[BioC] How to use biomaRt with RMySQL under Windows

[James W. MacDonald]

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.

Best,

Jim


-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623