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1. $R_HOME/bin/R
2. At the R prompts:
   • source("http://www.bioconductor.org/biocLite.R")
   • biocLite()
   • biocLite("RCurl")
   • biocLite("SJava")
   • biocLite("RWebServices")
   • biocLite("RUnit")
   • biocLite("DNAcopy")
   • q()
3. Build SJava links missed by install:
   • cd $R_HOME/lib64/R/library/SJava/libs
   • ln -s SJava.so libRInterpreter.so
   • ln -s SJava.so libSJava.so
4. Build and test SJava/RWebServices installation (as per Bioconductor Installation Guide page 10)Need link#* Link is https://gforge.nci.nih.gov/docman/view.php/175/20293/Installation_Guide.doc^{Image Added}
   • $R_HOME/bin/R#* At the R prompts:
   • #* library(RWebServices)#* unpackAntScript("/tmp/rservices")#** q()
   • cd /tmp/rservices
   • ant recompile-sjava
   • ant basic-prop#** Look for any errors)
   • ant rservices-test#** This step is optional

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• cd /usr/local/bioconductor
• $R_HOME/bin/R
• At the R prompts:
  • library(RWebServices)
  • unpackAntScript("caDNAcopy")
  • q()
• Optionally, fix timeout value for all R workers to be 2 hours instead of 60 seconds
  • Edit $R_HOME/lib64/R/library/RWebServices/scripts/RWebServicesTuning.properties
    • Change to: jms.timeout=7200000
• cd caDNAcopy
• ant map-package -Dpkg=caDNAcopy
• ant unpack-package -Dpkg=caDNAcopy
• ant precompile
• Optionally, test RWebService (as per Bioconductor Installation Guide page 11)Link is https://gforge.nci.nih.gov/docman/view.php/175/20293/Installation_Guide.doc^{Image Added}:
  • Start up Tomcat (shutdown if already running)
    • $CATALINA_HOME/bin/startup.sh
  • Start up ActiveMQ
    • $JMS_HOME/bin/activemq &
  • Start up R worker for caDNAcopy
    • nohup ant start-worker &
  • Run the test
    • ant local-test

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As per Bioconductor Installation Guide page 11: link?: Link is https://gforge.nci.nih.gov/docman/view.php/175/20293/Installation_Guide.doc^{Image Added}

1. Start up Tomcat (shutdown if already running)
   • $CATALINA_HOME/bin/startup.sh
2. Start up ActiveMQ
   • $JMS_HOME/bin/activemq &
3. Start up R worker for caDNAcopy (skip if only using caDNAcopy)
   • cd /usr/local/bioconductor/caDNAcopy
   • nohup ant start-worker &
4. Start up R worker for caCGHcall (skip if only using caCGHcall)
   • cd /usr/local/bioconductor/caCGHcall
   • nohup ant start-worker &

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