HI Oliver Until this issue is resolved at www.biomart.org, you can point your host to www.ensembl.org/biomart/martservice/ to get your data. Hope that helps Regards Rhoda
On 29 May 2013, at 08:39, Oliver Burren <[email protected]> wrote: > Hi, > > Not sure that this is the correct place to post but getting the following > error using biomaRt with following code. I notice that the host being > returned is for the BioMart portal hence why I'm posting here and not > directly to Steffen. > > Thanks for any help you can provide. > > Olly Burren > > #connect to BioMart > library(biomaRt) > ensembl <- useMart('ensembl') > ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl) > gene.details<-getGene(id='ENSG00000163599', > type="ensembl_gene_id",mart=ensembl) > Error in getBM(attributes = attrib, filters = type, values = id, mart = mart) > : > Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql > database ensembl_mart_71: DBI > connect('database=ensembl_mart_71;host=bm_mysql;port=3306','bmweb',...) > failed: Host '54.225.80.241' 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 > > > sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.16.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.95-4.1 XML_3.96-1.1 > > > > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users Rhoda Kinsella Ph.D. Ensembl Production Project Leader, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
