Interaction between callNextMethod() and selectMethod()

Fri, Aug 3, 2012 4:24 PM

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

Interaction between callNextMethod() and selectMethod()

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