[Biojava-l] location of biojava.jar on a linux system

[Michael Heuer]

Hello Alex,

Combining the java command line arguments -cp and -jar will not work as
you expect -- the -jar argument overrides the CLASSPATH.

"When you use this option, the JAR file is the source of all user
classes, and other user class path settings are ignored."

> http://java.sun.com/j2se/1.5.0/docs/tooldocs/solaris/java.html#options

   michael


On Fri, 11 Feb 2005, Alexandre Dionne-Laporte wrote:

> include the full path of the biojava archive in the definition of your
> classpath:
>
> #java -cp
> /uufs/inscc.utah.edu/common/home/ahammer/ext/xerces.jar:/uufs/inscc.utah.edu/common/home/ahammer/ext/biojava.jar -jar MotifSearch.jar
>
> Alex.
>
> On Fri, 2005-02-11 at 14:02, Andy Hammer wrote:
> > I think I am on the same page as everyone here.
> > But I still get:
> > >java -cp xerces.jar:biojava.jar -jar MotifSearch.jar
> > Exception in thread "main"
> > java.lang.NoClassDefFoundError:
> > org/biojava/bio/BioException
> >
> > More info:
> > ahammer at marchingmen2:~/ext> pwd
> > /uufs/inscc.utah.edu/common/home/ahammer/ext
> > ahammer at marchingmen2:~/ext>
> > ahammer at marchingmen2:~/ext> echo $CLASSPATH
> > .:/uufs/inscc.utah.edu/common/home/ahammer/ext/
> > ahammer at marchingmen2:~/ext>
> > ahammer at marchingmen2:~/ext> ls -l
> > total 4772
> > -rw-r--r--    1 ahammer  gestelan  2674782 2003-10-15
> > 10:37 biojava.jar
> > -rw-r--r--    1 ahammer  gestelan    93463 2003-10-07
> > 17:59 bytecode.jar
> > -rw-r--r--    1 ahammer  gestelan    30117 2003-10-07
> > 17:59 commons-cli.jar
> > -rw-r--r--    1 ahammer  gestelan   145563 2003-10-15
> > 10:04 grammars.jar
> > -rw-r--r--    1 ahammer  gestelan    46056 2003-10-07
> > 17:59 htmlparser.jar
> > -rw-r--r--    1 ahammer  gestelan    50962 2005-02-10
> > 11:38 MotifSearch.jar
> > -rw-r--r--    1 ahammer  gestelan  1808885 2005-02-11
> > 11:55 xerces.jar
> > ahammer at marchingmen2:~/ext>
> >
> > I don't understard why this doesn't work.  It works
> > fine on a windows box.  It makes me think it wouldn't
> > work even if I had access to the jre/ext directory.
> >
> > Andy
> >
> >
> >
> > __________________________________
> > Do you Yahoo!?
> > Yahoo! Mail - Easier than ever with enhanced search. Learn more.
> > http://info.mail.yahoo.com/mail_250
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>