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

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")