[R] RMySQL problem on Windows 7 32 bit

[byzin]

I am attempting to analyze Affymetrix exonchip data using the exon map
package.  I have installed this package but have had problems installing the
associated programs, specifically RMySQL since no windows binary exists.  

I have followed the directions for compiling the package as found on -
http://biostat.mc.vanderbilt.edu/wiki/Main/RMySQL - but still have an error
when executing the install.package command.  

RTools, and MSQL 5.5 have been installed on my computer. Path environment
altered to include RTools and R, verified to be working.  

Thanks in advance,

Mike

o ‘C:\Users\Mike\Documents/R/win-library/2.12’
(as ‘lib’ is unspecified)
trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/RMySQL_0.7-5.tar.gz'
Content type 'application/x-gzip' length 160769 bytes (157 Kb)
opened URL
downloaded 157 Kb

* installing *source* package 'RMySQL' ...
checking for $MYSQL_HOME... C:/Program Files/MySQL/MySQL Server 5.5
cygwin warning:
  MS-DOS style path detected: C:/Program
  Preferred POSIX equivalent is: /cygdrive/c/Program
  CYGWIN environment variable option "nodosfilewarning" turns off this
warning.
  Consult the user's guide for more details about POSIX paths:
    http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
test: Files/MySQL/MySQL: unknown operand
** libs
Warning: this package has a non-empty 'configure.win' file,
so building only the main architecture

cygwin warning:
  MS-DOS style path detected: C:/PROGRA~1/R/R-212~1.1/etc/i386/Makeconf
  Preferred POSIX equivalent is:
/cygdrive/c/PROGRA~1/R/R-212~1.1/etc/i386/Makeconf
  CYGWIN environment variable option "nodosfilewarning" turns off this
warning.
  Consult the user's guide for more details about POSIX paths:
    http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
gcc -I"C:/PROGRA~1/R/R-212~1.1/include" -I"C:/Program Files/MySQL/MySQL
Server 5.5"/include        -O3 -Wall  -std=gnu99 -c RS-DBI.c -o RS-DBI.o
gcc -I"C:/PROGRA~1/R/R-212~1.1/include" -I"C:/Program Files/MySQL/MySQL
Server 5.5"/include        -O3 -Wall  -std=gnu99 -c RS-MySQL.c -o RS-MySQL.o
gcc -shared -s -static-libgcc -o RMySQL.dll tmp.def RS-DBI.o RS-MySQL.o
C:/Program Files/MySQL/MySQL Server 5.5/lib/opt/libmysql.lib
-LC:/PROGRA~1/R/R-212~1.1/bin/i386 -lR
gcc.exe: C:/Program Files/MySQL/MySQL Server 5.5/lib/opt/libmysql.lib: No
such file or directory
ERROR: compilation failed for package 'RMySQL'
* removing 'C:/Users/Mike/Documents/R/win-library/2.12/RMySQL'
* restoring previous 'C:/Users/Mike /Documents/R/win-library/2.12/RMySQL'

The downloaded packages are in
        ‘C:\Users\Mike \AppData\Local\Temp\Rtmp56pouO\downloaded_packages’
Warning messages:
1: running command 'C:\PROGRA~1\R\R-212~1.1/bin/i386/R CMD INSTALL -l
"C:\Users\Mike \Documents/R/win-library/2.12"  
C:\Users\MIKEBY~1\AppData\Local\Temp\Rtmp56pouO/downloaded_packages/RMySQL_0.7-5.tar.gz'
had status 1 
2: In install.packages("RMySQL", type = "source") :
  installation of package 'RMySQL' had non-zero exit status
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
LC_TIME=English_United States.1252    

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

loaded via a namespace (and not attached):
[1] tools_2.12.1
> 




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