From hpages at fhcrc.org  Thu Jul 16 04:15:22 2009
From: hpages at fhcrc.org (=?ISO-8859-1?Q?Herv=E9_Pag=E8s?=)
Date: Wed, 15 Jul 2009 19:15:22 -0700
Subject: [Rd] Resizing a named vector crashes
	R	with	gctorture(TRUE)	(PR#13837)
In-Reply-To: <4A5E7E07.8040203@fhcrc.org>
References: <20090716004516.0A505282BE84@mail.pubhealth.ku.dk>
	<4A5E7E07.8040203@fhcrc.org>
Message-ID: <4A5E8D3A.30206@fhcrc.org>

I have to confess that I'm a little bit puzzled by how the
PROTECT/UNPROTECT mechanism is used in the C code of R.
Duncan, you say the problem you just fixed was an easy one.
I looked at the C code too and was able to recognize a pattern
that is indeed easy to identify as problematic:

   an unprotected call to allocVector() followed by a call
   that can trigger garbage collection (in that case another
   call to allocVector())

It only took me 1 minute to find another occurrence of this pattern.
It's in the do_grep() function (src/main/character.c, line 1168):

   > gctorture(TRUE)
   > grep("b", c(A="aa", B="aba"), value=TRUE)
     B
   "B"

Given that the overhead of PROTECTing the SEXP returned by
allocVector() can really be considered 0 (or almost), I'm
wondering why this is not done in a more systematic way.
Even when nothing between PROTECT(allocVector()) and the
corresponding UNPROTECT could trigger garbage collection
(e.g. PROTECT(allocVector()) is close to the return statement).
Because making exceptions like this can make your code
really hard to maintain in the long term.

Cheers,
H.


Herv? Pag?s wrote:
> murdoch at stats.uwo.ca wrote:
>> On 15/07/2009 8:30 PM, murdoch at stats.uwo.ca wrote:
>>> On 15/07/2009 8:08 PM, Herv? Pag?s wrote:
>>>> Hi,
>>>>
>>>>    > x <- c(a=10, b=20)
>>>>    > length(x) <- 1
>>>>    > x
>>>>     a
>>>>    10
>>>>
>>>> But with gctorture turned on, I get:
>>>>
>>>>    > gctorture(TRUE)
>>>>    > x <- c(a=10, b=20)
>>>>    > length(x) <- 1
>>>>    > x
>>>>      a
>>>>    "a"   <---- ???
>>>>
>>>>    > x <- c(a=10, b=20)
>>>>    > length(x) <- 3
>>>>
>>>>     *** caught segfault ***
>>>>    address (nil), cause 'unknown'
>>>>
>>>>    Possible actions:
>>>>    1: abort (with core dump, if enabled)
>>>>    2: normal R exit
>>>>    3: exit R without saving workspace
>>>>    4: exit R saving workspace
>>>>
>>>> This seems to have been around for a while (I get this with R 2.10,
>>>> 2.9 and 2.8). Note that I don't get this with an unnamed vector.
>>>>
>>>> This problem affects the methods package. I found it while
>>>> troubleshooting the "Protection stack overflow" I reported earlier
>>>> (see https://stat.ethz.ch/pipermail/r-devel/2009-July/054030.html)
>>>> but I can't tell yet whether the 2 issues are related or not.
>>> That's clearly a bug (reproducible in today's R-devel build); I've 
>>> cc'd this reply to r-bugs.  I'll take a look and see if I can track 
>>> it down.
>>
>> That's got to be the easiest low-level bug I've worked on in a while. 
>> Just a missing PROTECT.  Now fixed, about to be committed to R-devel.
> 
> Thanks Duncan! And the "Protection stack overflow" issue that was affecting
> the methods package is gone now :)
> 
> Cheers,
> H.
> 
>>
>> Duncan Murdoch
>>
>>>> It would be nice to see some reaction from the R developers
>>>> about these issues. Thanks in advance!
>>> You should post them as bug reports if they are as clearly bugs as 
>>> this one; otherwise they can easily get lost in the noise.  I'm not 
>>> going to offer to look into the other one; I don't know the insides 
>>> of the methods package.
>>>
>>> Duncan Murdoch
>>>
>>>> H.
>>>>
>>>>
>>>> hpages at fhcrc.org wrote:
>>>>> Hi,
>>>>>
>>>>>   > gctorture(TRUE)
>>>>>   > setGeneric("foo", function(x, y) standardGeneric("foo"))
>>>>>   [1] "foo"
>>>>>   > setMethod("foo", c("ANY", "ANY"),
>>>>>   +   function(x, y) cat("calling foo,ANY,ANY method\n")
>>>>>   + )
>>>>>   Error: protect(): protection stack overflow
>>>>>
>>>>> Sorry this is something I already reported one week ago here
>>>>>   https://stat.ethz.ch/pipermail/r-devel/2009-July/053973.html
>>>>> but I just had a 2nd look at it and realized that the problem
>>>>> can in fact be reproduced out of the .onLoad() hook. So I'm
>>>>> reporting it again with a different subject.
>>>>>
>>>>> See my sessionInfo() below. Thanks!
>>>>> H.
>>>>>
>>>>>
>>>>>> sessionInfo()
>>>>> R version 2.10.0 Under development (unstable) (2009-06-26 r48837)
>>>>> x86_64-unknown-linux-gnu
>>>>>
>>>>> locale:
>>>>>  [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C
>>>>>  [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8
>>>>>  [5] LC_MONETARY=C              LC_MESSAGES=en_CA.UTF-8
>>>>>  [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C
>>>>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>>>> [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
>>>>>
>>>>> attached base packages:
>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>>
>>>>> ______________________________________________
>>>>> 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
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> 

-- 
Herv? Pag?s

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: hpages at fhcrc.org
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[Rd] Resizing a named vector crashes R with gctorture(TRUE) (PR#13837)
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