R devel - Dec 2011 - Reference class finalize() fails with 'attempt to apply non-function'

This bug appears intermittently in R CMD check when reference classes 
have finalize methods. The problem is that garbage collection can be run 
after the methods package is no longer available. It affects 
(periodically) the Bioconductor AnnotationDbi package as well as 
packages that contain Rcpp classes. To reproduce:

   library(methods)
   a = setRefClass("A", methods=list(finalize=function()
cat("A\n")))
   b = setRefClass("B", contains="A")

repeat b = setRefClass("B", contains="A") until finalize
does not run
(no garbage collection triggered during setRefClass)

   b = setRefClass("B", contains="A")
   b = setRefClass("B", contains="A")

and then

 > detach("package:methods")
 > gc()
Error in function (x)  : attempt to apply non-function
Error in function (x)  : attempt to apply non-function

 > traceback()
1: function (x)
    x$.self$finalize()(<environment>)

I believe a variant of the same type of problem generates an error

Error in function (x)  : no function to return from, jumping to top level

also seen in AnnotationDbi and Rcpp packages
-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

On Thu, Dec 8, 2011 at 2:52 PM, Martin Morgan <mtmorgan at fhcrc.org>
wrote:
> This bug appears intermittently in R CMD check when reference classes have
> finalize methods. The problem is that garbage collection can be run after
> the methods package is no longer available. It affects (periodically) the
> Bioconductor AnnotationDbi package as well as packages that contain Rcpp
> classes. To reproduce:
>
> ?library(methods)
> ?a = setRefClass("A", methods=list(finalize=function()
cat("A\n")))
> ?b = setRefClass("B", contains="A")
>
> repeat b = setRefClass("B", contains="A") until
finalize does not run (no
> garbage collection triggered during setRefClass)
>
> ?b = setRefClass("B", contains="A")
> ?b = setRefClass("B", contains="A")
>
> and then
>
>> detach("package:methods")
>> gc()
> Error in function (x) ?: attempt to apply non-function
> Error in function (x) ?: attempt to apply non-function
>
>> traceback()
> 1: function (x)
> ? x$.self$finalize()(<environment>)
>
> I believe a variant of the same type of problem generates an error
>
> Error in function (x) ?: no function to return from, jumping to top level
>
> also seen in AnnotationDbi and Rcpp packages
Here is a self-contained reproducible example that immediately and
consistently produces the error on R 2.14 and R-devel:

library(methods)
a = setRefClass("A",
  methods=list(finalize=function() options("finalized"=TRUE)))
b = setRefClass("B", contains="A")

while (TRUE) {
    options("finalized" = FALSE)
    b = setRefClass("B", contains="A")
    if (!getOption("finalized")) break
}

detach("package:methods")
gc()



Thanks!
Dan



> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>
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