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

[Julie Zhu]

Hi Seth,

Thank you so much for your excellent help!

Best regards,

Julie


On 2/11/10 12:46 AM, "Seth Falcon" <sfalcon at fhcrc.org> wrote:

> 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
>> 
> 
>