Hi Seth, Thank you so much for your excellent help!
Best regards, Julie On 2/11/10 12:46 AM, "Seth Falcon" <[email protected]> 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 >> > > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
