[BioC] How to use biomaRt with RMySQL under Windows

James W. MacDonald jmacdon at med.umich.edu
Thu Jan 26 21:38:50 CET 2006


Earl F. Glynn wrote:

> I'm confused.  There is no libs/libMySQL.dll but only a libs/libMySQL.lib
> file.

Odd. Maybe you got a bum download? I checked my RMySQL installation, and 
also re-downloaded the binary package, and I have


in R_HOME\library\RMySQL\libs.

> After installation I'm seeing a libmysql.lib (not a .DLL) and a RMySQL.dll
> in this directory:
> C:\Program Files\R\R-2.2.1\library\RMySQL\libs.  I checked the libs in the
> original ZIP and it has the same two files.
> The file libmysql.lib is only 34 KB while the file
> C:\WINDOWS\system32\lilbMySQL.DLL is 1,128 KB (for the MySQL Version version
> 4.1.12a).  How does this 34 KB LIB file do the work of the 1,128 KB DLL?
> The RMySQL.dll isn't very large either, only 37 KB.

The lib file doesn't - there should be a dll there as well.

> I am not aware of any other R package that requires a path change or file
> movement after installation (perhaps there are others).  Shouldn't any
> dependency like this be taken care of by the installation program?

Normally, to use RMySQL on Windows you need to have MySQL installed and 
do a bunch of manipulations to get things to work (I have never been 
successful). Really it is a *NIX package that David James is kind enough 
to compile and make available for Windows users.

Ideally the installation of the package would take care of everything, 
but I don't know if there is a reasonable way to modify your PATH during 
the installation process. Somebody like Seth or Robert might know if 
this is possible.

Anyway, given how difficult it is to compile a binary RMySQL package on 
Windows, I am just happy that there is an easy work around.



> efg
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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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