From mtmorgan at fhcrc.org  Wed Aug  8 01:00:10 2012
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Tue, 07 Aug 2012 16:00:10 -0700
Subject: [Rd] setMethod sometimes fails to set package slot when
 signature has trailing 'ANY'
In-Reply-To: <50218C0F.5050101@stat.stanford.edu>
References: <501F0263.8050700@fhcrc.org> <50218C0F.5050101@stat.stanford.edu>
Message-ID: <50219DFA.2060103@fhcrc.org>

On 08/07/2012 02:43 PM, John Chambers wrote:
> 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.

Thank you for the fix. Martin

>
> 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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[Rd] setMethod sometimes fails to set package slot when signature has trailing 'ANY'
Martin Morgan