[BioC] biomaRt

[Durinck, Steffen (NIH/NCI) [F]]

Hi Joao,

>From the error it seems like you don't have the latest version.
The packages were updated only yesterday and it looks like the builds are not yet available via the Bioconductor website.
They are available via SVN and I hope they will be downloadable via the BioC website by tommorow.

Here is how you can get the latest biomaRt version via SVN.
http://wiki.fhcrc.org/bioc/SvnHowTo

Alternatively if you work on a linux platform I could send you the latest version by mail, let me know.

Best regards,
Steffen


-----Original Message-----
From: João Fadista [mailto:Joao.Fadista at agrsci.dk]
Sent: Thu 11/30/2006 9:27 AM
To: Durinck, Steffen (NIH/NCI) [F]
Cc: bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] biomaRt
 
Dear Steffen Durinck,

I downloaded today the biomaRt package from Bioconductor website and my R version is also the latest.
When I use biomaRt without setting my proxy it gives me this error:

> library(biomaRt)
Loading required package: XML
Loading required package: RCurl
> ensembl <- useMart("ensembl")
Error in validObject(.Object) : invalid class "Mart" object: invalid object for slot "vschema" in class "Mart": got class "NULL", should be or extend class "character"


Best regards

João Fadista
Ph.d. student


Danish Institute of Agricultural Sciences
Research Centre Foulum
Dept. of Genetics and Biotechnology
Blichers Allé 20, P.O. BOX 50
DK-8830 Tjele

Phone:   +45 8999 1900
Direct:  +45 8999 8999

E-mail:  Joao.Fadista at agrsci.dk
Web:	   http://www.agrsci.org				

This email may contain information that is confidential.
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-----Original Message-----
From: Durinck, Steffen (NIH/NCI) [F] [mailto:durincks at mail.nih.gov] 
Sent: Thursday, November 30, 2006 3:23 PM
To: João Fadista; bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] biomaRt

Hi Joao,

Are you sure you need to set your proxy?
Try first to use biomaRt without setting it.

library(biomaRt)
ensembl <- useMart("ensembl")

Also make sure you use the latest available version of biomaRt (biomaRt 1.8.1 in the release version or biomaRt 1.9.8 in the devel repository.  The BioMart suite upgraded to version 0.5 this week and you'll need the latest biomaRt release to work with it.

Best regards,
Steffen 


-----Original Message-----
From: João Fadista [mailto:Joao.Fadista at agrsci.dk]
Sent: Thu 11/30/2006 9:01 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] biomaRt
 
Dear all,
 
I am having some trouble using the biomaRt useMart function. I do not know what seems to be the problem. Here is what I got:
 
 
> Sys.putenv("http\_proxy" = "http://my.proxy.org:9999") ensembl <- 
> useMart("ensembl")
Error in curlPerform(curl = curl, .opts = opts) : 
        Could not resolve proxy: my.proxy.org; Host not found
 


Best regards

João Fadista
Ph.d. student


 	
 	 Danish Institute of Agricultural Sciences	
Research Centre Foulum	
Dept. of Genetics and Biotechnology	
Blichers Allé 20, P.O. BOX 50	
DK-8830 Tjele	
 	
Phone:	 +45 8999 1900	
Direct:	 +45 8999 8999	
E-mail:	 Joao.Fadista at agrsci.dk <mailto:Joao.Fadista at agrsci.dk> 	
Web:	 www.agrsci.org <http://www.agrsci.org/> 	
________________________________

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This email may contain information that is confidential. Any use or publication of this email without written permission from DIAS is not allowed. If you are not the intended recipient, please notify DIAS immediately and delete this email.


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