First remove /var/lib/alternatives/java file by typing;
You don't need to do this.
rm /var/lib/alternatives/java
Why, you just add the same entry below, and not in the complete context?
Now to create the new (corrected) alternatives file for java type the following commands as root (modify for jdk as needed);
Again, you can have multiples, and in fact this is what the jpackage compatibility rpm does for you.
/usr/sbin/alternatives --install /usr/bin/java java /usr/lib/jvm/jre-1.4.2-gcj/bin/java 1
/usr/sbin/alternatives --install /usr/bin/java java /usr/java/j2re1.5.0_06/bin/java 2
/usr/sbin/alternatives --config java
These all leave out loads of options that you should have. While it does provide a functioning java setup, it does not provide a complete one, and also removes functionality provided by the original gcj setup.
Next you might want to create (or edit) /etc/profile.d/java.sh file, example below;
export JAVA_HOME="/usr/java/jre1.5.0_06/bin" export JAVA_PATH="$JAVA_HOME" export PATH="$PATH:$JAVA_HOME"
If you're using the alternatives framework you listed above, there's no need to add java to the path. This is redundant. Also, if alternatives is used properly, the other things will be taken care of automagically.
which java
This works before you even install java, as it's a null file provided by gcj. It's simply not competely functional
and the results should read something like; /usr/java/jre1.5.0_06/bin/java
This is because you've made your java path redundant in previous statements. If you're using alternatives correctly, and not screwing with the path after the fact, it should still return the original file, which is: /usr/bin/java
That's it, all done.
It might work, but it's a very broken implementation.
Not meant to be harsh, simply meant to correct bad information.
Also, please don't top post. It's bad for the flow of such messages.