Dear Xianyong,

Thanks for the feedback!

Regarding the error you got, it seems to be a memory issue. Could you please take a look at the post at http://www.mail-archive.com/r-help@stat.math.ethz.ch/msg91461.html? I am ccing the list to get input from the experts in memory setting and management.

Best regards,

Julie


On 5/4/12 3:07 PM, "Ma, Xian-Yong" <xian-yong.ma@yale.edu> wrote:

Hi, Dear Dr.Zhu:

I got nice results by using your software, and I am still using this soft ware to analyze other data, now I have the following problem and tried two days, I
can't figured out, would you please help me to solve this problem, I am really appreciate! since the file is bigger than 60 Mb (after compressed), I can't send it
directly.

When I used the CHIPAnno software to analysis my data, as problem always exist as following:


> test1.bed=read.table("/Users/xm5/Downloads/ChIPpeakAnno/data/CHIPJ3.bed", sep="\t", skip=0, header=FALSE)
> CHIPJ3 = BED2RangedData(test1.bed, header=FALSE)
> data(TSS.human.GRCh37)
> annotatedPeak = annotatePeakInBatch(CHIPJ3, AnnotationData=TSS.human.GRCh37)
Error: cannot allocate vector of size 14.4 Mb
R(365,0xa0416540) malloc: *** mmap(size=15118336) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug


I don't know what's reason, and I checked the file using other program, it looks OK, would you please help me to figure out, I appreciate your nice help please see the
attached file that I used for this analysis.






Best wishes,

Xianyong


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