R help - Oct 2008 - Installing RWeka package in CentOS 5: problems with JAVA?

Hi,

I am a R user, with some experience in MacOS, Linux, etc, but I am 
having a problem that I cannot solve:

I have a linux server (CentOS 5) and I installed sun jdk1.6. For instance:

$ java -version
Java version "1.6.0_10-rc2"
Java(TM) SE Runtime Environment (build 1.6.0_10-rc2-b32)
Java HotSpot(TM) Server VM (build 11.0-b15, mixed mode)

I also installed the latest version of R:
 > R version 2.7.2 (2008-08-25)

I need to install the package tm, which requires RWeka.
So my first attempt was:

 > 
install.packages("tm",repos="http://cran.cnr.berkeley.edu/",dependencies=TRUE)

Under R. Yet, I got an error related with the RWeka package. Hence, I
downloaded directly the .tgz file and tryed to install it (as root):

$ wget http://cran.cnr.berkeley.edu/src/contrib/RWeka_0.3-14.tar.gz
$ R CMD INSTALL RWeka_0.3-14.tar.gz

* Installing to library '/usr/lib/R/library'
* Installing *source* package 'RWeka' ...
Exception in thread "main" java.lang.NoClassDefFoundError: getsp
Caused by: java.lang.ClassNotFoundException: getsp
	at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
	at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
Could not find the main class: getsp.  Program will exit.
./configure: line 50: test: -ge: unary operator expected
./configure: line 51: test: -eq: unary operator expected
RWeka needs at least Java version 1.5/5.0.
ERROR: configuration failed for package 'RWeka'
** Removing '/usr/lib/R/library/RWeka'

After surfing the web, I found a japanese/chinese(?) page with the same 
problem and I followed their advice (as I understood):

$ R CMD javareconf
Java interpreter : /usr/java/latest//jre/bin/java
Java version     : 1.6.0_10-rc2
Java home path   : /usr/java/latest/
Java compiler    : /usr/java/latest//bin/javac
Java headers gen.: /usr/java/latest//bin/javah
Java archive tool: /usr/java/latest//bin/jar
Java library path: 
/usr/java/jdk1.6.0_10/jre/lib/i386/server:/usr/java/jdk1.6.0_10/jre/lib/i386:/usr/java/jdk1.6.0_10/jre/../lib/i386::/usr/java/packages/lib/i386:/lib:/usr/lib
JNI linker flags : -L/usr/java/jdk1.6.0_10/jre/lib/i386/server 
-L/usr/java/jdk1.6.0_10/jre/lib/i386 
-L/usr/java/jdk1.6.0_10/jre/../lib/i386 -L -L/usr/java/packages/lib/i386 
-L/lib -L/usr/lib -ljvm
JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux

Updating Java configuration in /usr/lib/R
Done.

Then I tryed to repeat the $ R CMD INSTALL RWeka_0.3-14.tar.gz
but I received the previous error. What is wrong? Any help please?


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

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 Azur?m, 4800-058 Guimaraes, Portugal
http://www.dsi.uminho.pt/~pcortez +351253510313 Fax:+351253510300

Em Ter, 2008-10-21 ?s 15:36 +0100, Paulo Cortez
escreveu:
> 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.
  (...)

Hi Paulo

I think you need install JDK and JRE for using rJava


-- 
Bernardo Rangel Tura, M.D,MPH,Ph.D
National Institute of Cardiology
Brazil

On Wed, Oct 22, 2008 at 04:51:13AM -0200, Bernardo Rangel Tura
wrote:
> Em Ter, 2008-10-21 ?s 15:36 +0100, Paulo Cortez escreveu:
> > 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...
...
>   (...)
> 
> Hi Paulo
> 
> I think you need install JDK and JRE for using rJava
> 
http://wiki.centos.org/HowTos/JavaOnCentOS is the recommended way 
to install java on CentOS
see also
http://wiki.centos.org/AdditionalResources/Repositories
http://wiki.centos.org/PackageManagement/SourceInstalls

Tru
-- 
Dr Tru Huynh          | http://www.pasteur.fr/recherche/unites/Binfs/
mailto:tru at pasteur.fr | tel/fax +33 1 45 68 87 37/19
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France