[R] Installing R in Linux: problems with JAVA packages (rJava, RWeka, ...) ?

Paulo Cortez pcortez at dsi.uminho.pt
Tue Oct 21 16:36:16 CEST 2008


While in MacOS it is quite simple to install R and Java packages, the 
same is not true for Linux. I surfed the web and it seems that other 
users also have similar problems. Perhaps a nice FAQ answer or HOWTO 
would help...

But here is my situation: I have 2 linux servers, one with Fedora 9 and 
the other with CentOS5.

I have installed R (2.7.2 version, with yum) and I tryed to install the 
RWeka and rJava packages.

After receiving an error, I installed jdk1.6 from java (file:
in both machines.

Then, I had to manually set the java links, using something like:

# rm /usr/bin/java
# ln -sv /usr/java/default/bin/java /usr/bin/java

(repeat these lines for javac, javadoc, javah, etc..)

Finally I performed (in both machines):

R CMD javareconf (as root)

In Fedora9, I opened R and the package installation went well.
But in the CentOS5 machine, I received the error:
checking Java support in R... configure: error: absent
R was configured without Java support. Please run
R CMD javareconf
as root to add Java support to R.

If you don't have root privileges, run
R CMD javareconf -e
Since the R CMD javareconf did not work, I tryed instead:
R CMD javareconf -e

And now I receive the error:
checking whether JNI programs can be compiled... configure: error: 
Cannot compile a simple JNI program. See config.log for details.

Currently, I do not know how to resolve this error. Where is the 
config.log file? As a root, I did: # find / -name config.log .print
and find no file regarding this JNI error. Also, it is quite difficult 
for a non expert to resolve this type of errors... Any help?

Paulo Alexandre Ribeiro Cortez  (PhD, MSc)
Lecturer (Prof. Auxiliar) at the Department of Information Systems (DSI)
University of Minho, Campus de AzurÈm, 4800-058 Guimaraes, Portugal
http://www.dsi.uminho.pt/~pcortez +351253510313 Fax:+351253510300

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