[BioC] Query Error in biomaRt package on Mac R 2.15.1

[James W. MacDonald]

This was just asked about an hour ago. You can use a different server:

mart <- useMart("ENSEMBL_MART_ENSEMBL","hsapiens_gene_ensembl", 
host="www.ensembl.org")

Best,

Jim





On 10/4/2012 4:05 PM, Simon Senkewicz [guest] wrote:
> I apologize if this message has already been asked; however, I have yet to find an answer. I am trying to re-annotate some of my gene lists following release version 68 for the human datasets.
>
> library("biomaRt")
> ensembl<- useMart("ensembl", dataset="hsapiens_gene_ensembl")
>
> but with I use the 'getBM' function I receive the following error message:
>
> Error in getBM(attributes = c("ensembl_gene_id", "hgnc_symbol", "refseq_mrna"),  :
>    Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_68: DBI connect('database=ensembl_mart_68;host=bmdccdb.oicr.on.ca;port=3306','bm_web',...) failed: Host 'bmdcc1.oicr.on.ca' is blocked because of many connection errors; unblock with 'mysqladmin flush-hosts' at /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98
>
>
> Is there a simple workaround to fix this problem? I have used the exact same code previously without any errors.
>
> Thanks in advance to anyone and everyone for their help.
>
>   -- output of sessionInfo():
>
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] biomaRt_2.12.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.91-1 tools_2.15.1 XML_3.9-4
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099