Issue with hdbscan (ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject)

Question

I know a number of people have posted about this before but I still can't resolve my error. I'm trying to import hdbscan but it keeps returning the following error

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-12-bf3184c2d1a0> in <module>
      2 import numpy as np
      3 from pyproj import Transformer
----> 4 import hdbscan
      5 from scipy.spatial.qhull import ConvexHull
      6 from shapely.geometry import Point

~/Library/Python/3.7/lib/python/site-packages/hdbscan/__init__.py in <module>
----> 1 from .hdbscan_ import HDBSCAN, hdbscan
      2 from .robust_single_linkage_ import RobustSingleLinkage, robust_single_linkage
      3 from .validity import validity_index
      4 from .prediction import (approximate_predict,
      5                          membership_vector,

~/Library/Python/3.7/lib/python/site-packages/hdbscan/hdbscan_.py in <module>
     19 from scipy.sparse import csgraph
     20 
---> 21 from ._hdbscan_linkage import (single_linkage,
     22                                mst_linkage_core,
     23                                mst_linkage_core_vector,

hdbscan/_hdbscan_linkage.pyx in init hdbscan._hdbscan_linkage()

ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject

I have tried uninstalling numpy 1.19.5 and installing numpy 1.20 but it hasn't worked for me. I have installed the package hdbscan 0.8.27, I'm using Python 3.7.2 and I do not have admin rights to my MacBook. Appreciate any help!!

Answer 1

I had the same issue.

I installed the hdbscan using the below method:

!pip install hdbscan --no-build-isolation --no-binary :all:

also installed the numpy 1.9.2

It works for me.