[BioC] biomaRt not working?

[Steve Pederson]

Hi John,

I had some similar trouble with RCurl_0.95-1, but everything worked fine 
again when I rolled back to RCurl_0.94-1.

The command listMarts() would work, but getBM() gave me a similar error.

Hope that's vaguely useful,

Steve


john seers (IFR) wrote:
> 
> 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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