[BioC] Bioconductor error

[Dan Tenenbaum]

On Fri, May 17, 2013 at 4:48 AM, Alexia Cardona
<alexia.cardona at gmail.com> 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.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)
>

Sounds like Biomart is down, which happens occasionally. I suggest
trying again, and if you still have problems, contact Biomart via
http://www.biomart.org/.

Dan


> Thanks
>
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>
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