Environment: Ubuntu 9.04 + latestest R-devel
SJava package can be installed by biocLite('SJava'), but it resuses to start and moans it cannot find the 'libjvm.so' file.
(1) Set a link by:
sudo ln -s /usr/lib/jvm/java-6-sun-184.108.40.206/jre/lib/i386/client/libjvm.so /usr/local/lib/libjvm.so
(2) Install the SJava package again. Now it should start.
The reason for this is by default the libjvm library is not linked in the default library search path /usr/local/lib.