I also have the same problem with older versions of graphviz.
I really need graphviz for OMNeT++
[ellson] For a quick workaround, configure --disable-java
but first, please send me you config.log
[andrei romanov] I'm getting the same error as described in bug #1212 while compiling graphviz 2.12. To find out more about this error, I downloaded version 2.16 from your website and tried compiling it myself. The weird thing is, if I run configure with the --disable-java parameter, the build fails with the "gv_java.cpp:138:17: error: jni.h: No such file or directory" message, just like the gentoo ebuild. But if I _don't_ use the --disable-java parameter, the build compiles just fine.
Since I do have Java installed on my system, I would like to suggest
to look into the possibility that the --disable-java parameter works
incorrectly on systems with Java available.