[Biojava-dev] Installation Problems

[Salvo Camiolo]

Hi,
I am experiencing some problem with the biojava installation. I use a 
linux machine with  PcLinuxOs distro. I downloaded the file biojava.jar 
from the following website

http://biojava.org/wiki/BioJava:Download

and I have put it in the folder /home/salvo. I then entered that folder 
and typed the following command:

export 
CLASSPATH=/home/salvo/biojava.jar:/home/salvo/bytecode.jar:/home/salvo/commons-cli.jar:/home/salvo/commons-collections-2.1.jar:/home/salvo/commons-dbcp-1.1.jar:/home/salvo/commons-pool-1.1.jar:. 


I need biojava in order to use CAI software by Carbone et al. I 
downloaded the java files for this software and had to compile it. The 
CAI website advice to use javac which I don't have. I used jikes instead 
and got the following error message:

Found 1 system error:

*** Semantic Error: You need to modify your classpath, sourcepath, 
bootclasspath, and/or extdirs setup. Jikes could not find package 
"java.lang" in:
               /home/salvo/biojava.jar
               /home/salvo/bytecode.jar
               /home/salvo/commons-cli.jar
               /home/salvo/commons-collections-2.1.jar
               /home/salvo/commons-dbcp-1.1.jar
               /home/salvo/commons-pool-1.1.jar
               .
               .

If I use the gcj compiler I get several errors, all related to the class 
`org::biojava::bio::seq.


What's can be the problem in your opinion?
Thank you very much in helping me
kind regards
Salvo C.