[Rd] dgTMatrix Segmentation Fault

[Dario Strbenac]

Good day,

Thanks to handy hints from Martin Morgan, I ran R under gdb and checked for any numeric overflow. We pinpointed the cause:

(gdb) info locals
i = 0
j = 10738
m = 200000
n = 50000
ans = 0x55555b332790
aa = 0x55555b3327c0

There is a line of C code in dgeMatrix.c for (i = 0; i < m; i++) aa[i] += xx[i + j * m];

i  + j * m are all int, and overflow
(lldb) print 0 + 10738 * 200000
(int) $5 = -2147367296

So, either the code should check that this doesn't occur, or be adjusted to allow for large indexes.

If anyone is interested, this is in the context of single-cell ATAC-seq data, which typically has about 200000 genomic regions (rows) and perhaps 100000 biological cells (columns).

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Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia