ERROR: Failed building wheel for hdbscan #47
Description
Hi there,
I'd love to install FSCT to try out the leaf/wood segmentation and its other tools, but I have an error when creating the conda environment. It seems that on my machine and using a python 3.9 env as advised in the installation instructions, the hdbscan library cannot be compiled, see below ! I use Ubuntu 25.04.
I'd appreciate your help with that, thank you very much!
Cyril
Building wheels for collected packages: hdbscan
Building wheel for hdbscan (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for hdbscan (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [180 lines of output]
/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite'
warnings.warn(msg)
/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require'
warnings.warn(msg)
/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!
********************************************************************************
Please consider removing the following classifiers in favor of a SPDX license expression:
License :: OSI Approved
See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
********************************************************************************
!!
self._finalize_license_expression()
running bdist_wheel
running build
running build_py
creating build/lib.linux-x86_64-cpython-39/hdbscan
copying hdbscan/validity.py -> build/lib.linux-x86_64-cpython-39/hdbscan
copying hdbscan/robust_single_linkage_.py -> build/lib.linux-x86_64-cpython-39/hdbscan
copying hdbscan/prediction.py -> build/lib.linux-x86_64-cpython-39/hdbscan
copying hdbscan/plots.py -> build/lib.linux-x86_64-cpython-39/hdbscan
copying hdbscan/hdbscan_.py -> build/lib.linux-x86_64-cpython-39/hdbscan
copying hdbscan/flat.py -> build/lib.linux-x86_64-cpython-39/hdbscan
copying hdbscan/__init__.py -> build/lib.linux-x86_64-cpython-39/hdbscan
creating build/lib.linux-x86_64-cpython-39/hdbscan/tests
copying hdbscan/tests/test_rsl.py -> build/lib.linux-x86_64-cpython-39/hdbscan/tests
copying hdbscan/tests/test_prediction_utils.py -> build/lib.linux-x86_64-cpython-39/hdbscan/tests
copying hdbscan/tests/test_hdbscan.py -> build/lib.linux-x86_64-cpython-39/hdbscan/tests
copying hdbscan/tests/test_flat.py -> build/lib.linux-x86_64-cpython-39/hdbscan/tests
copying hdbscan/tests/__init__.py -> build/lib.linux-x86_64-cpython-39/hdbscan/tests
running build_ext
Compiling hdbscan/_hdbscan_tree.pyx because it changed.
[1/1] Cythonizing hdbscan/_hdbscan_tree.pyx
building 'hdbscan._hdbscan_tree' extension
creating build/temp.linux-x86_64-cpython-39/hdbscan
gcc -pthread -B /home/cbozonnet/miniconda3/envs/FSCT/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/cbozonnet/miniconda3/envs/FSCT/include -fPIC -O2 -isystem /home/cbozonnet/miniconda3/envs/FSCT/include -fPIC -I/home/cbozonnet/miniconda3/envs/FSCT/include/python3.9 -I/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/numpy/core/include -c hdbscan/_hdbscan_tree.c -o build/temp.linux-x86_64-cpython-39/hdbscan/_hdbscan_tree.o
In file included from /tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
from /tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from hdbscan/_hdbscan_tree.c:1136:
/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
gcc -pthread -B /home/cbozonnet/miniconda3/envs/FSCT/compiler_compat -Wl,--sysroot=/ -shared -Wl,-rpath,/home/cbozonnet/miniconda3/envs/FSCT/lib -Wl,-rpath-link,/home/cbozonnet/miniconda3/envs/FSCT/lib -L/home/cbozonnet/miniconda3/envs/FSCT/lib -Wl,-rpath,/home/cbozonnet/miniconda3/envs/FSCT/lib -Wl,-rpath-link,/home/cbozonnet/miniconda3/envs/FSCT/lib -L/home/cbozonnet/miniconda3/envs/FSCT/lib build/temp.linux-x86_64-cpython-39/hdbscan/_hdbscan_tree.o -o build/lib.linux-x86_64-cpython-39/hdbscan/_hdbscan_tree.cpython-39-x86_64-linux-gnu.so
Error compiling Cython file:
------------------------------------------------------------
...
import numpy as np
cimport numpy as np
from libc.float cimport DBL_MAX
from dist_metrics cimport DistanceMetric
^
------------------------------------------------------------
hdbscan/_hdbscan_linkage.pyx:12:0: 'dist_metrics.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
import numpy as np
cimport numpy as np
from libc.float cimport DBL_MAX
from dist_metrics cimport DistanceMetric
^
------------------------------------------------------------
hdbscan/_hdbscan_linkage.pyx:12:0: 'dist_metrics/DistanceMetric.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
cpdef np.ndarray[np.double_t, ndim=2] mst_linkage_core_vector(
np.ndarray[np.double_t, ndim=2, mode='c'] raw_data,
np.ndarray[np.double_t, ndim=1, mode='c'] core_distances,
DistanceMetric dist_metric,
^
------------------------------------------------------------
hdbscan/_hdbscan_linkage.pyx:58:8: 'DistanceMetric' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
continue
right_value = current_distances[j]
right_source = current_sources[j]
left_value = dist_metric.dist(&raw_data_ptr[num_features *
^
------------------------------------------------------------
hdbscan/_hdbscan_linkage.pyx:129:42: Cannot convert 'double_t *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
right_value = current_distances[j]
right_source = current_sources[j]
left_value = dist_metric.dist(&raw_data_ptr[num_features *
current_node],
&raw_data_ptr[num_features * j],
^
------------------------------------------------------------
hdbscan/_hdbscan_linkage.pyx:131:42: Cannot convert 'double_t *' to Python object
Compiling hdbscan/_hdbscan_linkage.pyx because it changed.
[1/1] Cythonizing hdbscan/_hdbscan_linkage.pyx
Traceback (most recent call last):
File "/home/cbozonnet/miniconda3/envs/FSCT/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
main()
File "/home/cbozonnet/miniconda3/envs/FSCT/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
json_out["return_val"] = hook(**hook_input["kwargs"])
File "/home/cbozonnet/miniconda3/envs/FSCT/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 280, in build_wheel
return _build_backend().build_wheel(
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 435, in build_wheel
return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)])
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 423, in _build
return self._build_with_temp_dir(
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 404, in _build_with_temp_dir
self.run_setup()
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 512, in run_setup
super().run_setup(setup_script=setup_script)
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 317, in run_setup
exec(code, locals())
File "<string>", line 96, in <module>
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 115, in setup
return distutils.core.setup(**attrs)
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 186, in setup
return run_commands(dist)
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
dist.run_commands()
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 1002, in run_commands
self.run_command(cmd)
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 1102, in run_command
super().run_command(command)
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/command/bdist_wheel.py", line 370, in run
self.run_command("build")
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 357, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 1102, in run_command
super().run_command(command)
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 357, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 1102, in run_command
super().run_command(command)
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
cmd_obj.run()
File "<string>", line 26, in run
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 368, in run
self.build_extensions()
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 484, in build_extensions
self._build_extensions_serial()
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 510, in _build_extensions_serial
self.build_extension(ext)
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/Cython/Distutils/build_ext.py", line 131, in build_extension
new_ext = cythonize(
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
cythonize_one(*args)
File "/tmp/pip-build-env-zs_dooqn/overlay/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1298, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: hdbscan/_hdbscan_linkage.pyx
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for hdbscan
Failed to build hdbscan
ERROR: Failed to build installable wheels for some pyproject.toml based projects (hdbscan)