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U.S. Department of Health and Human Services

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Local R-Server Installation Instructions

Optional R-Server Installation for Apache Tomcat in Linux/Unix/Windows Systems

The installation of R/Bionconductor on the Windows platform is completely automated within the ArrayTrack™ application. R server installation is not required. However, it may be beneficial to install an R server in order to handle memory-intensive analysis on large datasets.
Recommended Hardware Configuration

  • Memory: 4 or more gigabytes
  • Operating Systems: 64-Bit Linux/Unix/Windows
  • Free disk space for Apache Tomcat: At least two gigabytes

Software Requirements for R Server

  • R and Bioconductor (see http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/documents/R_Install
    InstructionsLinuxSys.pdf).
  • Java servlets container: Apache Tomcat (see documents on http://tomcat.apache.org/)

Installation of R server in Linux/Unix Systems
1. Create a folder “RLink” in $TOMCAT_HOME/webapps
2. Copy all files/directories in the folder “RLink” on CD to $TOMCAT_HOME/webapps/RLink/
3. Setup the environment variable $R_HOME for the tomcat server process. In bash or bourne shell, this is done by executing the following command prior to starting Tomcat.
>export R_HOME=”…”
4. Add $R_HOME/bin to PATH environment variable for the tomcat server process
5. Make sure that the owner of $TOMCAT_HOME/webapps/RLink/ is the same user who starts the tomcat service
6. Make sure that the user who starts the tomcat service has the read/write/execution permissions in the path $R_HOME.
7. Make sure that the user who starts the tomcat service has the read/write/executions permissions in the path $TOMCAT_HOME/temp/
Installation of R server in Windows Systems
1. Create a folder “RLink” in $TOMCAT_HOME/webapps
2. Copy all files in folder RLink on CD to $TOMCAT_HOME/webapps/RLink/
3. Add $R_HOME/bin to PATH environment variable
R server connection string: http://IP:Port/RLink/RLinker
Testing of R Server Connection
Enter http://IP:port/RLink/RLinker in the address bar of your web browser:
The R server is installed correctly if you can see “Bioconductor link is ready!!!”