@quiet-ice-72984 so, you find something like:

jsirois@gill ~/dev/pantsbuild/pants (1.2.x) $ ./pants options --scope=python-repos
python-repos.indexes = ['<https://pypi.python.org/simple/>'] (from HARDCODED)
python-repos.repos = [] (from HARDCODED)

Your description (builds on OSX, not Ubuntu) implies the

python_binary

target(s) you're building are not multi-platform; ie: you are not trying to build a single pex that can run on both mac and linux. Can you confirm these details?