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 message is attached below. I searched for similar problems but my issue is a little trickier and many proposed solutions either didnt work or I could not try, because I am working on a server which I do not have write access to system libraries.
OS: Linux 2.6.18-348.6.1.el5 #1 SMP Tue May 21 15:44:27 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux (info given by typing "uname -a" sorry I couldn't quite understand this info)
R: R3.0.1, I downloaded the source, put in my home directory, and built R from source.
rJava: I ran 'install.packages("rJava")', during installation I got:
=========================
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver : '/usr/bin/jar'
compiler : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : '-I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.9.x86_64/jre/../include -
I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.9.x86_64/jre/../include/linux'
java libs : '-L/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.9.x86_64/jre/lib/amd64/se
rver -ljvm'
checking whether JNI programs can be compiled... yes
checking JNI data types... configure: error: One or more JNI types differ from the
corresponding native type. You may need to use non-standard compiler flags or
a different compiler in order to fix this.
ERROR: configuration failed for package 'rJava'
* removing '/home/me/R-3.0.1/library/rJava'
==================================
Since I can only access the server remotely, I do not have write access to anything outside my home directory /home/me.
Any information would be highly appreciated!