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[Rcpp-devel] simple Rcpp function produces: "AddressSanitizer: attempting free on address which was not malloc"

Nick Matzke 
I have an R package, cladoRcpp, which is up on CRAN.  After 
a minor update, which compiled without errors on R CMD check 
on my machine, I submitted the update.

Brian Ripley got an error that I didn't get:


==================================================================
We still see

 > Rcpp_combn_zerostart(n_to_choose_from=4, k_to_choose=2, 
maxlim=1e+07)
=================================================================
==14369== ERROR: AddressSanitizer: attempting free on 
address which was not malloc()-ed: 0x0000040541d0
     #0 0x7fe61090caca in ?? ??:0
     #1 0x7fe6138ba858 in 
_ZN9__gnu_cxx13new_allocatorIiE10deallocateEPim 
/usr/local/gcc48x/include/c++/4.8.1/ext/new_allocator.h:110
     #2 0x7fe613896fd4 in cpp_combn_zerostart 
/data/gannet2/ripley/R/packages/incoming/cladoRcpp.Rcheck/00_pkg_src/cladoRcpp/src/calc_anclikes_sp.cpp:75
     #3 0x472b5f in do_dotcall 
/data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:587

using AddressSanitizer, as before.
==================================================================


I gather that this is from him using the new gcc4.8 and the 
AddressSanitizer option on compile:

http://r.789695.n4.nabble.com/Linux-distribution-with-gcc-4-8-and-AddressSanitizer-td4664629.html

http://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Using-gctorture-and-memory-access


I will attempt to download/install gcc48 and reproduce the 
error, although this is a somewhat major project.


The C++ function, though, is quite simple -- I wonder if 
anyone might be able to spot easily what is going on?





R function which calls C++ function:

======================================
Rcpp_combn_zerostart <- function(n_to_choose_from, 
k_to_choose, maxlim=1e+07)
	{
	n = n_to_choose_from
	m = k_to_choose
	
	# HEAD OFF ERROR
	predicted_number_of_cells_to_fill = choose(n,m)
	
	if (predicted_number_of_cells_to_fill > maxlim)
		{
		txt = paste("ERROR: n=", n_to_choose_from, ", k=", 
k_to_choose, ", n choose k=", 
predicted_number_of_cells_to_fill, " > maxlim=", maxlim, 
"\nCalculating something this big may crash your computer!", 
sep="")
		stop(txt)
		}
	
	
	outarray = .Call("cpp_combn_zerostart", as.integer(n), 
as.integer(m), as.double(maxlim))

	#R_states_list <- matrix(out$res,nrow=m,byrow=F)

	return(outarray)
	}
======================================



C++ function:
======================================

RcppExport SEXP cpp_combn_zerostart(SEXP R_n, SEXP R_m, SEXP 
R_maxval)
	{
	using namespace std;
	
	// Convert to plain C++
	int cpp_nval = Rcpp::as<int>(R_n);
	int cpp_mval = Rcpp::as<int>(R_m);
	double cpp_maxval = Rcpp::as<double>(R_maxval);
	
	// Create pointer variables to hold the addresses to each
	int* n = &cpp_nval;
	int* m = &cpp_mval;
	
	// Choose n by m; calculate from the values stored at 
addresses n and m
	double Cnm;
	Cnm = nChoosek(*n, *m);
	
	// Error check
	if (Cnm > cpp_maxval)
		{
		//cout << "\nERROR: n=" << cpp_nval << ", k=" << cpp_mval 
<< ", n choose k=" << Cnm << " > maxval=", cpp_maxval;
		//cout << "\nCalculating something this big may crash your 
computer!  Returning 0.";
		return 0;
		}
	
	
	// Declare and populate empty array of addresses to hold 
the combn results
	// Addresses for a 10x3 array; 30 total
	int* combmat;
	combmat = new int[(int)Cnm**(m+0)];
	
	// Run moncombn_zerostart; this will update the stuff in 
the addresses
	// stored in combmat
	moncombn_zerostart(combmat,n,m);
	
	// Write the contents of each of the Cnm times *m addresses 
to cout
	// convert double (float) Cnm to int
	int nrows;
	int ncols;
	nrows = *m;
	ncols = (int)Cnm;
	int vecsize;
	vecsize = nrows * ncols;
	//int combmat_vals[nrows * ncols];
	
	//Rcpp::NumericVector combmat_vals(vecsize);	// vector of 
size vecsize filled with 0s
	Rcpp::NumericMatrix combmat_vals(nrows,ncols);	// vector of 
size vecsize filled with 0s

	// initialize row & column numbers, and the temporary number	
	int rownum = 0;
	int colnum = 0;
	int tmpnum = 0;
	
	//cout << nrows << " rows, " << ncols << "cols...\n";
	
	for (int j = 1; j <= Cnm**(m+0); j++)
		{
		//cout << "\n";
		//cout << *(combmat+j-1) << " ";
		//combmat_vals[rownum][colnum] = *(combmat+j-1);
		//tmpnum = Rcpp::as<int>(*(combmat+j-1));
		tmpnum = *(combmat+j-1);
		//combmat_vals[j-1] = tmpnum;

		//cout << "\n" << rownum << "," << colnum << ", ncols=" << 
ncols << ": " << tmpnum;
		combmat_vals(rownum, colnum) = tmpnum;
		
		// Increment column
		rownum++;
		
		// Reset column when you reach the end; increment the row.
		// Reset of rows is not necessary
		if (rownum >= (nrows))
			{
			rownum = 0;
			colnum++;
			}
		} // end forloop

	// Convert to an int
	//Rcpp::Matrix outcombs(combmat_vals);
	
	// example use Armadillo matrix
	// http://dirk.eddelbuettel.com/blog/2011/04/23/
	//arma::mat outcombs = Rcpp::as<arma::mat>(combmat_vals);
	
	return Rcpp::wrap(combmat_vals);
	}
======================================
	

Thanks for any and all help!  These memory errors are tough 
for us biologists!!

Cheers, Nick

Thread (5 messages)

Nick Matzke simple Rcpp function produces: "AddressSanitizer: attempting free on address which was not malloc" Jul 8 Darren Cook simple Rcpp function produces: "AddressSanitizer: attempting free on address which was not malloc" Jul 8 Dirk Eddelbuettel simple Rcpp function produces: "AddressSanitizer: attempting free on address which was not malloc" Jul 8 Smith, Dale (Norcross) simple Rcpp function produces: "AddressSanitizer: attempting free on address which was not malloc" Jul 9 Smith, Dale (Norcross) simple Rcpp function produces: "AddressSanitizer: attempting free on address which was not malloc" Jul 9