[BioC] Biomart server down?

Fri May 20 17:44:12 CEST 2011

Hi Alistair
Glad it now works.
Regards
Rhoda

On 20 May 2011, at 16:41, Alistair Rust wrote:

> Hi Rhoda,
>
> Yep, indeed adding the following bit of magic into my simple test
> script did the trick for that.
>
> listMarts(mart, host="www.ensembl.org")
>
> The 'real' script I'm working with however uses a R package that is
> hardcoded
> to run off the Biomart.org databases.
>
> Though it looks as if things are now back as my test script seems to  
> run
> without
> complaining...
>
> Best
>
> Alistair
>
>
> On Fri, May 20, 2011 at 3:58 PM, Rhoda Kinsella <rhoda at ebi.ac.uk>  
> wrote:
>
>> Hi Alistair
>> You can set your host to www.ensembl.org and use the Ensembl Biomart
>> databases there.
>> Regards
>> Rhoda
>>
>>
>>
>> On 20 May 2011, at 15:44, Alistair Rust wrote:
>>
>> Hi,
>>>
>>> I've had an R script playing nicely with biomaRt for a while
>>> Today there seem to be a few wee problems.  Is the result
>>> of the server being down in Toronto?
>>>
>>> SessionInfo, a simple test and output below.  I downloaded
>>> and installed the 2.8.0 version of biomaRt this morning.
>>> Also tried the 2.9.0 development version with the same
>>> results.
>>>
>>> Cheers
>>>
>>> Alistair
>>>
>>> Team113: Experimental Cancer Genetics,
>>> Wellcome Trust Sanger Institute,
>>> Hinxton, Cambridge, UK
>>>
>>>
>>> sessionInfo()
>>>>
>>> R version 2.11.1 (2010-05-31)
>>> x86_64-unknown-linux-gnu
>>>
>>> locale:
>>> [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>>> [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>>> [5] LC_MONETARY=C              LC_MESSAGES=C
>>> [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>>> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] biomaRt_2.8.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] RCurl_1.4-2 XML_3.1-0
>>>
>>>
>>> Simple test from the R script on the BioConductor biomaRt webpage
>>> ========
>>> library(biomaRt)
>>>
>>> listMarts()
>>>
>>> ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
>>>
>>> affyids=c("202763_at","209310_s_at","207500_at")
>>>
>>> getBM(attributes=c('affy_hg_u133_plus_2', 'entrezgene'), filters =
>>> 'affy_hg_u133_plus_2', values = affyids, mart = ensembl)
>>> =========
>>>
>>>
>>>
>>> Output
>>> =========
>>>
>>>    V1
>>>
>>> 1 <!DOCTYPE html PUBLIC -//W3C//DTD HTML 4.01//EN
>>> http://www.w3.org/TR/html4/strict.dtd>
>>> 2
>>> <html><head>
>>> 3                        <meta http-equiv=Content-Type  
>>> content=text/html;
>>> charset=utf-8>
>>> 4                         <title>ERROR: The requested URL could  
>>> not be
>>> retrieved</title>
>>> 5                                                             <style
>>> type=text/css><!--
>>> 6
>>> /*
>>> Error in getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"),
>>> filters
>>> = "affy_hg_u133_plus_2",  :
>>> The query to the BioMart webservice returned an invalid result: the
>>> number
>>> of columns in the result table does not equal the number of  
>>> attributes in
>>> the query. Please report this to the mailing list.
>>>
>>>       [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
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>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>> Rhoda Kinsella Ph.D.
>> Ensembl Bioinformatician,
>> European Bioinformatics Institute (EMBL-EBI),
>> Wellcome Trust Genome Campus,
>> Hinxton
>> Cambridge CB10 1SD,
>> UK.
>>
>>
>
> 	[[alternative HTML version deleted]]
>
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.