This is a real noob question.
When I set up JAVA_HOME using the command line interface I used set JAVA_HOME = C:\Program Files\Java\jdk1.6.0_13
However when I open the JAVA_HOME variable from System>Advanced>Environment Variables the change is not visible. Are these two different settings?
I have this question every time I set up a new Jdk and have never fully understood why the two seem to be different.
The variable you set on command line is for that command shell and any other processes it starts. When you set it from System/Advanced/Environment Variables it affects any other process you start, including command shell, after setting it. Depending on where you set it, it will be available to the same user or any other use who logs in as well.
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