Using the pypy fedora package, it seems pip install --user is confused about ~/.local/lib/python3.5/site-packages. It should be using it's own directory, ~/.local/lib/pypy3.5/site-packages, or something like that. pypy3 $(which pip) install --user matplotlib ... Traceback (most recent call last): File "/home/nbecker/.local/lib/python3.5/site-packages/numpy/core/__init__.py", line 16, in <module> from . import multiarray ImportError: cannot import name 'multiarray' Don't know if the pypy default for --user is wrong, or if it's a fedora packaging problem. I can use pypy with virtualenv, but I think this issue shouldn't happen.