rJava fails to install (MacOS, Red Hat)

Question

I am experiencing the same rJava problem that many other people seem to of had at one point or another. The error occurs when R CMD INSTALL tests whether JNI programs can be compiled.

The output recommends running R CMD javareconf -ed or sudo R CMD javareconf The output of the latter is :

computer: home$ sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 1.6.0_31
Java home path   : /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Java library path: 
JNI linker flags : -framework JavaVM
JNI cpp flags    : -I$(JAVA_HOME)/include

Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.

And when trying to install rJava afterwards,

computer: home$ R CMD INSTALL ~/Downloads/rJava_0.9-4.tar.gz 
* installing to library ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
* installing *source* package ‘rJava’ ...
checking for gcc... gcc -arch x86_64 -std=gnu99
checking for C compiler default output file name... a.out
/* Passes all checks */
configure: checking whether gcc -arch x86_64 -std=gnu99 supports static inline...yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
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/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/include'
java libs   : '-framework JavaVM'
checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details.

Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root.

ERROR: configuration failed for package ‘rJava’
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rJava’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rJava’

An alternative attempt where /usr/bin/javac is replaced by /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Homefails just the same.

I am running Mac OS 10.7.3 and

computer: home$ java -version
java version "1.6.0_31"
Java(TM) SE Runtime Environment (build 1.6.0_31-b04-415-11M3646)
Java HotSpot(TM) 64-Bit Server VM (build 20.6-b01-415, mixed mode)

The following is in my .bash_profile

export JAVA_HOME=/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home

Additionally, I have the same problem on Red-Hat. I hope any fix provided will work there too, but if it won't and why it won't is know, please explain.

I've been using this site's incredible knowledge base for a couple of years now, but this is my first post. Mucho thanks in advance.

Some (not all) of the resources I have already browsed through are

• https://stat.ethz.ch/pipermail/r-devel/2008-November/051224.html
• https://stat.ethz.ch/pipermail/r-help/2008-October/177688.html
• R: rJava package install failing

Please note that the apt-get solution in the last link is of no use to me (I think) unless there is an equiv solution for port and/or yum.

Answer 1

I am using Redhat Linux 7.1

I was getting the same problem as above and I performed the following steps

1) Edit /usr/lib64/R/etc/Renviron and add "CPPFLAGS=${CPPFLAGS-'-ldl'}" to the end of the file

2) Then find the java home and set it like below ( set java home till /jre)

$export JAVA_HOME=/usr/lib/jvm/java-1.7.1-ibm-1.7.1.3.10-1jpp.1.el7_1.x86_64/jre
$export PATH=$PATH:$JAVA_HOME/bin
$R CMD javareconf

3) invoke R from commandline

$R
> install.packages("rJava")
> install.packages("RJDBC",dep=TRUE)
> q()
Save workspace image? [y/n/c]: y

Answer 2

I had a recent variation on this same problem with RHEL 6.5. I reviewed this thread and many others. The ptoblem was that the dynamic load modules were not found when testing the complile of the JNI programs. My fix was to insert "CPPFLAGS=${CPPFLAGS-'-ldl'}" into file

/usr/lib64/R/etc/Renviron