[BioC] biomaRt package listMarts() error

[Ye, Bin]

Thank you Steffen, and thank you Sean! I really appreciate all your help!


Bin


-----Original Message-----
From: Steffen Durinck [mailto:sdurinck at ebi.ac.uk]
Sent: Thu 6/30/2005 3:47 AM
To: Ye, Bin
Cc: Sean Davis; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] biomaRt package listMarts() error
 
Hi Bin,

Thanks for reporting this, it is a bug the listMarts function and I will 
fix it.
The BioMarts that are currently accessible with the biomaRt package are 
ensembl, vega, snp and sequence.
If you want to connect to all or some of these you can do the following:

 > mart<-martConnect(biomarts=c("ensembl","snp","vega","sequence"))
connected to:  ensembl_mart_31
connected to:  snp_mart_31
connected to:  vega_mart_31
connected to:  sequence_mart_31

Cheers,
Steffen


Sean Davis wrote:

>Is RMySQL installed?
>
>If so, what happens when you do:
>
>driv <- dbDriver('MySQL', force.reload=FALSE)
>conn <-  
>dbConnect(driv,user='anonymous',password='',host='ensembldb.ensembl.org' 
>)
>res <- dbGetQuery(conn,"show databases like '%mart%'")
>dbDisconnect(conn)
>res
>
>Do you get something that lists the databases like:
>ensembl_mart_27_1
>ensembl_mart_28_1
>....
>
>Sean
>
>
>On Jun 29, 2005, at 3:33 PM, Ye, Bin wrote:
>
>  
>
>>Hi, everyone,
>>
>>I met an error message when I using biomaRt package.
>>    
>>
>>>listMarts()
>>>      
>>>
>>Error in if (is.na(pattern)) { : argument is of length zero
>>In addition: Warning message:
>>is.na() applied to non-(list or vector) in: is.na(pattern)
>>
>>Does anyone know what's wrong? I'm running windows 2k, R 2.0.1,  
>>bioconductor 1.6, and biomaRt 1.1.2.
>>
>>Thanks a lot!
>>
>>
>>Bin
>>
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>>    
>>
>
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>