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
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Location: M1-B861
Telephone: 206 667-2793
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