From hpages at fhcrc.org  Sat Aug  4 01:24:50 2012
From: hpages at fhcrc.org (=?windows-1252?Q?Herv=E9_Pag=E8s?=)
Date: Fri, 03 Aug 2012 16:24:50 -0700
Subject: [Rd] Interaction between callNextMethod() and selectMethod()
In-Reply-To: <501C5C5F.6050900@fhcrc.org>
References: <501C5C5F.6050900@fhcrc.org>
Message-ID: <501C5DC2.4040400@fhcrc.org>

FWIW, here is my sessionInfo:

   > sessionInfo()
   R Under development (unstable) (2012-07-25 r59963)
   Platform: x86_64-unknown-linux-gnu (64-bit)

   locale:
    [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
    [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
    [7] LC_PAPER=C                 LC_NAME=C
    [9] LC_ADDRESS=C               LC_TELEPHONE=C
   [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

   attached base packages:
   [1] stats     graphics  grDevices utils     datasets  methods   base

BTW, it's funny that the VERSION file in the R source tree says:

   hpages at latitude:~/src/R-2.16.r59963$ cat VERSION
   2.16.0 Under development (unstable)
   ^^^^^^

H.

On 08/03/2012 04:18 PM, Herv? Pag?s wrote:
> Hi,
>
> Strange things happen. Here is a simple example:
>
>    > setClass("A", contains="integer")
>    > setMethod("as.matrix", "A", function(x, ...) t(callNextMethod()))
>    Creating a generic function for ?as.matrix? from package ?base? in
> the global environment
>    [1] "as.matrix"
>    > a <- new("A", 1:3)
>    > as.matrix(a)
>         [,1] [,2] [,3]
>    [1,]    1    2    3
>
> Everything fine so far. But:
>
>    > selectMethod("as.matrix", "A")(a)
>    Error in callNextMethod() :
>      c("a call to callNextMethod() appears in a call to
> \"selectMethod\", but the call does not seem to come from either a
> generic function or another 'callNextMethod'", "a call to
> callNextMethod() appears in a call to \"as.matrix\", but the call does
> not seem to come from either a generic function or another
> 'callNextMethod'", "a call to callNextMethod() appears in a call to
> \"A\", but the call does not seem to come from either a generic function
> or another 'callNextMethod'")
>    In addition: Warning message:
>    In if (is.na(i)) { :
>      the condition has length > 1 and only the first element will be used
>
> 2 things about this:
>
> (1) Sure callNextMethod() needs some context in order to know what to
>      do but it seems that the MethodDefinition object returned by
>      selectMethod() carries that context i.e. it seems to contain
>      all the information that callNextMethod() would need (name of the
>      generic and defined signature) to actually work:
>
>        > mymethod <- selectMethod("as.matrix", "A")
>        > class(mymethod)
>        [1] "MethodDefinition"
>        attr(,"package")
>        [1] "methods"
>        > mymethod at generic
>        [1] "as.matrix"
>        attr(,"package")
>        [1] "base"
>        > mymethod at defined
>        An object of class "signature"
>          x
>        "A"
>
> (2) If for whatever reason callNextMethod() really needs to fail, could
>      the error handling be fixed so it produces the same output as:
>
>      > mymethod(a)
>      Error in callNextMethod() :
>        a call to callNextMethod() appears in a call to "mymethod", but
> the call does not seem to come from either a generic function or another
> 'callNextMethod'
>
> Thanks!
> H.
>


-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



[Rd] Interaction between callNextMethod() and selectMethod()
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