install rJava - “configure: error: One or more JNI types differ from the corresponding native type”

Question

I have came across this problem while installing rJava on R3.0.1: \"configure: error: One or more JNI types differ from the corresponding native type\"

The detailed

Answer 1

I ran into the same problem trying to install.packages("rJava") in R version 3.0.2, as long as I tried to install as ordinary user (Linux, Debian). There was no problem running install.packages("rJava") as root. Then, trying library(rJava) worked for root but not for me as a user:

Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/usr/usr.local.original.Debian/lib/R/site-library/rJava/libs/rJava.so':
  libjvm.so: cannot open shared object file: No such file or directory

This problem required to add the environment variables JAVA_HOME and LD_LIBRARY_PATH to ~/.login (following instructions found at Trouble in Setting Java Environment Path on Ubuntu (libjvm.so: cannot open shared object file: No such file or directory)):

setenv JAVA_HOME /usr/lib/jvm/java-7-oracle/
setenv LD_LIBRARY_PATH $JAVA_HOME/jre/lib/amd64:$JAVA_HOME/jre/lib/amd64/server

# For c-shell; for bash, it would have to be:
export JAVA_HOME=/usr/lib/jvm/java-7-oracle/
export LD_LIBRARY_PATH=$JAVA_HOME/jre/lib/amd64:$JAVA_HOME/jre/lib/amd64/server

So, you would have to have a system administrator install rJava for you, then set your environment variables and, of course, set your own .libPaths() in R such as to find rJava.