From luke at stat.uiowa.edu  Tue Jun  2 17:34:47 2009
From: luke at stat.uiowa.edu (luke at stat.uiowa.edu)
Date: Tue, 2 Jun 2009 10:34:47 -0500 (CDT)
Subject: [Rd] formal argument "envir" matched by multiple actual
 arguments
In-Reply-To: <59d7961d0906020125w5b399755j594a018ca608318c@mail.gmail.com>
References: <4A24839C.50403@fhcrc.org>
	<20090602010540.k6d93dfdycc884wg@webmail.fhcrc.org>
	<59d7961d0906020125w5b399755j594a018ca608318c@mail.gmail.com>
Message-ID: <alpine.LFD.2.00.0906021031000.7161@nokomis.stat.uiowa.edu>

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.

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


[Rd] formal argument "envir" matched by multiple actual arguments
luke at stat.uiowa.edu