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Plastid 0.4.7 completing installation but not importable on OSX #13

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joshuagryphon opened this issue Mar 28, 2017 · 2 comments
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@joshuagryphon
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Two users have reported that Plastid passes installation, but fails during runtime on OSX. This appears to be conda-independent, and occurs even when installing inside virtualenv. After a successful install, import plastid yields:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/username/env/lib/python2.7/site-packages/plastid/__init__.py", line 40, in <module>
    from plastid.genomics.roitools import (GenomicSegment,
ImportError: dlopen(/Users/username/env/lib/python2.7/site-packages/plastid/genomics/roitools.so, 2): Library not loaded: @rpath/pysam/libctabixproxies.so
  Referenced from: /Users/username/env/lib/python2.7/site-packages/plastid/genomics/roitools.so
  Reason: image not found

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@joshuagryphon
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Looking into this a bit, it seems like clang is making dynamically-linked libraries, which is weird because on Linux GCC makes static libs for all of Plastid's extensions.

@joshuagryphon joshuagryphon self-assigned this Mar 28, 2017
@joshuagryphon
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Fixed by removing EXTRA_LINK_ARGS from setup.py. See commit 340e6c6

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