[BioC] BiomaRt connection error

[Steffen Durinck]

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
>
>"EMF <COH.ORG>" made the following annotations.
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>  
>