Hi Budi and Bill,
As a workaround, you could try setting your stack limit to a larger
limit (ulimit -s). I'll change that to a heap allocation.
Thanks,
Marcus
William Dunlap wrote:
This is probably due to the code in hdf5.c allocating a huge
matrix, buf, on the stack with
883 unsigned char buf[rowcount][size];
It dies with the segmentatio fault (stack overflow, in particular)
at line 898, where it tries to access this buf.
885 for (ri = 0; ri < rowcount; ri++)
886 for (pos = 0; pos < colcount; pos++)
887 {
888 SEXP item = VECTOR_ELT (val, pos);
889 SEXPTYPE type = TYPEOF (item);
890 void *ptr = &buf[ri][offsets[pos]];
891
892 switch (type)
893 {
894 case REALSXP:
895 memcpy (ptr, &REAL (item)[ri], sizeof
(double));
896 break;
897 case INTSXP:
898 memcpy (ptr, &INTEGER (item)[ri], sizeof
(int));
899 break;
The code should use one of the allocators in the R API instead
of putting the big memory block on the stack.
========
The data example, the list continue for more than 250,000
rows: sample.txt
========
Date Time f1 f2 f3 f4 f5
20070328 07:56 463 463.07 462.9 463.01 1100
20070328 07:57 463.01 463.01 463.01 463.01 200
....
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