You've got the right Michael Lawrence. I'm not getting that warning, so
please send your sessionInfo() output. Also, I hope you don't mind that
I've cc'd the Bioc list.

Michael


On Thu, Mar 27, 2014 at 8:07 PM, David Ghosh, PhD <dghosh@ifti.org> wrote:

>
> A specific example of the error:
>
> > tTrack<- import("testB3.bed")
> > gr<-GenomicData(tTrack, genome="hg19", asRangedData=TRUE)
> > sessionNew<-browserSession("UCSC")
> Warning message:
> In .local(.Object, ...) : NAs introduced by coercion
> > track(sessionNew, "test track")<-gr
> Error in UseMethod("xpathApply") :
>   no applicable method for 'xpathApply' applied to an object of class
> "NULL"
> >
>
> This is from an AWS EC2 instance in the us-east (Virginia) availability
> zone.
>
> David Ghosh, PhD
> President, Institute for Transcriptional Informatics
> Woodland Hills, CA 91365
> Telephone:  412-682-0550
> Website:  http://www.ifti.org/
>
> -----Original Message-----
> From: Michael Lawrence [mailto:lawrence.michael@gene.com]
> Sent: March 27, 2014 12:23:AM
> To: dghosh@ifti.org
> Cc: Michael Lawrence
> Subject: Re: rtracklayer connect problems
>
> Please send me the details of the connection issues. A lot of times, this
> is
> some sort of proxy getting in the way.
>
> Michael
>
>
>
> On Wed, Mar 26, 2014 at 7:59 PM, David Ghosh, PhD <dghosh@ifti.org> wrote:
>
>
>
>
>         Michael
>
>
>
>         Is there anything that's changed on the server side at the UCSC
> genome browser and how it might interact with Curl / rtracklayer?  There's
> a
> new connection problem that I've run into recently.
>
>
>
>         About the issue of connecting to specific UCSC sessions and the
> problems with that, I'll send the details/ code in the very near future.
>
>
>
>         David
>
>
>
>         David Ghosh, PhD
>
>         President/Owner
>         Institute for Transcriptional Informatics
>         Woodland Hills, CA 91365
>
>         Telephone:  412-682-0550
>
>         Website:  http://www.ifti.org/
>
>
>
>
>
>

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