Hmm. With stock settings I’m seeing:
Build tree
% otool -L lib/java/vtk-Darwin-x86_64/libvtkCommonCoreJava.jnilib
lib/java/vtk-Darwin-x86_64/libvtkCommonCoreJava.jnilib:
@rpath/libvtkCommonCoreJava.jnilib (compatibility version 0.0.0, current version 0.0.0)
@rpath/libvtkJava-9.0.1.dylib (compatibility version 1.0.0, current version 9.0.0)
@rpath/libvtkCommonCore-9.0.1.dylib (compatibility version 1.0.0, current version 9.0.0)
@rpath/libvtksys-9.0.1.dylib (compatibility version 1.0.0, current version 9.0.0)
/System/Library/Frameworks/JavaVM.framework/Versions/A/JavaVM (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 400.9.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.50.4)
% otool -l lib/java/vtk-Darwin-x86_64/libvtkCommonCoreJava.jnilib | grep -A2 LC_RPATH
cmd LC_RPATH
cmdsize 72
path /Users/boeckb/code/depot/group-kitware/vtk/build/lib (offset 12)
The install tree looks the same; looking into that. But it looks OK here. I’d look to see if you have something not making @rpath/ be used in your build. What CMake are you using?