[BioC] problem connecting to bioMart - NOT proxy error
Jenny Drnevich
drnevich at illinois.edu
Thu Nov 19 17:47:09 CET 2009
Hi Seth and James,
Thanks for your help. I'm on a desktop, so I don't think I can
connect from a different network. The odd thing is that when I
started my computer this morning, I was able to get
http://www.biomart.org/ up on my browser, pretty quickly. However,
then I opened a fresh session of R and had the same problems as
before. After that, I wasn't able to get http://www.biomart.org/
again on my browser! I just rebooted my machine, and tried
http://www.biomart.org/ on the browser again before starting R; it
took several minutes but it finally came up, but then I couldn't get
it to re-load (still not having started R). I don't know why I'm
having these weird connection problems - maybe my machine is
establishing a connection through R, but when it gets hung up it
doesn't relinquish the connection even after killing R and rebooting?
Time to call in my IT people - any suggestions for things to check
out would be appreciated!
Thanks,
Jenny
At 10:08 PM 11/18/2009, Seth Falcon wrote:
>Hi Jenny,
>
>On 11/18/09 2:25 PM, Jenny Drnevich wrote:
>>I don't know if this is related, but I
>>can't get http://www.biomart.org/ to come up on my browser, either,
>>although I have no trouble with http://www.ensembl.org/biomart/martview/.
>
>Hmm, that sounds suspicious. I can browse to that site without
>problem and seem to be able to connect to both marts quickly (see
>below). I wonder if you can try connecting from a cafe to try a
>different network?
>
>
>
> > library("biomaRt")
> > system.time(ensembl <- useMart("ensembl"))
> user system elapsed
> 0.103 0.006 0.479
> > system.time(ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl))
>Checking attributes ... ok
>Checking filters ... ok
> user system elapsed
> 0.032 0.008 1.902
>
> > sessionInfo()
>R version 2.11.0 Under development (unstable) (--)
>i386-apple-darwin10.0.0
>
>locale:
>[1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8
>
>attached base packages:
>[1] stats graphics grDevices datasets utils methods base
>
>other attached packages:
>[1] biomaRt_2.3.0
>
>loaded via a namespace (and not attached):
>[1] RCurl_1.2-1 XML_2.6-0
Jenny Drnevich, Ph.D.
Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign
330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA
ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at illinois.edu
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