[BioC] too many biomaRt connections

Elizabeth Purdom epurdom at stat.Berkeley.EDU
Wed Apr 9 21:09:42 CEST 2008


Hi,
I am using biomaRt to get information regarding genes. I use it pretty 
frequently and recently have gotten the error:

Too many connections at 
/ebi/www/biomart/www/biomart-perl-06/lib/BioMart/Configuration/DBLocation.pm 
line 98

I assume that I've hit some sort of wall in terms of how often I have 
queried the database?

I don't really use biomart except through R; at what point do you get 
booted off and what can I do to regain access? I often run queries on a 
few hundred genes and don't think twice about rerunning such a query or 
running several such queries in a day plus I use functions that call on 
biomaRt repeatedly that I also apply to around 100 genes. So I could 
easily send a thousand queries in a day. I can be more careful, but it 
would be useful to know what the limits are. And does it matter how many 
times you call a 'mart<-useMart(...)' command? (lately, I've been 
calling it frequently rather than using the one I've already opened, 
largely through programming laziness).

By the way, it took me quite some time to track down the error, because 
I was using getGene which just gave me the confusing error:
"Error: ncol(result) == length(attributes) is not TRUE"
I think this must be because something like try(...) is used within 
getBM() and so the output is the error message which is then transferred 
down the line and at some point causes a problem when the function tries 
to bundle it into a data.frame, etc.

Thanks,
Elizabeth



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