Update all subprocess.check_output functions in CI scripts to be Python 3.4 compatible

Removing the 'universal_newlines' and 'encoding' args from the subprocess.check_outputs fuction. 'universal_newlines' is supported in 3.4, but 'encoding' is not. Without specifying 'encoding' it will make a guess at encoding, which can break things on BSD systems. We must handle encoding/decoding ourselves until we can use Python 3.6

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