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

[Julie Zhu]

Hi Seth,

Thank you so much for being so resourceful and helpful!

Best regards,

Julie


*******************************************
Lihua Julie Zhu, Ph.D
Research Associate Professor
Program Gene Function and Expression
University of Massachusetts Medical School
364 Plantation Street, Room 613
Worcester, MA 01605
508-856-5256
http://www.umassmed.edu/pgfe/faculty/zhu.cfm




On 2/9/10 4:43 PM, "Seth Falcon" <sfalcon at fhcrc.org> wrote:

> 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