[Bioc-sig-seq] Annotation of ChIP-Seq peaks

[Seth Falcon]

On 2/9/10 1:21 PM, Julie Zhu wrote:
> BTW, have you encountered the error: segfault from C stack overflow?

I did some looking into the segfault reported by P. Terry.  I believe 
that the root cause here is in R's gsub implementation and I am trying 
to track it down.

The crash comes from a call to gsub inside biomaRt's getBM function 
where it tries to eliminate newline characters in a long string.  The 
call is essentially:

     gsub("\n", "", big)

where big is a length one character vector containing ~16M characters 
and ~33.5K newlines.

I'll try to report back when I have more details.

+ seth

-- 
Seth Falcon
Bioconductor Core Team | FHCRC