I've also come across this bug and investigating further, I found the
problem is with the sun-java6-* packages, not with gpsprune per-se.

When the system is configured to use openjdk by default, gpsprune works

The issue with Sun Java is that it does not find libraries located in
the /usr/lib/jni directory.

This was discussed in this thread:

Failing a system-wide solution to the Sun Java problem, a workaround is
to patch the gpsprune startup script to add the following line:
export LD_LIBRARY_PATH=/usr/lib/jni

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