Installation issues with mac

[mortonjt]

I'm having a bit of a problem trying to install this on my mac

(bio)pyemd mortonjt$ nosetests .
EE
======================================================================
ERROR: Failure: ImportError (dlopen(/Users/mortonjt/Documents/software/python/pyemd/pyemd/emd.cpython-35m-darwin.so, 2): Symbol not found: __ZNSt8__detail15_List_node_base7_M_hookEPS0_
  Referenced from: /Users/mortonjt/Documents/software/python/pyemd/pyemd/emd.cpython-35m-darwin.so
  Expected in: dynamic lookup
)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/mortonjt/miniconda2/envs/bio/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/Users/mortonjt/miniconda2/envs/bio/lib/python3.5/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/Users/mortonjt/miniconda2/envs/bio/lib/python3.5/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/Users/mortonjt/miniconda2/envs/bio/lib/python3.5/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/Users/mortonjt/miniconda2/envs/bio/lib/python3.5/imp.py", line 244, in load_module
    return load_package(name, filename)
  File "/Users/mortonjt/miniconda2/envs/bio/lib/python3.5/imp.py", line 216, in load_package
    return _load(spec)
  File "<frozen importlib._bootstrap>", line 693, in _load
  File "<frozen importlib._bootstrap>", line 673, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 662, in exec_module
  File "<frozen importlib._bootstrap>", line 222, in _call_with_frames_removed
  File "/Users/mortonjt/Documents/software/python/pyemd/pyemd/__init__.py", line 60, in <module>
    from .emd import emd
ImportError: dlopen(/Users/mortonjt/Documents/software/python/pyemd/pyemd/emd.cpython-35m-darwin.so, 2): Symbol not found: __ZNSt8__detail15_List_node_base7_M_hookEPS0_
  Referenced from: /Users/mortonjt/Documents/software/python/pyemd/pyemd/emd.cpython-35m-darwin.so
  Expected in: dynamic lookup

pip install gives the exact same issue.
I'm also using python3.5.

Do you have any suggestions around this? Thanks!

[wmayner]

I can't seem to reproduce this. Does it work when you try installing it into a fresh, empty virtualenv?

[mortonjt]

Nope. I tried installing it with a fresh conda environment.

Are you testing this out on an osx machine?

I know another way to reproduce this is to have an osx environment installed on travis.

[wmayner]

Yes, I use OSX. Not sure what the problem is—I've never used Conda or the OSX environment on Travis, so I'm afraid I probably won't be much help.

[wmayner]

There was a similar problem in #5; installing from source seemed to be a workaround in that case. I'd give that a shot.

[mortonjt]

Ok. Good to know that there is a working solution out there. I'll just tinker around with it. Thanks!

[mortonjt]

Ok. Looks like I had some remnants of a homebrew install that overlapped with macports.
After uninstalling homebrew, the linking issues were resolved.