[BioC] Can't access biomaRt with mysql

Richard Pearson richard.pearson at postgrad.manchester.ac.uk
Fri Jul 25 16:53:28 CEST 2008


I've not been able to access biomaRt using the mysql interface this week. I'm 
seeing this both in release and devel. Is this a problem at the EBI end? If so, 
who should I contact?

 > library(biomaRt)
Loading required package: RCurl
 > listMarts(mysql=TRUE)
Loading required package: RMySQL
Loading required package: DBI
Error in mysqlNewConnection(drv, ...) :
   RS-DBI driver: (could not connect anonymous at martdb.ebi.ac.uk on dbname "(null)"
Error:Can't connect to MySQL server on 'martdb.ebi.ac.uk' (110)

 > sessionInfo()

R version 2.7.1 (2008-06-23)


attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] RMySQL_0.6-0   DBI_0.2-4      biomaRt_1.14.0 RCurl_0.9-3

loaded via a namespace (and not attached):
[1] XML_1.95-3  tools_2.7.1

Best wishes


Richard D. Pearson             richard.pearson at postgrad.manchester.ac.uk
School of Computer Science,    http://www.cs.man.ac.uk/~pearsonr
University of Manchester,      Tel: +44 161 275 6178
Oxford Road,                   Mob: +44 7971 221181
Manchester M13 9PL, UK.        Fax: +44 161 275 6204

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