Entering edit mode
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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