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please check linksThe following software packages must be installed prior to beginning the instructions:

• Java Development Kit (JDK) 1.6.x
  • Ensure that JAVA_HOME is defined, preferably in the user or system profile
  • Ensure that $JAVA_HOME/bin is in PATH

• Ant 1.7.x
  • Ensure that ANT_HOME is defined, preferably in the user or system .profile
  • Ensure that $ANT_HOME/bin is in PATH

• Tomcat 5.5.x need link** Instructions assume Tomcat is configured to run on port 8080. If you are using another port, substitute it into later instructions
  • Ensure that CATALINA_HOME is set
  • Tomcat may be autostarted or started as part of the Bioconductor launch script (provided later in these instructions)

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1. Download
2. Unpack tar file in home directory
3. Configure, build, and install
   • cd R-2.9.0
   • ./configure --enable-R-shlib --with-readline=no --with-x=no
   • Fix src/modules/Makefile as follows (fix is from http://tolstoy.newcastle.edu.au/R/e6/devel/09/04/1434.html)
     • Change lines that read:

       Code Block
       for d in "$(R_MODULES)"; do \ (cd $${d} && $(MAKE) $@) || exit 1; \ done

     • To read:

       Code Block
       @if test "$(R_MODULES)" != ""; then \ for d in "$(R_MODULES)"; do \ (cd $${d} && $(MAKE) $@) || exit 1; \ done; \ fi

       Warning
       title Warning
       Be very careful of tabs in the lines, one tab to start each line, indent beyond that with spaces. Be careful to have no spaces at the end of the lines too. Use rest of Makefile as an example.

4. make Should this be here by itself?
   When I printed this document off, there was a "made install prefix+/usr/local/R-2.90" here, but I see it's gone. Did you delete it? Just wanted to make sure I didn't do anything I shouldn't.

Dependent R packages (RCurl, SJava, RWebServices, RUnit, DNAcopy)

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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#* $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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