Despite running the configure script with the option --with-java, HAVE_JAVA is not passed if java is not installed on the system. Would it be possible to have an error instead? The current behaviour gives me problems on Debian, where java support can be silently dropped by accident when compiling architecture-specific components of the EMBOSS packages. You can find a bit more explanations on the following message:
http://lists.debian.org/msgid-search/20100722081340.GB3417@glandium.org
Have a nice day,
--
Charles
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