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
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