Hi, I used "rtracklayer' and ran into some problems in using browserSession() function. I traced back the code and found somthing might wrong in the "hguid" slot of a "ucscSession" object. Followin was the code I used. ======================================== library(rtracklayer) #browserSession("ucsc") ##error!!! Class<-"ucscSession" ClassDef <- getClass(Class, where = topenv(parent.frame())) value <- .Call("R_do_new_object", ClassDef, PACKAGE = "base") value at url <- "http://genome.ucsc.edu/cgi-bin/" value at views<-new.env() handle<-getCurlHandle() getURL("http://genome.ucsc.edu/cgi-bin/hgGateway", cookiefile = tempfile(),curl = handle) cart <- getURL("http://genome.ucsc.edu/cgi-bin/hgTracks", curl = handle) vlaue at hguid<-as.numeric(gsub(".*hguid=([^\n]*).*","\\1", cart)) #[1] NA #Warning message: #NAs introduced by coercion grep("hguid",cart) #integer(0) ======================================== As shown in the above result, "hguid" will be NA as will lead to the subsequent underling code of browserSession("ucsc") to be failed. How to fix this problem? Or this might related to 'cookie' or 'handle'? Thanks! ---- LiGang

Just for the record, I responded to an email about this problem sent directly to me. However, I still have not learned what the original error actually was... it's true that the code below does not work, but that's because it's incorrect and not the code in any version of rtracklayer, so I'm a bit confused :) On Wed, Aug 6, 2008 at 7:50 PM, LiGang <luzifer.li@gmail.com> wrote: > Hi, > > I used "rtracklayer' and ran into some problems in using > browserSession() function. > > I traced back the code and found somthing might wrong in the "hguid" > slot of a "ucscSession" object. > > Followin was the code I used. > > ======================================== > library(rtracklayer) > > #browserSession("ucsc") > > ##error!!! > > > Class<-"ucscSession" > ClassDef <- getClass(Class, where = topenv(parent.frame())) > value <- .Call("R_do_new_object", ClassDef, PACKAGE = "base") > > > value@url <- "http://genome.ucsc.edu/cgi-bin/" > value@views<-new.env() > handle<-getCurlHandle() > > getURL("http://genome.ucsc.edu/cgi-bin/hgGateway", cookiefile = > tempfile(),curl = handle) > cart <- getURL("http://genome.ucsc.edu/cgi-bin/hgTracks", curl = handle) > > vlaue@hguid<-as.numeric(gsub(".*hguid=([^\n]*).*","\\1", cart)) > > #[1] NA > #Warning message: > #NAs introduced by coercion > > > grep("hguid",cart) > > #integer(0) > ======================================== > > As shown in the above result, "hguid" will be NA as will lead to the > subsequent underling code of browserSession("ucsc") to be failed. > > How to fix this problem? Or this might related to 'cookie' or 'handle'? > > Thanks! > > ---- > LiGang > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]