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require ATLAS at build time
This should enable building with the system-wide ATLAS instead of the partial version shipped by scikit-learn, which contains reference implementations of BLAS algorithms.
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debian/control

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@@ -10,7 +10,8 @@ Build-Depends: debhelper (>= 7.0.50), dh-autoreconf,
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python-numpy, python-scipy,
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python-nose,
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python-matplotlib,
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python-joblib (>= 0.4.5), python-support
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python-joblib (>= 0.4.5), python-support,
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libatlas-dev
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Build-Depends-Indep:
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python-sphinx (>= 1.0), python-imaging, graphviz,
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Standards-Version: 3.9.4

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