Dear Alexia, There seems to be an issue with the biomart.org server today. If you don't want to wait until biomart.org is fixed, I will suggest you to change your host in to ensembl.org by doing the following: mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path="/biomart/martservice") This will allow you to access our most recent data (ensembl_mart_71). If you want to use the same version of our databases present on biomart central(ensembl_mart_69), then please change your host to our release 69 archive: mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="oct2012.archive.ensembl.org", path="/biomart/martservice"). To load the biomaRt package, you should use "library(biomaRt)" instead of "source("http://bioconductor.org/biocLite.R")" Hope this helps, Thomas On 17 May 2013, at 16:19, Steve Lianoglou wrote: > Hi alexia, > > Couple points inline: > > On Friday, May 17, 2013, Alexia Cardona wrote: > >> Dear all, >> I am getting a strange error this morning from Bioconductor. I am trying >> to connect from different servers and I'm still getting the same error. >> Are there some database connection problems from Bioconductor? >> >> 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.pmline >> 98 > > > The Bioconductor team does not host biomart. The biomaRt package is simply > a library that interfaces with an external web server. It seems as if that > resource is having trouble now? > > I'm not at a CPU right now so I cannot provide the exact details, but you > should be able to chose another mirror to connect to via the biomaRt > package. Details On how to do so are likely in the biomaRt vignette. > > Also: > > Code example: >> >> #load Bioconductor >> source("http://bioconductor.org/biocLite.R") > > > You don't have to source the bioclite script every time. It does not, in > fact, load bioconductor. You only need to source it when you want to > install new packages. > > HTH, > -steve > > > > -- > Steve Lianoglou > Computational Biologist > Department of Bioinformatics and Computational Biology > Genentech > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton Cambridge - CB10 1SD - UK [[alternative HTML version deleted]]