Great news ! This bug was driving me mad.
I have some scripts that had _high_ probability of running into the
bug. I'll recompile and check it out over the weekend.
Kasper
On Jun 12, 2009, at 10:25 , Henrik Bengtsson wrote:
Thank you Luke! I know you made many people happy by fixing this one,
especially over at BioC.
Is this a candidate for the contest of the bug that survived the
longest without being caught?
I reported on its symptoms in April 2006, but I think I first observed
them in 2003-2004 (thinking for a long time that it was a problem with
my code).
/Henrik
On Fri, Jun 12, 2009 at 9:01 AM, <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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--
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics and Fax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: l...@stat.uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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