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Appendix: MeV R Integration

MeV has integrated a R (CRAN) hook where by R functions and libraries can be called within the Java instance using shared libraries. Mev developed a library around the JRI (rForge) API which uses JNI, to make this happen. The user in *most cases would not have to set up or configure anything to run R dependent modules and it should be completely transparent. Please also note that MeV does not produce a command line interface to run R commands. This integration was done to leverage the R environment where many algorithms are readily available and does not need to be re-implemented in Java. MeV would use R internally as appropriate and the user should not expect to see any change in behavior of MeV.

**Notes**

  1. On Windows and Mac OS X (10.6) where the default JVM is 64 Bit, the user will be thrown a warning to change to 32 bit JVM. This is required because the API is not ready for 64 Bit environment yet and we are working on a solution. However once the default JVM is set to 32 Bit, the R dependent modules would run. To help the users setup the 32 bit JVM we will be providing help and assistance to do the following:
    1. On Windows: To install 32 Bit Java if not already installed and to modify the launch script TMEV.sh to point to it.
    2. On Mac OS X we would provide instructions on how to set up 32bit JVM as default. The default in OS X 10.6 (Snow leopard is 64 bit).
  2. On Mac we expect the user to have R 2.11.1 universal binary installed in the Application Framework. We do not expect such for Windows and Linux systems.
  3. Please use MeV SourceForge page for submitting queries, questions and issues. We have set up a page for this particular JVM issue named R MeV Integration, JVM issues.

Multiple R Versions on a Mac

MeV for Mac OS requires that R2.11 be pre-installed. For users who already have another version of R installed, this requirement sometimes presents a difficulty as Macs generally do not allow two versions of the same program to be installed alongside one another. We recommend using the RSwitch utility to overcome this problem.

Windows users do not have this restriction; an appropriate version of R comes bundled with MeV for Windows. This R instance will not interfere with other installed copies of R. 

  
** RSwitch: 
      Util from http://r.research.att.com/#other 
      to switch between different version of R installed on MAC OS X
      
      After evry install remember to use appropriate method described
      below to setup next version of install as a separate install
      instead of an upgrade of the previous install.

** OS X 10.4 Tiger & OS X 10.5 Leopard
      Remove /Library/Receipts/R-Framework.pkg for fresh install and 
      to avoid an upgrade.
      rm -rf /Library/Receipts/R-Framework.pkg

** OS X 10.5 and higher you have to use 
   ** For 32/64 Bit Binary pkg
      pkgutil --forget org.r-project.R.Leopard.fw.pkg

   ** For the 32 bit Tiger binary dmg:
      pkgutil --forget org.r-project.R.framework
      pkgutil --forget org.r-project.R

** Etc:
   ** Check for pkgs:
      pkgutil --pkgs | grep r-project
      
** UNinstall R
   rm -rf /Library/Frameworks/R.framework
   rm -rf /Applications/R.app
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