Currently, I have a machine on which I am working in Eclipse, it says that the JRE System Library version is sun-jdk-1.5.0.11 but on my active development machine, it is java-6-sun-1.6.0.16. Is there any way I can make the first machine to use the same "java-6-sun-1.6.0.16" version without having sudo permissions on the machine?
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You can install the JDK in a non-standard directory, for example under your own home directory, without special permissions.
You just need to point PATH and JAVA_HOME and Eclipse at it.
The great thing with Java on Linux (and quite some other Unices) is that you don't need the "root" password to install it. I do this all the time. This is in sharp contrast with Windows where, last time I checked, it was impossible to install Java without having an admin password.
All you need is a repertory in which you put the JRE (or JDK) and then put it on the path:
In the same vein, you can keep several JVM in the same user account and simply change the path as needed (or point your IDE to the correct JVM: for example I'm running IntelliJ IDEA with an 1.6 VM but compiling and runnning all my unit tests using a 1.5 VM).