Qiime --help throws error after installing qiime2 on Mac

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From your attached log:

(qiime2-2017.10) Colleen-Kelloggs-MacBook-Pro:~ polarmicrobes$ python -c "import numpy; print(numpy.__version__)"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/polarmicrobes/miniconda2/envs/qiime2-2017.10/lib/python3.5/site-packages/numpy/__init__.py", line 142, in <module>
    from . import add_newdocs
  File "/Users/polarmicrobes/miniconda2/envs/qiime2-2017.10/lib/python3.5/site-packages/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/Users/polarmicrobes/miniconda2/envs/qiime2-2017.10/lib/python3.5/site-packages/numpy/lib/__init__.py", line 8, in <module>
    from .type_check import *
  File "/Users/polarmicrobes/miniconda2/envs/qiime2-2017.10/lib/python3.5/site-packages/numpy/lib/type_check.py", line 11, in <module>
    import numpy.core.numeric as _nx
  File "/Users/polarmicrobes/miniconda2/envs/qiime2-2017.10/lib/python3.5/site-packages/numpy/core/__init__.py", line 34, in <module>
    from . import umath
ImportError: dlopen(/Users/polarmicrobes/miniconda2/envs/qiime2-2017.10/lib/python3.5/site-packages/numpy/core/umath.cpython-35m-darwin.so, 2): Symbol not found: ___sincos_stret
  Referenced from: /Users/polarmicrobes/miniconda2/envs/qiime2-2017.10/lib/python3.5/site-packages/numpy/core/umath.cpython-35m-darwin.so
  Expected in: /usr/lib/libSystem.B.dylib
 in /Users/polarmicrobes/miniconda2/envs/qiime2-2017.10/lib/python3.5/site-packages/numpy/core/umath.cpython-35m-darwin.so

Of particular interest is this line:

2): Symbol not found: ___sincos_stret

I think we found the culprit! It looks like you are running Mac OS X 10.8 (Mountain Lion), which is a very old version of Mac OS X (relatively speaking!). Apparently there are issues with running numpy on that version of OS X. I am not sure what version of Mac OS X the conda-supplied numpy builds are built against (one of us will follow-up here if we find that information). Moving forward, one of the following options should work for you:

  • Upgrade your Mac to a recent version of macOS/OS X (High Sierra just came out, that might be a good place to start, if your hardware supports it)
  • Use a QIIME 2 Virtual Machine. The AWS and Virtualbox options should work well for you, but, the Docker VM is probably not a great idea, given how old your OS X is --- I suspect it will be more trouble than it is worth.

Keep us posted! :t_rex:

EDIT: I opened an issue on our issue tracker.

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