That's great news Luke! Thanks for finding and fixing that one!
I will do some testing and update the BioC build system with
the latest R.
H.
l...@stat.uiowa.edu wrote:
On Tue, 2 Jun 2009, l...@stat.uiowa.edu wrote:
On Tue, 2 Jun 2009, Henrik Bengtsson wrote:
Nice case - I think you're onto something. /Henrik
2009/6/2 <hpa...@fhcrc.org>:
In fact reg.finalizer() looks like a dangerous feature.
If the finalizer itself triggers (implicitely or
explicitely) garbage collection, then bad things happen.
In the following example, garbage collection is triggered
explicitely (using R-2.9.0):
setClass("B", representation(bb="environment"))
newB <- function()
{
ans <- new("B", bb=new.env())
reg.finalizer(a...@bb,
function(e)
{
gc()
cat("cleaning", class(ans), "object...\n")
}
)
return(ans)
}
> for (i in 1:500) {cat(i, "\n"); b1 <- newB()}
1
2
3
4
5
6
...
13
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
14
...
169
170
171
Error: not a weak reference
Error: not a weak reference
[repeat the above line thousands of times]
...
Error: not a weak reference
Error: not a weak reference
cleaning B object...
Error: SET_VECTOR_ELT() can only be applied to a 'list', not a
'integer'
Error: SET_VECTOR_ELT() can only be applied to a 'list', not a
'integer'
[repeat the above line thousands of times]
...
Error: SET_VECTOR_ELT() can only be applied to a 'list', not a
'integer'
Error: SET_VECTOR_ELT() can only be applied to a 'list', not a
'integer'
172
...
246
247
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
cleaning B object...
*** caught segfault ***
address 0x41, cause 'memory not mapped'
Traceback:
1: gc()
2: function (e) { gc() cat("cleaning", class(ans),
"object...\n")}(<environment>)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 2
Save workspace image? [y/n/c]: n
Segmentation fault
So apparently, if the finalizer triggers garbage collection,
then we can end up with a corrupted session. Then anything can
happen, from the strange 'formal argument "envir" matched by
multiple actual arguments' error I reported in the previous post,
to a segfault. In the worse case, nothing apparently happens but
the output produced by the code is wrong.
Maybe garbage collection requests should be ignored during the
execution of the finalizer? (and more generally during garbbage
collection itself)
Thanks for the report. The gc proper does not (or should not) do
anything that could cause allocation or trigger another gc. The gc
proper only identifies objects ready for finalization; running the
finalizers happens outside the gc proper where allocation and gc calls
should be safe. This looks like either a missing PROTECT call in the
code for running finalizers or possibly a more subltle bug in managing
the lists of objects in different states of finalization. I will look
more carefully when I get a chance.
This is now fixed in R-devel and the R-patched (it was essentially a
missing PROTECT call).
luke
luke
Cheers,
H.
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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