R devel - Jun 2021 - dgTMatrix Segmentation Fault

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).

--------------------------------------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia

Nice!

On 6/9/21 9:00 PM, Dario Strbenac via R-devel wrote:
> 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).
> 
> --------------------------------------
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>