From nabble.30.miller_2555 at spamgourmet.com  Sun Nov 15 19:41:49 2009
From: nabble.30.miller_2555 at spamgourmet.com (nabble.30.miller_2555 at spamgourmet.com)
Date: Sun, 15 Nov 2009 13:41:49 -0500
Subject: [Rd] Segmentation faults on SEXP conversion
Message-ID: <1dd941090911151041q58de5995y281885f7afcdc48c@mail.gmail.com>

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));
  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!



[Rd] Segmentation faults on SEXP conversion
nabble.30.miller_2555 at spamgourmet.com