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

Simon Senkewicz [guest] guest at bioconductor.org
Thu Oct 4 22:05:02 CEST 2012

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. 

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)

[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 

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