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It's needed to have JAVA_HOME environmental variable set (and pointing to jdk home directory) before running cmake. After
export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64
(path may differ in your system), cmake generated both:
build/bin/opencv-249.jar
build/lib/libopencv_java249.so
Note: 'build'is the temp file where I run cmake and make. make install didn't copy these files to anywhere.