[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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