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.

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=ensem bl_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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099