Re: [Rd] Segmentation faults on SEXP conversion

From: Duncan Murdoch <murdoch_at_stats.uwo.ca>
Date: Sun, 15 Nov 2009 14:52:18 -0500

On 15/11/2009 1:41 PM, nabble.30.miller_2555_at_spamgourmet.com wrote:
> Hello -
>
> I am making a first attempt at writing a simple C++ routine to print
> out R objects (this is a simple proof-of-concept as part of a larger
> package development). The relevant C++ routine is as follows:
>
> void Rwrite(SEXP fd, SEXP msg) {
> int *ofd = INTEGER(fd);
> const char * omsg = CHAR(asChar(msg));

The "character" type in R corresponds to STRSXP in C, which is a vector of CHARSXPs. So you need an extra step to get to the C string:

const char * omsg = CHAR(STRING_ELT(msg, 0));

Duncan Murdoch

> printf("[%i] %s",*ofd,omsg);
> }
>
> And the corresponding interface in R is as follows:
>
> ptest <- function()
> {
> cfd <- as.integer(2);
> cmsg <- as.character("Hi");
> storage.mode(cfd) <- "integer";
> storage.mode(cmsg) <- "character";
> .Call("Rwrite",
> fd=cfd,
> msg=cmsg,
> PACKAGE="forkex"
> );
> }
>
> Upon running the above code as a call to `ptest()`, I receive a
> segmentation fault. Building the package as `R CMD check
> --use-valgrind ...` provides the following memcheck output:
>

>> ptest();

> ==12591== Invalid read of size 1
> ==12591== at 0x4D04209: SET_SYMVALUE (in /usr/lib64/R/lib/libR.so)
> ==12591== by 0x4D01E51: Rf_ReplIteration (in /usr/lib64/R/lib/libR.so)
> ==12591== by 0x4D020B7: (within /usr/lib64/R/lib/libR.so)
> ==12591== by 0x4D027CF: run_Rmainloop (in /usr/lib64/R/lib/libR.so)
> ==12591== by 0x40083A: main (in /usr/lib64/R/bin/exec/R)
> ==12591== Address 0x9 is not stack'd, malloc'd or (recently) free'd
> [2] Hi
> *** caught segfault ***
> address 0x9, cause 'memory not mapped'
> aborting ...
> ==12591==
> ==12591== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 18 from 1)
> ==12591== malloc/free: in use at exit: 22,564,238 bytes in 10,614 blocks.
> ==12591== malloc/free: 29,096 allocs, 18,482 frees, 44,702,479 bytes allocated.
> ==12591== For counts of detected errors, rerun with: -v
> ==12591== searching for pointers to 10,614 not-freed blocks.
> ==12591== checked 19,665,464 bytes.
> ==12591==
> ==12591== LEAK SUMMARY:
> ==12591== definitely lost: 0 bytes in 0 blocks.
> ==12591== possibly lost: 0 bytes in 0 blocks.
> ==12591== still reachable: 22,564,238 bytes in 10,614 blocks.
> ==12591== suppressed: 0 bytes in 0 blocks.
> ==12591== Rerun with --leak-check=full to see details of leaked memory.
>
> The same segmentation fault occurs whether I try passing either the
> `int` or `character` or both (as in the above). I have not tried other
> types. However, I have attempted various type conversions in the
> Rdefines.h header, but cannot avoid the segmentation fault. This is
> the only code in the proof-of-concept pacakage (aside from useDynLoad
> related registration structures and the R_init_??? call).
>
> I have a feeling it is something simple, but I am not well versed in R
> package development at this point. Please let me know if other
> information is helpful.
>
> I am running Linux 2.6.27.30-170.2.82.fc10.x86_64 with R 2.10.0.
>
> Thanks!
>
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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Sun 15 Nov 2009 - 19:55:30 GMT

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