R help - Nov 2010 - warning creating an as.array method in a package

[Env:  R 2.11.1, Win Xp, using Eclipse/StatET]

In a package I'm working on, I want to create as.matrix() and as.array() 
methods for a particular kind of
object (log odds ratios). These are returned in a loddsratio object as 
the $coefficients component,
a vector, but really reflect an underlying (R-1)x(C-1)xstrata array, 
whose attributes are contained in other
components.

I define coef, dim and dimnames methods, and then want an as.array method,

## dim methods
dimnames.loddsratio <- function(object, ...) object$dimnames
dim.loddsratio <- function(object, ...) object$dim
coef.loddsratio <- function(object, log = object$log, ...)
   if(log) object$coefficients else exp(object$coefficients)

as.array.loddsratio <- function (x, log=x$log, ...)
     drop(array(coef(x, log = log), dim = dim(x), dimnames=dimnames(x)))

I believe everything is declared properly in the NAMESPACE file, e.g.,
...
S3method(dim, loddsratio)
S3method(dimnames, loddsratio)
S3method(print, loddsratio)
S3method(vcov, loddsratio)
S3method(as.matrix, loddsratio)
S3method(as.array, loddsratio)


All my tests work correctly when run in the R console, but R CMD check 
gives me a perplexing warning:

* checking whether package 'vcdExtra' can be installed ... WARNING
Found the following significant warnings:
   Warning: found an S4 version of 'as.array' so it has not been 
imported correctly
See 'C:/eclipse/vcdExtra.Rcheck/00install.out' for details.

It's just a warning, so maybe I can ignore it, but I can't figure out 
where this might have come from.
Has anyone seen this before?  Where might an S4 version of as.array be 
found?

-- 
Michael Friendly     Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street    Web:   http://www.datavis.ca
Toronto, ONT  M3J 1P3 CANADA

On Nov 30, 2010, at 5:43 PM, Michael Friendly wrote:
> [Env:  R 2.11.1, Win Xp, using Eclipse/StatET]
>
> In a package I'm working on, I want to create as.matrix() and  
> as.array() methods for a particular kind of
> object (log odds ratios). These are returned in a loddsratio object  
> as the $coefficients component,
> a vector, but really reflect an underlying (R-1)x(C-1)xstrata array,  
> whose attributes are contained in other
> components.
>
> I define coef, dim and dimnames methods, and then want an as.array  
> method,
>
> ## dim methods
> dimnames.loddsratio <- function(object, ...) object$dimnames
> dim.loddsratio <- function(object, ...) object$dim
> coef.loddsratio <- function(object, log = object$log, ...)
>  if(log) object$coefficients else exp(object$coefficients)
>
> as.array.loddsratio <- function (x, log=x$log, ...)
>    drop(array(coef(x, log = log), dim = dim(x), dimnames=dimnames(x)))
>
> I believe everything is declared properly in the NAMESPACE file, e.g.,
> ...
> S3method(dim, loddsratio)
> S3method(dimnames, loddsratio)
> S3method(print, loddsratio)
> S3method(vcov, loddsratio)
> S3method(as.matrix, loddsratio)
> S3method(as.array, loddsratio)
>
>
> All my tests work correctly when run in the R console, but R CMD  
> check gives me a perplexing warning:
>
> * checking whether package 'vcdExtra' can be installed ... WARNING
> Found the following significant warnings:
>  Warning: found an S4 version of 'as.array' so it has not been  
> imported correctly
> See 'C:/eclipse/vcdExtra.Rcheck/00install.out' for details.
>
> It's just a warning, so maybe I can ignore it, but I can't figure  
> out where this might have come from.
> Has anyone seen this before?  Where might an S4 version of as.array  
> be found?
Have you looked in the ".out" file in which you were told there were  
details?

I'm guessing from this behavior on my system that it may be Matrix.

 > showMethods(as.array)
Function: as.array (package base)
x="ANY"
x="Matrix"

-- 
David Winsemius, MD
West Hartford, CT