One may see the messages
... checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details. ... ERROR: configuration failed for package ‘rJava'
so quit R and run
R CMD javareconf Rscript -e 'install.packages("rJava")'
It might well be that the procedure above fails to work – a further attempt is to download rJava locally.
Rscript -e 'download.packages("rJava",".")' tar xvfz rJava_1.0-6.tar.gz R CMD INSTALL rJava
With Bioconductor package
rJava.so could not be loaded but can be installed inside R, namely.