gluegen-rt.jar shipped depends on gluegen-rt-natives-linux-i586.jar which is actually compiled, but not installed by the current ebuild. I attached a small patch to fix the issue. Reproducible: Always The ebuild is from the java-overlay.
Created attachment 315159 [details, diff] ebuild patch
Created attachment 315161 [details, diff] ebuild patch
We are installing the shared libraries to /usr/lib instead. Please describe what exactly fails or why they need to be on classpath as well.
I'm sorry I can't reproduce the bug at the moment. I thought I needed the patch at the time for a package depending on gluegen, but it's working fine now. I'll reopen the bug if it props up again.