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conda-forge / msprime-feedstock

A conda-smithy repository for msprime.
BSD 3-Clause "New" or "Revised" License
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HDF5 linkage issues #6

Closed jakirkham closed 6 years ago

jakirkham commented 6 years ago

Copying from @alimahmoudi29's comment.

I received the following error: 

Traceback (most recent call last):
  File "/anaconda3/bin/mspms", line 4, in <module>
    import msprime.cli
  File "/anaconda3/lib/python3.6/site-packages/msprime/__init__.py", line 26, in <module>
    from _msprime import FORWARD  # NOQA
ImportError: dlopen(/anaconda3/lib/python3.6/site-packages/_msprime.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libhdf5.10.dylib
  Referenced from: /anaconda3/lib/python3.6/site-packages/_msprime.cpython-36m-darwin.so
  Reason: image not found

I fixed the issue by mv libhdf5.101.dylib libhdf5.10.dylib in directory /usr/local/lib .

jakirkham commented 6 years ago

Would add that it appears that hdf5 is not pinned in this package as it should be. The package should be rebuilt with hdf5 correctly pinned. We will need to pull the packages that were not pinned once this is done.

jeromekelleher commented 6 years ago

Ugh, sorry for this @jakirkham, my bad. I was trying to muddle my way through without bothering you and the other maintainers, but it appears this has done more harm than good...

I've pinned HDF5 following the examples in other feedstocks, so hopefully it's OK now. Let me know if there's anything I can do to help clear up the mess.

jakirkham commented 6 years ago

No worries. If you see this issue other places, please us know.

Looks better. Have pulled the packages that didn't have hdf5 pinned, which should avoid users getting these accidentally. Please double check that we got them all and got the right ones.

jeromekelleher commented 6 years ago

Great, thanks. Just checked the packages on anaconda cloud, and they look right to me.

alimahmoudi29 commented 6 years ago

It works now, thanks