[BioC] problems connecting to Biomart today?

[Rhoda Kinsella]

Hi Jose
I should also have mentioned in my previous email that if you are  
having difficulties doing other queries, this may be a server issue at www.biomart.org 
  and you should try running your query against www.ensembl.org marts  
by setting host=www.ensembl.org.
I hope that helps,
Regards
Rhoda

On 21 Feb 2011, at 12:38, Hans-Rudolf Hotz wrote:

> Hi Jose
>
> it is the Biomart server...the web site is up, but you can't do any  
> queries (ie they will produce the same error message as you got  
> through the biomaRt interface). you should contact the Biomart team.
>
> Regards, Hans
>
>
>
> On 02/21/2011 01:19 PM, J.delasHeras at ed.ac.uk wrote:
>> I seem to be unable to use biomaRt today (working fine Friday) but I
>> don't see anything on the Biomart website wbout downtime, so I am not
>> sure if the problem lies at my end. Any ideas?
>>
>> Jose
>>
>> example:
>>
>> library(biomaRt)
>> ensembl=useMart("ensembl")
>> dataset="hsapiens_gene_ensembl"
>> ensembl=useDataset(dataset, mart=ensembl)
>>
>> getBM(attributes="hgnc_curated_gene_name", filters="entrezgene",
>> values=c(1,33), mart=ensembl)
>>
>> I get:
>> Error in getBM(attributes = "hgnc_curated_gene_name", filters =
>> "entrezgene", :
>> Query ERROR: caught BioMart::Exception::Database: Could not connect  
>> to
>> mysql database ensembl_mart_61: DBI
>> connect('database=ensembl_mart_61;host=dcc-qa- 
>> db.oicr.on.ca;port=3306','bm_web',...)
>> failed: Can't connect to MySQL server on 'dcc-qa- 
>> db.oicr.on.ca' (113) at
>> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/ 
>> Configuration/DBLocation.pm
>> line 98
>>>
>>
>>
>> my sessionInfo()
>>
>> R version 2.11.0 (2010-04-22)
>> i386-pc-mingw32
>>
>> locale:
>> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
>> Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
>> [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] xtable_1.5-6 GO.db_2.4.1 org.Hs.eg.db_2.4.1 annotate_1.26.0
>> GOstats_2.14.0
>> [6] RSQLite_0.9-0 DBI_0.2-5 graph_1.28.0 Category_2.14.0
>> AnnotationDbi_1.10.1
>> [11] Biobase_2.8.0 biomaRt_2.4.0
>>
>> loaded via a namespace (and not attached):
>> [1] genefilter_1.30.0 GSEABase_1.10.0 RBGL_1.26.0 RCurl_1.4-2
>> splines_2.11.0 survival_2.35-9
>> [7] tools_2.11.0 XML_3.1-0
>>
>>
>
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.