[BioC] problems connecting to Biomart today?

[Hans-Rudolf Hotz]

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
>
>