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

[Seth Falcon]

Hi all,

This should be fixed in latest R-devel.  I was able to run the following
example without error:

library(biomaRt)
library(ChIPpeakAnno)
mart = useMart(biomart="plant_mart_3", dataset="athaliana_eg_gene")
x = getAnnotation(mart, featureType="TSS")


+ seth


On 2/9/10 1:43 PM, Seth Falcon 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
>