<p>For what it's worth, I just tried compiling <code>armadillo</code> by hand (i.e., Homebrew is not involved, except that we hope <code>armadillo</code> picks up the HDF5 that was installed via Homebrew). It turns out that <code>tmp/include/armadillo_bits/config.hpp</code> has</p>

<pre><code>#define ARMA_USE_HDF5_ALT
</code></pre>

<p>but after I run <code>make</code>, things change:</p>

<pre><code>$ diff tmp/include/armadillo_bits/config.hpp include/armadillo_bits/config.hpp
27c27
&lt; #define ARMA_USE_ARPACK
---
&gt; // #define ARMA_USE_ARPACK
32c32
&lt; #define ARMA_USE_WRAPPER
---
&gt; // #define ARMA_USE_WRAPPER
56,57c56,57
&lt; /* #undef ARMA_USE_ATLAS */
&lt; #define ARMA_ATLAS_INCLUDE_DIR /
---
&gt; // #define ARMA_USE_ATLAS
&gt; // #define ARMA_ATLAS_INCLUDE_DIR /usr/include/
93c93
&lt; #define ARMA_USE_HDF5_ALT
---
&gt; // #define ARMA_USE_HDF5_ALT
98c98
&lt;   #define ARMA_HDF5_INCLUDE_DIR /usr/local/Cellar/hdf5/1.8.14/include/
---
&gt;   // #define ARMA_HDF5_INCLUDE_DIR /usr/include/
171c171
&lt; /* #undef ARMA_USE_EXTERN_CXX11_RNG */
---
&gt;       // #define ARMA_USE_EXTERN_CXX11_RNG
</code></pre>

<p>Does that make any sense to you?</p>

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