[Rcpp-devel] R CMD BATCH - segfault (was: Create and access several instances of a C++ class from R)

[romain at r-enthusiasts.com]

Le 20 mai 2011 à 12:01, soeren.vogel at uzh.ch a écrit :

> On 18.05.2011, at 15:17, Douglas Bates wrote:
> 
>> On May 18, 2011 2:53 AM, <soeren.vogel at uzh.ch> wrote:
>> 
>>> [...]
>>> 
>>> When librarying the class, assigning an object, do some calculations,
>>> whatever -- everything goes fine. Yet, when using R CMD BATCH on a file
>>> listing the same commands as by hand, R produces some nice information at
>>> the end, however, here it produces an segmentation fault, which does --
>>> according to my small knowledge -- say something bad:
>>> 
>>> proc.time()
>>> user  system elapsed
>>> 0.702   0.017   0.714
>>> R(72992) malloc: *** error for object 0x2c9b604: incorrect checksum for
>>> freed object - object was probably modified after being freed.
>>> *** set a breakpoint in malloc_error_break to debug
>>> 
>>> *** caught segfault ***
>>> address 0x4909d58, cause 'memory not mapped'
>>> 
>>> Traceback:
>>> 1: save(list = ls(envir = .GlobalEnv, all.names = TRUE), file = outfile,
>>>   version = version, ascii = ascii, compress = compress, envir =
>>> .GlobalEnv,     precheck = FALSE)
>>> 2: save.image(name)
>>> 3: sys.save.image(".RData")
>>> aborting ...
>>> 
>>> Any idea what goes wrong there?
>> 
>> As you can see, the problem occurs when R is saving the worksheet.  At
>> present an instance of a Rcpp module class cannot be saved. It is likely
>> that this will need to be addressed by the person designing each C++ class
>> that will be expressed in a module.  R can't serialize the contents of
>> memory that it doesn't "own".
>> 
>> The current fix is "don't do that".  Add the --no-save or --vanilla in your
>> call to R CMD BATCH to suppress saving the worksheet.
> 
> Hello Douglas
> 
> Ah, I see. Thanks for this tip.
> 
> However, I am wondering why removing objects and detaching the package (where the Rcpp module resides) do not resolve the issue in the same way:
> 
> x <- new(FOO)
> do_something_with_x()
> rm(x)
> detach("package:GUTS")

My guess is this is related to garbage collection. Removing an object makes it candidate for GC, but it does not necessarily occur right away. 

Maybe forcing it through gc() would do the trick ...


> Regards
> *S*
> 
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