[BioC] BiomaRt connection error

[Wu, Xiwei]

Steffen,

Thank you very much for your reply. I think it might be due to firewall
issue, but a little confused on how MySQL qyeries works here. I thought
firewall usually does not block out-going traffic. 

How to enable mysql queries in the firewall? Are there any specific
ports need to be opened?  

Xiwei

-----Original Message-----
From: Steffen Durinck [mailto:sdurinck at ebi.ac.uk] 
Sent: Wednesday, November 16, 2005 1:55 AM
To: Wu, Xiwei
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] BiomaRt connection error

Hi Xiwei,

Are you behind a firewall?
Keep in mind that the current biomaRt will try to do MySQL queries to
the databases, if you are behind a firewall then these queries won't go
through and you get the error you show.
You can either ask your systems to enable mysql queries or install a
local version of the BioMart database you want to query with biomaRt.

best,
Steffen

On which platform are you working? Do you have the XML package
installed?

Wu, Xiwei wrote:

>Dear list: 
>
>I just installed biomaRt1.4.0, RMySQL, and DBI. I am using R2.2.0 with 
>BioC 1.7. I got error message when trying to connect mart:
>
>  
>
>>mart <- martConnect()
>>    
>>
>Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not 
>connect anonymous at ensembldb.ensembl.org on dbname "(null)")
>
>Or
>
>  
>
>>marts <- listMarts()
>>    
>>
>Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not 
>connect anonymous at ensembldb.ensembl.org on dbname "(null)")
>
>IS there any special settings that I missed? Any help will be highly 
>appreciated.
>
>Xiwei Wu, MD, PhD
>Assistant Research Scientist
>Department of Biomedical Informatics
>Beckman Research Institute
>City of Hope National Medical Center
>Duarte, CA 91010
>
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