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
--
====================================================
Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley
Graduate Student Instructor, IB200B
Principles of Phylogenetics: Ecology and Evolution
http://ib.berkeley.edu/courses/ib200b/
http://phylo.wikidot.com/
Lab websites:
http://ib.berkeley.edu/people/lab_detail.php?lab=54
http://fisher.berkeley.edu/cteg/hlab.html
Dept. personal page:
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page:
http://fisher.berkeley.edu/cteg/members/matzke.html
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: mat...@berkeley.edu
Mailing address:
Department of Integrative Biology
1005 Valley Life Sciences Building #3140
Berkeley, CA 94720-3140
-----------------------------------------------------
"[W]hen people thought the earth was flat, they were wrong.
When people thought the earth was spherical, they were
wrong. But if you think that thinking the earth is spherical
is just as wrong as thinking the earth is flat, then your
view is wronger than both of them put together."
Isaac Asimov (1989). "The Relativity of Wrong." The
Skeptical Inquirer, 14(1), 35-44. Fall 1989.
http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
