[Rcpp-devel] Segfault, is it because of iterators/pointers?

Alessandro Mammana mammana at molgen.mpg.de
Tue Feb 11 15:18:23 CET 2014

Hi all,
I got another segfault using Rcpp. It is very difficult to understand
where it happens and to reduce it to a minimal example, so for now I
am not posting very precise code here, but I have a suspicion, maybe
you could help me saying if my suspect is right.

I am doing something similar:

in a .cpp file:
struct GapMat {
    int* ptr;
    int* colset;
    int nrow;
    int ncol;

    inline int* colptr(int col){
        return ptr + colset[col];


    GapMat(int* _ptr, int* _colset, int _nrow, int _ncol):
        ptr(_ptr), colset(_colset), nrow(_nrow), ncol(_ncol){}

// [[Rcpp::export]]
IntegerVector colSumsGapMat(Rcpp::IntegerVector vec,
Rcpp::IntegerVector pos, int nrow){
   GapMat mat(vec.begin(), pos.begin(), nrow, pos.length());
   IntegerVector res(pos.length());

    for (int i = 0; i < pos.length(); ++i){
        for (int j = 0; j < nrow; ++j){
            res[i] += mat.colptr(i)[j];

    return res;

from R:

vec <- a very big integer vector
nrow <- 80
pos <- a very big subset of positions, such that max(pos) + nrow < length(vec)
colsums <- colSumsGapMat(vec, pos, nrow)

from time to time I get a segfault.
Note: this is not exactly the code that produces the segfault (because
that one is very complicated), so it might be that this code is
totally fine.

My suspicion:

I am using the pointer "vec.begin()", but then I am allocating new
memory in the R area of memory with "IntegerVector res(pos.length())"
and R decides to move the original values of "vec" to some other
place, making the pointer invalid.

Is that possible????

Sorry for being very vague and thx in advance!!!

Alessandro Mammana, PhD Student
Max Planck Institute for Molecular Genetics
Ihnestraße 63-73
D-14195 Berlin, Germany

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