#1259·umap

Importing umap throws "SystemError: CPUDispatcher(<function make_heap at 0x0000020B1ACFEE80>) returned a result with an exception set"

Author: actopozipcCreated May 19, 2026Updated May 20, 2026

Hi, When I write

import umap

it throws the error


TypeError: expected dtype object, got 'numpy.dtypes.UInt8DType'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\philip\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.12_qbz5n2kfra8p0\LocalCache\local-packages\Python312\site-packages\\\umap\__init__.py", line 2, in <module>
    from .umap_ import UMAP
  File "C:\Users\philip\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.12_qbz5n2kfra8p0\LocalCache\local-packages\Python312\site-packages\\\umap\\\umap_.py", line 48, in <module>
    from pynndescent import NNDescent
  File "C:\Users\philip\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.12_qbz5n2kfra8p0\LocalCache\local-packages\Python312\site-packages\pynndescent\__init__.py", line 5, in <module>
    from .pynndescent_ import NNDescent, PyNNDescentTransformer
  File "C:\Users\philip\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.12_qbz5n2kfra8p0\LocalCache\local-packages\Python312\site-packages\pynndescent\pynndescent_.py", line 22, in <module>
    import pynndescent.sparse as sparse
  File "C:\Users\philip\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.12_qbz5n2kfra8p0\LocalCache\local-packages\Python312\site-packages\pynndescent\sparse.py", line 9, in <module>
    from pynndescent.utils import norm, tau_rand
  File "C:\Users\philip\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.12_qbz5n2kfra8p0\LocalCache\local-packages\Python312\site-packages\pynndescent\\\utils.py", line 162, in <module>
    EMPTY_GRAPH = make_heap(1, 1)
                  ^^^^^^^^^^^^^^^
SystemError: CPUDispatcher(<function make_heap at 0x0000020B1ACFEE80>) returned a result with an exception set

Looking for this error only lead to other packages throwing the same error due to mismatches with numpy, scipy or numba. However, for me as an "end-user" of umap it is quite hard to tell what actually could cause the missmatch and it would be delightful to receive some input from someone who knows it better than me.

umap-learn version: 0.5.12
numba version: 0.64.0
numpy version: 1.26.4
scipy version: 1.12.0

When creating a new fresh environment and freshly installing umap-learn, these versions:

colorama 0.4.6
joblib 1.5.3
llvmlite 0.47.0
numba 0.65.1
numpy 2.4.6
pip 25.0.1
pynndescent 0.6.0
scikit-learn 1.8.0
scipy 1.17.1
threadpoolctl 3.6.0
tqdm 4.67.3
umap-learn 0.5.12

throw me the SAME error as previously.

Source: lmcinnes/umap

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