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
> 
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> 
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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK


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