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 
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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Touch seeded packages, which is subscribed to mesa in Ubuntu.

  Scilab does not start after some upgrades on Ubuntu Xenial

Status in Mesa:
Status in libjogl2-java package in Ubuntu:
  Fix Released
Status in mesa package in Ubuntu:
Status in scilab package in Ubuntu:
Status in libjogl2-java source package in Xenial:
  Fix Committed
Status in mesa source package in Xenial:
Status in scilab source package in Xenial:
Status in libjogl2-java source package in Artful:
  Fix Committed
Status in mesa source package in Artful:
Status in scilab source package in Artful:
Status in scilab package in Debian:
  Fix Released

Bug description:

  Software that use libjogl2-java (Scilab, Matlab,...) fail to run,
  because Mesa dropped 'Gallium' from the renderer string.

  [Test case]
  Steps to reproduce:
  1. have installed Scilab on Ubuntu Xenial system
  2. install system updates
  3. try to launch Scilab from GUI - it does not start
  4. try to launch Scilab from terminal - it does not start with the following 
output in the terminal:

  $ scilab
  Could not create a Scilab main class. Error:
  Exception in thread "main" java.lang.InternalError: XXX0 profile[1]: GL3bc -> 
profileImpl GL4bc !!! not mapped
   at com.jogamp.opengl.GLProfile.computeProfileMap(GLProfile.java:2071)
   at com.jogamp.opengl.GLProfile.initProfilesForDevice(GLProfile.java:1875)
   at com.jogamp.opengl.GLProfile.access$000(GLProfile.java:80)
   at com.jogamp.opengl.GLProfile$1.run(GLProfile.java:230)
   at java.security.AccessController.doPrivileged(Native Method)
   at com.jogamp.opengl.GLProfile.initSingleton(GLProfile.java:216)
   at com.jogamp.opengl.GLProfile.getProfileMap(GLProfile.java:2297)
   at com.jogamp.opengl.GLProfile.get(GLProfile.java:988)
   at com.jogamp.opengl.GLProfile.getDefault(GLProfile.java:722)
   at com.jogamp.opengl.GLProfile.getDefault(GLProfile.java:733)
   at org.scilab.modules.gui.SwingView.<init>(Unknown Source)
   at org.scilab.modules.gui.SwingView.registerSwingView(Unknown Source)
   at org.scilab.modules.core.Scilab.<init>(Unknown Source)

  Scilab cannot create Scilab Java Main-Class (we have not been able to
  find the main Scilab class. Check if the Scilab and thirdparty
  packages are available).

  Expected results:
  Scilab works normally on Ubuntu 16.04 LTS system.

  Actual results:
  see error above.

  [Regression potential]
  The fix is a simple oneliner that allows libjogl2-java to detect Mesa with 
both new and original version of Mesa.

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