[BioC] biomaRt problem

Wed Aug 23 10:54:53 CEST 2006

hi Steffen,
thanks for your help.
now biomart.org is up, but there are still some problems.

> mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
Error in file(file, "r") : unable to open connection
In addition: Warning message:
unable to resolve 'web50-node4.ebi.ac.uk'.

and in fact, if i try to open in browser the address 
http://www.biomart.org/biomart/martservice

i get this internal error message:
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<HTML><HEAD>
<TITLE>200 OK</TITLE>
</HEAD><BODY>
<H1>OK</H1>
The server encountered an internal error or
misconfiguration and was unable to complete
your request.<P>
Please contact the server administrator,
 webmaster&amp;#064;mydomain.org and inform them of the time the error 
occurred,
and anything you might have done that may have
caused the error.<P>
More information about this error may be available
in the server error log.<P>
</BODY></HTML>

what to do?

thanks again for your kind help
sincerely
Dario

On Tuesday 22 August 2006 15:58, Durinck, Steffen (NIH/NCI) [F] wrote:
> Hi Dario,
>
> Yes it looks like the website has been down for a few days which explains
> why useMart fails. I've CC'd Arek (BioMart developer) maybe he can shed
> more light on what is happening.
>
> best.
> Steffen
>
>
> -----Original Message-----
> From: Dario Greco [mailto:dario.greco at helsinki.fi]
> Sent: Tue 8/22/2006 4:59 AM
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] biomaRt problem
>
> dear list,
> i am trying to annotate some genes using biomaRt, but i am running in the
>
> following problem:
> > library(biomaRt)
>
> Loading required package: XML
> Loading required package: RCurl
>
> > mart <- useMart("ensembl")
>
> Error in curlPerform(curl = curl, .opts = opts) :
>         Couldn't resolve host 'www.biomart.org'
>
> i have also updated to the 1.7.6 version of biomaRt, but no change in the
> result.
>
> > sessionInfo()
>
> Version 2.3.1 (2006-06-01)
> i686-redhat-linux-gnu
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
> [7] "base"
>
> other attached packages:
>  biomaRt    RCurl      XML
>  "1.7.6"  "0.6-2" "0.99-8"
>
> i am pretty sure my computer doesn't have any proxy issues. moreover, if i
> try to open the www.biomart.org website in my browser, it appears down. is
> there some problem with the biomart mirror? should i use an alternative
> host? if yes, which?
> do you have any other suggestions?
> thanks in advance for your kind help.
> sincerely
> Dario

-- 

Dario Greco

Institute of Biotechnology - University of Helsinki
Building Cultivator II
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FIN-00014       Finland

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