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 -e 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
Under R 4.3.2, we see error
/usr/bin/ld: cannot find -lintl collect2: error: ld returned 1 exit status make: *** [libjri.so] Error 1 make: Leaving directory `/rds/user/jhz22/hpc-work/work/RtmpwlPJIa/R.INSTALL1d07e7874480b/rJava/jri/src' make: *** [src/JRI.jar] Error 2 make: Leaving directory `/rds/user/jhz22/hpc-work/work/RtmpwlPJIa/R.INSTALL1d07e7874480b/rJava/jri' make: *** [jri] Error 2 ERROR: compilation failed for package ‘rJava' * removing ‘/rds/project/jmmh2/rds-jmmh2-public_databases/software/R/rJava' * restoring previous ‘/rds/project/jmmh2/rds-jmmh2-public_databases/software/R/rJava'
which is fixed with
module load ceuadmin/gettext/0.20 Rscript -e 'install.packages("rJava")'
With Bioconductor package
rJava.so could not be loaded but can be installed inside R, namely.