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
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.
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