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The Configuration(package_name).to_dict() result already includes the packages=[package_name] entry.
By including it in setup() and in the config_dict mapping, setup() is supplied that keyword twice. You could remove it from the setup() call (line 31):
setup(version='1.1-5',
description='Python wrappers for the GLMNET package',
author='David Warde-Farley',
author_email='dwf@cs.toronto.edu',
url='github.com/dwf/glmnet-python',
license='GPL2',
requires=['NumPy (>= 1.3)'],
**config_dict)
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