Tested the scilab 5.5.2 for ubuntu which works great. 
However, I did not test it before applying the jogl2 patch :-o.  

Had a look at the source and it seems that the Ubuntu version is patched to use 
the
generic version of jogl2. 

I would like to try and get this patch integrated in the Scilab source tree. 
Probably a difficult and slow process.

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https://bugs.launchpad.net/bugs/1742894

Title:
  Scilab does not start after some upgrades on Ubuntu Xenial

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