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Turns out, the problem was a previous installation of Eigen (probably from source), which wasn't cleaned up correctly. There was an invalid /usr/share/cmake/Eigen-3.0.1/eigen-config.cmake file which was setting Eigen_INCLUDE_DIRS instead of Eigen_INCLUDE_DIR (which orocos_kdl was expecting). The result was that the include flag for Eigen was set to -I instead of -I/usr/include/eigen3. Unfortunately the first error message led me way off the right trail.

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