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It is important that you checkout the source project side by side to its dependencies:
<pre>
- /home/dude/projects/jogamp> git clone git://jogamp.com/srv/scm/jocl.git jocl
+ /home/dude/projects/jogamp> git clone git://jogamp.org/srv/scm/jocl.git jocl
</pre>
Now you should have following directory structure:
<pre>