http://gcc.gnu.org/bugzilla/show_bug.cgi?id=55716
--- Comment #2 from Mark Wielaard <mark at gcc dot gnu.org> 2012-12-17 10:16:20 UTC --- Hmmm, it might be that it is picking up the wrong "bootclasspath" in this case. By default it tries to use System.getProperty("sun.boot.class.path") which I assume is set to file:/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre/lib/rt.jar in this case. Does it help to explicitly add it to the gjavah invocation like -bootclasspath ../../../libjava/classpath/lib ? It is a little strange if this (or maybe just -classpath ../../../libjava/classpath/lib) would work. I assume the directory on which you run --all is in the default classpath. And you seem to explicitly set the CLASSPATH environment variable (maybe that doesn't include all dirs/classes?)