Reference class finalize() fails with 'attempt to apply non-function'
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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