Thanks Herve and Michael,
I'll just use my linux box.
Sonali.
On 10/16/2015 1:15 PM, Hervé Pagès wrote:
Hi Sonali, Michael,
Tried on Linux and Windows with BioC 3.3 and couldn't reproduce
this either (got the expected/usual warning about the cds cumulative
length not being a multiple of 3).
Hi Sonali, Michael,
Tried on Linux and Windows with BioC 3.3 and couldn't reproduce
this either (got the expected/usual warning about the cds cumulative
length not being a multiple of 3).
BTW I think GenomicRanges is failing in the devel builds because
of some issues with AnnotationHub. I don't
Update , I just see a warning on my linux box ( see the error only on
windows)
> txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene")
Download the refGene table ... OK
Download the refLink table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ...
Seemed to work for me. Could just be a transient issue with UCSC?
On Fri, Oct 16, 2015 at 12:02 PM, Arora, Sonali wrote:
> Hi ,
>
> I get an error when creating a txdb object for hg19 from the refGene Table
>
>> txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene")
> Error in tableName
Hi ,
I get an error when creating a txdb object for hg19 from the refGene Table
> txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene")
Error in tableNames(ucscTableQuery(session, track = track)) :
error in evaluating the argument 'object' in selecting a method for
function 'tableN
