R devel - Dec 2009 - S4 and head() problems

Hi

I am having difficulty defining an S4 method for head() and tail().

I can't quite provide minimal self-contained code
because the problem appears to require the whole corpus
of my package; and there also appears to be a difference
between sourcing the lines directly, and having them
installed in a package.

The lines in question (I think) are:

setClass("mdm",
         representation = representation(
           xold  = "matrix",
           types = "factor"
           )
         )

"mdm" <- function(xold, types){
  new("mdm", xold=xold, types=types)
}

setGeneric("head",function(x,...){standardGeneric("head")})
setMethod("head",signature="mdm",function(x,n=6,...){
  mdm(head(x at xold,n=n,...) , types=factor(head(x at types,n=n,...)))
} )


If the above lines are part of the package source, and I install the package
then sometimes  I get errors like

 > head(toy_mm())
Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function "head", for
signature
"matrix"
 >

and sometimes it works as desired.

Why should head() not be able to take the first few lines of a matrix?
It seems to be "forgetting" that head.matrix() exists.

Can anyone give me some pointers for debugging this problem?

rksh







-- 
Robin K. S. Hankin
Uncertainty Analyst
University of Cambridge
19 Silver Street
Cambridge CB3 9EP
01223-764877

Hi Robin,
>>>>> "Robin" == Robin Hankin <rksh1 at
cam.ac.uk>
>>>>>     on Thu, 03 Dec 2009 11:04:03 +0000 writes:
    > Hi
    > I am having difficulty defining an S4 method for head() and tail().

    > I can't quite provide minimal self-contained code
    > because the problem appears to require the whole corpus
    > of my package; and there also appears to be a difference
    > between sourcing the lines directly, and having them
    > installed in a package.

    > The lines in question (I think) are:

    > setClass("mdm",
    > representation = representation(
    > xold  = "matrix",
    > types = "factor"
    > )
    > )

    > "mdm" <- function(xold, types){
    > new("mdm", xold=xold, types=types)
    > }

    >
setGeneric("head",function(x,...){standardGeneric("head")})

I would not use setGeneric() here
rather only setMethod() :

    >
setMethod("head",signature="mdm",function(x,n=6,...){
    > mdm(head(x at xold,n=n,...) , types=factor(head(x at types,n=n,...)))
    > } )


    > If the above lines are part of the package source, and I install the
package
    > then sometimes  I get errors like

    >> head(toy_mm())
    > Error in function (classes, fdef, mtable)  :
    > unable to find an inherited method for function "head", for
signature
    > "matrix"
    >> 

    > and sometimes it works as desired.

    > Why should head() not be able to take the first few lines of a matrix?
    > It seems to be "forgetting" that head.matrix() exists.

    > Can anyone give me some pointers for debugging this problem?

    > rksh

you did not mention if your package uses a NAMESPACE
and if yes, what exactly you import and export,
and that can matter quite a bit.

In the Matrix package, we do *not* call setGeneric() for head,
just setMethod(), and I'd advise you to do that too.

Why you get different behavior depending on how exactly you load
the code seems very had to diagnose from a distance.

Regards,
Martin