[BioC] biomaRt

[James W. MacDonald]

No, I am not talking about your internet connection, I am talking about 
the biomart web server at http://www.biomart.org/. The biomaRt package 
by default uses this web server, so if you cannot get the page to load 
in a browser, you will not be able to query using biomaRt either.

Best,

Jim



On 7/13/2010 12:43 PM, Fraser Sim wrote:
> My internet connection was fine if that's what you mean. I don't know how
> else to check bioMart directly? Is there a link which shows the status of
> the server?
>
> Cheers,
> Fraser
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of James W.
> MacDonald
> Sent: Tuesday, July 13, 2010 12:25 PM
> To: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] biomaRt
>
> Hi Fraser,
>
> On 7/13/2010 12:16 PM, Fraser Sim wrote:
>> I'm having a problem with biomaRt today. Is the service down? Or do I have
>> another problem? Thanks.
>
> Rather than asking here, wouldn't it be easier to just fire up a browser
> and see if the web service is available? That's what I just did, and I
> get no response, so there is your answer...
>
>
> Best,
>
> Jim
>
>
>>
>>> Hs.ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl")
>> Checking attributes ...Error in value[[3L]](cond) :
>>     Request to BioMart web service failed. Verify if you are still
> connected
>> to the internet.  Alternatively the BioMart web service is temporarily
> down.
>>
>>> sessionInfo()
>> R version 2.10.1 (2009-12-14)
>> i386-pc-mingw32
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] grid      stats     graphics  grDevices datasets  utils     methods
>> [8] base
>>
>> other attached packages:
>>    [1] biomaRt_2.2.0          annotationTools_1.18.0 Biobase_2.6.1
>>    [4] gplots_2.7.4           caTools_1.10           bitops_1.0-4.1
>>    [7] gdata_2.6.1            gtools_2.6.1           RColorBrewer_1.0-2
>> [10] RODBC_1.3-1            rcom_2.2-1             rscproxy_1.3-1
>>
>> loaded via a namespace (and not attached):
>> [1] RCurl_1.3-0 XML_2.6-0
>>
>> Thanks,
>> Fraser
>>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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