I'm having some trouble getting the hmmlearn package to install properly (in a virtual environment); it seems to have something to do with the underlying C code. The package installs fine with pip, but when I try to import the core class, I get an error:
In [1]: import hmmlearn
In [2]: from hmmlearn import hmm
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-2-8b8c029fb053> in <module>()
----> 1 from hmmlearn import hmm
/export/hdi3/home/krono/envs/sd/lib/python2.7/site-packages/hmmlearn/hmm.py in <module>()
19 from sklearn.utils import check_random_state
20
---> 21 from .base import _BaseHMM
22 from .utils import iter_from_X_lengths, normalize
23
/export/hdi3/home/krono/envs/sd/lib/python2.7/site-packages/hmmlearn/base.py in <module>()
11 from sklearn.utils.validation import check_is_fitted
12
---> 13 from . import _hmmc
14 from .utils import normalize, log_normalize, iter_from_X_lengths
15
ImportError: /export/hdi3/home/krono/envs/sd/lib/python2.7/site-packages/hmmlearn/_hmmc.so: undefined symbol: npy_expl
I've been reading other questions on SO which seem to treat this, but one solution (use Anaconda) won't work since hmmlearn isn't included. It seems like the answer has something to do with compiling the C code, but I'm not sure how to go about it. Any help would be much appreciated!
I ran into the same issue a while ago and found the solution by trying everything possible. For whatever reason in some cases pip skips building C-extensions, when a package is saved into the cache directory. If you force pip to ignore the cache, it always builds the package from scratch, so the solution is to uninstall the package in the first place and then run pip install --no-cache-dir <package>