<p>Hm, interesting.  Is there any way that you can grab the <code>config.hpp</code> file generated during the Armadillo build process and compare it?  It will be in <code>${ARMADILLO_BUILD_ROOT}/tmp/include/config.hpp</code>.</p>

<p>The fact that you are getting the message</p>

<pre><code>-- Set ARMA_HDF5_INCLUDE_DIR to /usr/local/include
</code></pre>

<p>implies that <code>ARMA_USE_HDF5_ALT</code> should be set in <code>config.hpp</code>, but it isn't, which is confusing to me.  Maybe it's accidentally being stripped somewhere?</p>

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