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

[Paulo Cortez]

Hi,

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:
jdk-6u10-linux-i586-rpm.bin?AuthParam=1224512972_e5a9932e886a02f44dfdfe48aad02db8&TicketId=B%2Fw2nBuFSltLQRRFM1JblgDk&GroupName=CDS&FilePath=%2FESD5%2FJSCDL%2Fjdk%2F6u10%2Fjdk-6u10-linux-i586-rpm.bin&File=jdk-6u10-linux-i586-rpm.bin)
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?

Regards,
-- 
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