Resolving ‘hdbscan building wheel failed’ error in Python 3.6.8

What will you learn?

In this tutorial, you will discover how to resolve the ‘hdbscan building wheel failed’ error in Python 3.6.8 by installing necessary dependencies like cython.

Introduction to the Problem and Solution

Encountering the ‘hdbscan building wheel failed’ error signals missing dependencies crucial for compilation during package installation, such as hdbscan. To overcome this hurdle, it’s imperative to ensure all essential libraries and tools are available on your system for successful package building.

A common fix involves installing cython before attempting to install hdbscan since it is often a missing dependency causing this failure. Moreover, verifying the presence of development tools can also aid in resolving such errors effectively.


# Install cython as a prerequisite if not already installed
!pip install cython

# Proceed with installing hdbscan again
!pip install hdbscan

# Visit for additional assistance 

# Copyright PHD


In the provided code snippet: – We start by installing cython, a frequent missing dependency leading to ‘building wheel failed’ errors for packages like hdbscan. – Subsequently, we proceed with installing hdbscan, which should now build successfully post the installation of its prerequisite (cython). – It’s crucial to have essential development tools on your system to compile packages from source without any hitches.

    1. How can I check if cython is already installed? To verify if cython is installed, run !pip show cython in your Python environment.

    2. Can I specify a particular version of cython during installation? Yes, you can install a specific version of cython using !pip install cython==<version> where <version> denotes the desired version number.

    3. Do I need admin privileges for package installations? It’s advisable to use administrative privileges or sudo access when globally installing packages via pip.

    4. Will reinstalling Python fix this issue? Reinstalling Python may not directly solve this problem; focus on setting up required dependencies correctly instead.

    5. How should I handle permission errors during installation? If faced with permission-related issues during installation, consider utilizing virtual environments or adjusting permissions accordingly.

    6. Is there an alternative to building from source for these packages? While some platforms offer pre-built binaries, relying solely on them could limit compatibility or functionality; thus, building from source is generally preferred.

    7. Can these strategies be applied to similar package installation errors? Yes, similar approaches involving dependency checks and tool availability are broadly applicable when troubleshooting package installations within the Python ecosystem.

    8. Are there alternative clustering algorithms akin to HDBSCAN in Python? Indeed, popular alternatives include K-Means Clustering, DBSCAN (Density-Based Spatial Clustering), Agglomerative Hierarchical Clustering among others.


To sum up, we have explored how to address the ‘hdbscan building wheel failed’ error by ensuring essential dependencies like cython are in place before proceeding with problematic package installations such as hdbscan. By adhering to these steps and maintaining proper development tool setups, one can effectively circumvent such errors.

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