[BioC] problem connecting to bioMart - NOT proxy error

[Seth Falcon]

Hi Jenny,

On Thu, Nov 19, 2009 at 8:47 AM, Jenny Drnevich <drnevich at illinois.edu> wrote:
> Thanks for your help. I'm on a desktop, so I don't think I can connect from
> a different network.

Hey, that's what extension cords are for ;-)

> 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!

One thing to be aware of is that I believe the biomart site imposes
some rate limits and possibly temporary blocks when it receives too
many requests in a short period of time.  I'm not up on the details so
might be getting this wrong.  If they are indeed doing some dynamic
blocking/limiting based on query rate, then a misbehaving colleague
could impact your access.

Otherwise, it would be worth asking for some local IT support to
assess general network connectivity to the biomart server.  For
example, if you get a lot of packet loss when pinging their server,
that might give you an idea that the problem is at a more generic
networking level.

+ seth

>
> 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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-- 
Seth Falcon | @sfalcon | http://userprimary.net/user