I found a temporary solution to this by using an archive instead of the biomart.org server today which seems to be experiencing some problems today. Use an archive instead eg: mart <- useMart(host="jan2013.archive.ensembl.org", biMBL", dataset="hsapiens_gene_ensembl")
On Fri, May 17, 2013 at 1:11 PM, Alexia Cardona <[email protected]>wrote: > Dear all, > there seems to be an error in the biomart connection. Can anyone look > into this please? > > Error: > Error in getBM(c("ensembl_gene_id", "ensembl_transcript_id", "ensembl_exon > : > Query ERROR: caught BioMart::Exception::Database: Could not connect to > matabase ensembl_mart_69: DBI > connect('database=ensembl_mart_69;host=bm_myst=3306','bmweb',...) failed: > Host '54.225.80.241' is blocked because of manection errors; unblock with > 'mysqladmin flush-hosts' at /srv/ > biomart_servmart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line > 98 > > > Code example: > > #load Bioconductor > source("http://bioconductor.org/biocLite.R";) > #load package GenomeGraphs > library(GenomeGraphs) > > mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl") > makeGeneRegion(start=105800000, end=107800000, strand="+", chromosome="7", > biomart=mart) > > Thanks >
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