libjava fails to cross-build because the Makefile includes an -I/usr/include. Removing that makes it work. I've seen this a number of times now, i386 to alpha-linux, i386 to m68-linux, etc. The problem is this in the Makefile: X_CFLAGS = -I/usr/include and X_CFLAGS is part of AM_CXXFLAGS which is where it causes the problem.
I configured gcc with: /home/tbm/scratch/gcc/configure --disable-bootstrap \ --enable-languages=c,c++,java --target=alpha-linux-gnu -- Summary: libjava cannot be cross-built; X_CFLAGS includes /usr/include Product: gcc Version: 4.2.0 Status: UNCONFIRMED Severity: normal Priority: P3 Component: libgcj AssignedTo: unassigned at gcc dot gnu dot org ReportedBy: tbm at cyrius dot com http://gcc.gnu.org/bugzilla/show_bug.cgi?id=28009