[BioC] biomaRt not working?

[john seers (IFR)]

Hi James

Thanks for the reply. That is useful to know it is probably not the
biomart end. I have run a traceback() and results are below. I have also
updated my sessionInfo() as that has changed. 

(I think I will also contact our IT department to see if something has
changed).

Regards

John

> 
> 
> listMarts()
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.
> traceback()
7: stop("Request to BioMart web service failed. Verify if you are still
connected to the internet.  Alternatively the BioMart web service is
temporarily down.")
6: value[[3L]](cond)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
4: tryCatchList(expr, classes, parentenv, handlers)
3: tryCatch(getURL(request), error = function(e) {
       stop("Request to BioMart web service failed. Verify if you are
still connected to the internet.  Alternatively the BioMart web service
is temporarily down.")
   })
2: bmRequest(paste("http://", host, ":", port, path,
"?type=registry&requestid=biomaRt", 
       sep = ""))
1: listMarts()
>



> sessionInfo()
R version 2.9.0 (2009-04-17) 
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] stats     graphics  grDevices datasets  utils     methods   base


other attached packages:
[1] biomaRt_2.0.0 RWinEdt_1.8-1

loaded via a namespace (and not attached):
[1] RCurl_0.97-3 XML_2.3-0   
>






-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: 04 June 2009 13:50
To: john seers (IFR)
Cc: bioconductor at stat.math.ethz.ch; maria traka (IFR)
Subject: Re: [BioC] biomaRt not working?

Hi John,



john seers (IFR) wrote:
> Hello All
> 
> Can anyone tell me why I get this error using Biomart? I am connected
to
> the internet (as in I can install R packages). So is the Biomart
website
> really down? I have been having this problem for at least 2 or 3 days.
> 
> If I access http://www.biomart.org/ using a web browser it appears to
be
> available.
> 
> 
>> listMarts()
> 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.

Works for me:

 > listMarts()
                      biomart
1                    ensembl
2                        snp
3                       vega
4                        msd
[snip]

 > 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] affy_1.22.0   Biobase_2.4.1 limma_2.18.1  biomaRt_2.0.0

loaded via a namespace (and not attached):
[1] affyio_1.12.0        preprocessCore_1.6.0 RCurl_0.97-3
[4] XML_2.3-0


If you are still having problems, run traceback() after the error and 
post the output.

Best,

Jim


> 
> If I access http://www.biomart.org/ using a web browser it appears to
be
> available.
> 
> 
> Any suggestions as to what is going on or things to try are very
> welcome.
> 
> Regards
> 
> John Seers
> 
> 
>> sessionInfo()
> R version 2.9.0 (2009-04-17) 
> 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] stats     graphics  grDevices datasets  utils     methods   base
> 
> 
> other attached packages:
> [1] biomaRt_2.0.0 limma_2.18.0  affy_1.22.0   Biobase_2.4.1
> RWinEdt_1.8-1
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.12.0        preprocessCore_1.6.0 RCurl_0.95-1
> tools_2.9.0          XML_2.3-0           
> 
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-- 
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