It's fixed. Thanks a lot for the speedy resolution.
O
On 29/05/13 09:28, Arek Kasprzyk wrote:
Hi Oliver,
the issue should be resolved now.
a
On 29 May 2013 08:39, Oliver Burren <[email protected]
<mailto:[email protected]>> wrote:
Hi,
Not sure that this is the correct place to post but getting the
following error using biomaRt with following code. I notice that
the host being returned is for the BioMart portal hence why I'm
posting here and not directly to Steffen.
Thanks for any help you can provide.
Olly Burren
#connect to BioMart
library(biomaRt)
ensembl <- useMart('ensembl')
ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl)
gene.details<-getGene(id='ENSG00000163599',
type="ensembl_gene_id",mart=ensembl)
Error in getBM(attributes = attrib, filters = type, values = id,
mart = mart) :
Query ERROR: caught BioMart::Exception::Database: Could not
connect to mysql database ensembl_mart_71: DBI
connect('database=ensembl_mart_71;host=bm_mysql;port=3306','bmweb',...)
failed: Host '54.225.80.241' is blocked because of many connection
errors; unblock with 'mysqladmin flush-hosts' at
/srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm
<http://biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm>
line 98
sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.16.0
loaded via a namespace (and not attached):
[1] RCurl_1.95-4.1 XML_3.96-1.1
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