Re: [Rd] formal argument "envir" matched by multiple actual arguments

From: Henrik Bengtsson <hb_at_stat.berkeley.edu>
Date: Fri, 12 Jun 2009 10:25:30 -0700

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, <luke_at_stat.uiowa.edu> wrote:
> On Tue, 2 Jun 2009, luke@stat.uiowa.edu wrote:
>
>> On Tue, 2 Jun 2009, Henrik Bengtsson wrote:
>>
>>> Nice case - I think you're onto something. /Henrik
>>>
>>> 2009/6/2  <hpages_at_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(ans_at_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.
>>>>
>>>> ______________________________________________
>>>> R-devel_at_r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>
>>>
>>> ______________________________________________
>>> R-devel_at_r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>
>>
>
> --
> 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:      luke_at_stat.uiowa.edu
> Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu
> ______________________________________________
> R-devel_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>



R-devel_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel Received on Fri 12 Jun 2009 - 17:32:32 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Fri 12 Jun 2009 - 22:35:44 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-devel. Please read the posting guide before posting to the list.

list of date sections of archive