[Biojava-dev] Installation Problems

[Richard Holland]

Jikes needs to have all the standard Java libraries on the classpath
as well as your downloaded BioJava+commons libraries. Read the Jikes
documentation for help with that if you're unsure.

We can't help with the errors you got from GCJ unless you can post
them to the list so that we can see what they are!

cheers,
Richard

2008/6/23 Salvo Camiolo <s.camiolo at uniss.it>:
> 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.
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>