R/rJava

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 Rcpi the rJava.so could not be loaded but can be installed inside R, namely.

> BiocManager::install("Rcpi")