<p>Sorry for the slow response.  The way the Armadillo configuration file should look is that <code>ARMA_USE_HDF5_ALT</code> should be set if <code>DETECT_HDF5</code> is set when CMake configures the project and HDF5 is found.</p>

<p>Nowthere is another shred of oddity here. Armadillo copies all of its sources temporarily to <code>tmp/</code> and modifies that <code>config.hpp</code> (<code>tmp/include/armadillo_bits/config.hpp</code>)</p>

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