From murdoch.duncan at gmail.com  Wed Feb  1 17:41:06 2012
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Wed, 01 Feb 2012 11:41:06 -0500
Subject: [Rd] Crash in R using embedded.
In-Reply-To: <CAM6_Vww=6SjgiDpZLQookKN=4jJCWz3HEBJyjTisq6yfAYaHMQ@mail.gmail.com>
References: <CAM6_Vww=6SjgiDpZLQookKN=4jJCWz3HEBJyjTisq6yfAYaHMQ@mail.gmail.com>
Message-ID: <4F296B22.4090607@gmail.com>

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);
>   }
>   UNPROTECT(2);
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] Crash in R using embedded.
Duncan Murdoch