On Fri, May 13, 2011 at 11:06 AM, byzin <[email protected]> wrote: > 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. >
1. Be sure to read the INSTALL file in the RMySQL*.tar.gz in the inst directory. 2. You may not have installed mysql completely. Be sure to install it from the mysql site. Distributions such as xampp won't work out of the box. 3. After installing mysql, download Rcmd.bat from the batchfiles distribution here: http://batchfiles.googlecode.com/svn/trunk/Rcmd.bat and run this (replacing whatever): Rcmd.bat INSTALL RMySQL.whatever.tar.gz If you have put MySQL in the standard place then Rcmd.bat will temporarily set MYSQL_HOME. It will also temporarily add rtools to the path, turn off cygwin warnings and do a number of other things for you so that basically the one line above is all you need to do (after installing r, rtools, miktex and mysql). Also, Rgui.bat (same file - just rename Rcmd.bat to Rgui.bat) will start up R with those defined. -- Statistics & Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
