package ".GlobalEnv"
> (the supplied definition differs from and overrides the implicit
generic
> in package "base": Signatures differ: (...), (deparse.level))
> [1] "rbind"
>
>> rbind(1)
>>
> Error in .Method(..., na.last = na.last, decreasing = decreasing,
> deparse.level = deparse.level) :
> object "na.last" not found
>
> ##############################################################
>
> It looks like something is trying to send the parameters of order() to an
> rbind() method. Weird..
>
> Thanks,
> Michael
>
>
>> sessionInfo()
>>
> R version 2.9.0 Under development (unstable) (--)
> i686-pc-linux-gnu
>
> locale:
> C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
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