[Rd] Crash in R using embedded.

Duncan Murdoch murdoch.duncan at gmail.com
Wed Feb 1 17:41:06 CET 2012

You posted this message already.  If you didn't get any responses based 
on that posting, I think it means nobody has any suggestions beyond what 
you're already doing.  Debugging is hard sometimes, even if you approach 
it in the right way.

A common source of hard-to-find bugs is the R garbage collection scheme: 
  if you don't PROTECT an allocation, sometimes it will be overwritten 
before you're done with it, because you haven't told R you're using it. 
  Running under gctorture() can sometimes trigger this sooner, but it's 
very slow.

Duncan Murdoch

On 12-02-01 10:24 AM, Dave Pugmire wrote:
> Hi,
> I'm new to R, and am trying to embed R into another application.
> I'm calling gev.fit() from the ismev package, and it is crashing somewhere
> inside it.
> gdb is not catching it, and valgrind is not showing any memory corruption
> issues.
> I suspect it's memory corruption, because it doesn't crash in exactly the
> same spot each time.
> I'm running R 2.12.2 on a 64 bit linux (Ubuntu 10.04)
> Also, before I make the gev.fit() call, I save out the R state using
> "save.image(....)", then load the image file into a standalone R on the
> console, and call gev.fit(), and it works fine.
> So, it's something to do with my app, and the R.
> I'm looking for hints/ideas/tricks/etc for debugging this.
> I'm starting to put print statements into the R code, and into the C code
> in R (src/main/optim.c), but it hasn't shown me the source of the problem.
> Thanks!
> Here is the code I'm using to initialize:
> putenv("R_HOME=/apps/R/install/lib64/R");
> const char *R_argv[]= {"RInterfaceTest", "--gui=none", "--no-save",
> "--no-readline", "--silent"};
> Rf_initialize_R(sizeof(R_argv)/sizeof(R_argv[0]), const_cast<char
> **>(R_argv));
> setup_Rmainloop();
> ParseStatus status;
> SEXP cmdSexp, cmdexpr = R_NilValue;
> int error;
> string rcommand = "f<-file(paste(tempdir(), \"/Routput.txt\", sep = \"\"),
> open=\"wt+\")\nsink(f)\n";
> PROTECT(cmdSexp = allocVector(STRSXP, 1));
> SET_STRING_ELT(cmdSexp, 0, mkChar(rcommand.c_str()));
> cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1,&status, R_NilValue));
> for(int i = 0; i<  length(cmdexpr); i++)
> {
>       R_tryEval(VECTOR_ELT(cmdexpr, i),NULL,&error);
>   }
> 	[[alternative HTML version deleted]]
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