[BioC] BiomaRt connection error

[Wu, Xiwei]

Francois,

Thank you for your help. I asked our network admin to open up outgoing
connection on port 3306, but I still got the same error. I am going to
try it tonight from my home computer to see if there is anything wrong
on my side first. Any other suggestions? 

Xiwei
-----Original Message-----
From: Francois Pepin [mailto:fpepin at cs.mcgill.ca] 
Sent: Wednesday, November 16, 2005 9:20 AM
To: Wu, Xiwei
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] BiomaRt connection error

Hi Xiwei,

yes, MySQL queries are outgoing connections.

On the other hand, it requires connection to a specific port (3306 if my
memory serves). It's not too uncommon to only allow connections to
predefined ports (say http, ftp and ssh).

The easiest for you would be to ask your network administrator if the
firewall would indeed be blocking an outgoing connection to an a server
on port 3306.

Francois

On Wed, 2005-11-16 at 08:44 -0800, Wu, Xiwei wrote:
> 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
> >
> >"EMF <COH.ORG>" made the following annotations.
> >---------------------------------------------------------------------
> >--
> >------- SECURITY/CONFIDENTIALITY WARNING:  This message and any 
> >atta...{{dropped}}
> >
> >_______________________________________________
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> >  
> >
> 
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