To build and install ==================== 1) (Windows only; required to build but not to install an already built SJava) Install the R Windows development tools, as described in the R Installation and Administration manual. Set an environment variable R_HOME, using c:/Progra~1/ -style file names 2) Install the Java Development Kit (in addition to the Java Runtime Environment) and ensure that the JAVA_HOME environment variable is set correctly. 3) Check that R understands the location of Java, with R CMD config JAVA_HOME R CMD config JAVA_LIBS R CMD config JAVA_CPPFLAGS It may be necessary to run R CMD javareconf or similar; see the R Installation and Administration Manual for further assistance. 4) Build and install SJava with the command R CMD INSTALL --clean SJava or source("http://bioconductor.org/biocLite.R") biocLite("SJava")