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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