[BioC] Problems with biomaRt

[michael watson (IAH-C)]

It is for me now, only I had to add:

Sys.setenv("http_proxy"="http://wwwcache.bbsrc.ac.uk:8080")

I didn't have to do this previously, and obviously R knows about my
proxy as it can use download.file (I am using the --internet2 switch to
get connection settings from IE).

Does biomaRt not use the proxy settings in some way that download.file
does?

Clearly this is not a huge problem as I can simply add
"Sys.setenv("http_proxy"="http://wwwcache.bbsrc.ac.uk:8080")" to all my
scripts, but this wasn't the case previously and I expect biomaRt should
be smart enough to pick up my proxy settings...

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: 13 July 2009 14:19
To: michael watson (IAH-C)
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Problems with biomaRt

It's working for me:

 > library(biomaRt)
 > mart <- useMart("ensembl","hsapiens_gene_ensembl")
Checking attributes ... ok
Checking filters ... ok
 > sessionInfo()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] biomaRt_2.0.0

loaded via a namespace (and not attached):
[1] RCurl_0.98-1 XML_2.5-1
 > Sys.time()
[1] "2009-07-13 09:17:58 EDT"

Maybe try again?

Best,

Jim



michael watson (IAH-C) wrote:
> I'm having problems connecting to biomaRt through R.
> 
>  
> 
> useMart reports an error and claims either the service is down or I am
> not connected to the internet:
> 
>  
> 
>> mart <- useMart(biomart="ensembl", dataset="ggallus_gene_ensembl")
> 
> Error in value[[3L]](cond) : 
> 
>   Request to BioMart web service failed. Verify if you are still
> connected to the internet.  Alternatively the BioMart web service is
> temporarily down.
> 
>  
> 
> But R can connect to martservice just fine:
> 
>  
> 
>> download.file(url="http://www.biomart.org/biomart/martservice",
> destfile="test.html")
> 
> trying URL 'http://www.biomart.org/biomart/martservice'
> 
> Content type 'text/plain' length 200 bytes
> 
> opened URL
> 
> downloaded 5810 bytes
> 
>  
> 
> So the problem is not R, it is biomaRt.
> 
>  
> 
> Any help appreciated
> 
>  
> 
> Mick
> 
>  
> 
>> sessionInfo()
> 
> R version 2.9.1 (2009-06-26) 
> 
> i386-pc-mingw32 
> 
>  
> 
> locale:
> 
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
> 
>  
> 
> attached base packages:
> 
> [1] tools     stats     graphics  grDevices utils     datasets
methods
> base     
> 
>  
> 
> other attached packages:
> 
> [1] CORNA_1.1      XML_2.5-3      GEOquery_2.8.0 RCurl_0.98-1
> bitops_1.0-4.1 biomaRt_2.0.0  Biobase_2.4.1
> 
>  
> 
> Head of Bioinformatics
> Institute for Animal Health
> Compton
> Berks
> RG20 7NN
> 01635 578411 
> 
>  
> 
> Please consider the environment and don't print this e-mail unless you
> really need to.
> 
> The information contained in this message may be
confide...{{dropped:26}}
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826