Yes you're right. Indeed what I need, or more what scilab 5.4.0 need, is jogl version 2.
checking jogl2... no configure: error: Could not find or use the Java package/jar jogl2 used by Scilab 3D rendering - Version 2.0 (looking for package javax.media.opengl.glu.GLUnurbs)
You could just try changing the PKGBUILD of jogl in AUR so that it builds version 2.
Time is a great teacher, but unfortunately it kills all its pupils ... - Louis Hector Berlioz