[BioC] How to use biomaRt with RMySQL under Windows

James W. MacDonald jmacdon at med.umich.edu
Thu Jan 26 20:36:05 CET 2006

Hi Earl,

Earl F. Glynn wrote:
> I wanted to extract data using the biomaRt package, but ran into a problem
> with the Windows installation.
> This page shows that biomaRt requires RMySQL and XML.
> http://www.bioconductor.org/packages/bioc/stable/src/contrib/html/biomaRt.html
> The XML package for Windows was easily available from CRAN
> http://cran.r-project.org/src/contrib/Descriptions/XML.html
> But the RMySQL package for Windows is NOT available from CRAN:
> http://cran.r-project.org/src/contrib/Descriptions/RMySQL.html
> A friend here at Stowers told me about the Windows version of RMySQL here:
> http://stat.bell-labs.com/RS-DBI/download/
> I downloaded RMySQL 0.5-6.zip and installed it
> http://stat.bell-labs.com/RS-DBI/download/RMySQL_0.5-6.zip
> For some reason a DLL was missing:  libMySQL.dll.  I tried moving this DLL
> from the most current version of the MySQL Query Browser, but that caused a

That binary *does* contain the libMySQL.dll in the libs directory (I 
just downloaded and checked). INSTALL.win in the top directory of that 
package contains the following hint from BDR:

You need to move libs/libMySQL.dll into the PATH, or add
...\library\mysql\libs to the path.

BDR 2002-06-19

I simply added R_HOME\library\RMySQL\libs to my path and it works out of 
the box.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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