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Building wheel for hdbscan (pyproject.toml) did not run successfully. #1411

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Ricksanchez000 opened this issue Jul 17, 2023 · 5 comments
Open

Building wheel for hdbscan (pyproject.toml) did not run successfully. #1411

Ricksanchez000 opened this issue Jul 17, 2023 · 5 comments

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@Ricksanchez000
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WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv class="ansi-yellow-fg">
error: subprocess-exited-with-error

× Building wheel for hdbscan (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [168 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-310
creating build/lib.linux-x86_64-cpython-310/hdbscan
copying hdbscan/validity.py -> build/lib.linux-x86_64-cpython-310/hdbscan
copying hdbscan/init.py -> build/lib.linux-x86_64-cpython-310/hdbscan
copying hdbscan/hdbscan_.py -> build/lib.linux-x86_64-cpython-310/hdbscan
copying hdbscan/robust_single_linkage_.py -> build/lib.linux-x86_64-cpython-310/hdbscan
copying hdbscan/prediction.py -> build/lib.linux-x86_64-cpython-310/hdbscan
copying hdbscan/plots.py -> build/lib.linux-x86_64-cpython-310/hdbscan
copying hdbscan/flat.py -> build/lib.linux-x86_64-cpython-310/hdbscan
creating build/lib.linux-x86_64-cpython-310/hdbscan/tests
copying hdbscan/tests/test_prediction_utils.py -> build/lib.linux-x86_64-cpython-310/hdbscan/tests
copying hdbscan/tests/init.py -> build/lib.linux-x86_64-cpython-310/hdbscan/tests
copying hdbscan/tests/test_hdbscan.py -> build/lib.linux-x86_64-cpython-310/hdbscan/tests
copying hdbscan/tests/test_flat.py -> build/lib.linux-x86_64-cpython-310/hdbscan/tests
copying hdbscan/tests/test_rsl.py -> build/lib.linux-x86_64-cpython-310/hdbscan/tests
running build_ext
/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-install-2wkh6f67/hdbscan_d9282b91d1024c7d897cc0e02360a19f/hdbscan/_hdbscan_tree.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
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-310
creating build/temp.linux-x86_64-cpython-310/hdbscan
gcc -pthread -B /opt/conda/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.10 -I/tmp/pip-build-env-ymbqos4/overlay/lib/python3.10/site-packages/numpy/core/include -c hdbscan/hdbscan_tree.c -o build/temp.linux-x86_64-cpython-310/hdbscan/hdbscan_tree.o
In file included from /tmp/pip-build-env-ymbqos4/overlay/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
from /tmp/pip-build-env-ymbqos4/overlay/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /tmp/pip-build-env-ymbqos4/overlay/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from hdbscan/hdbscan_tree.c:1097:
/tmp/pip-build-env-ymbqos4/overlay/lib/python3.10/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 /opt/conda/compiler_compat -shared -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib build/temp.linux-x86_64-cpython-310/hdbscan/_hdbscan_tree.o -o build/lib.linux-x86_64-cpython-310/hdbscan/hdbscan_tree.cpython-310-x86_64-linux-gnu.so
/tmp/pip-build-env-ymbqos4/overlay/lib/python3.10/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-install-2wkh6f67/hdbscan_d9282b91d1024c7d897cc0e02360a19f/hdbscan/_hdbscan_linkage.pyx
tree = Parsing.p_module(s, pxd, full_module_name)

  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 "/opt/conda/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
      main()
    File "/opt/conda/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/opt/conda/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
      return _build_backend().build_wheel(wheel_directory, config_settings,
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 416, in build_wheel
      return self._build_with_temp_dir(['bdist_wheel'], '.whl',
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 401, in _build_with_temp_dir
      self.run_setup()
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 487, in run_setup
      super(_BuildMetaLegacyBackend,
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 338, in run_setup
      exec(code, locals())
    File "<string>", line 96, in <module>
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/__init__.py", line 107, in setup
      return distutils.core.setup(**attrs)
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 185, in setup
      return run_commands(dist)
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
      dist.run_commands()
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
      self.run_command(cmd)
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1234, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/wheel/bdist_wheel.py", line 343, in run
      self.run_command("build")
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
      self.distribution.run_command(command)
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1234, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build.py", line 131, in run
      self.run_command(cmd_name)
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
      self.distribution.run_command(command)
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1234, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "<string>", line 26, in run
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 345, in run
      self.build_extensions()
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 467, in build_extensions
      self._build_extensions_serial()
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 493, in _build_extensions_serial
      self.build_extension(ext)
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/Cython/Distutils/build_ext.py", line 122, in build_extension
      new_ext = cythonize(
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
      cythonize_one(*args)
    File "/tmp/pip-build-env-ymbqos4_/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1301, 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
ERROR: Could not build wheels for hdbscan, which is required to install pyproject.toml-based projects
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv class="ansi-yellow-fg">
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv class="ansi-yellow-fg">

Hi, I meet this problem today ,not sure what happened, I can run the same code yesterday, and today just keep meeting this problem with hdbscan , can you please help me with it?
@MaartenGr
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I believe this is [a known issue with HDBSCAN for which a new version was released that hopefully resolved the issue. I also just checked Pypi and saw that a minute ago a new version of HDBSCAN was released. That might just solve the issue.

@jburdo1
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jburdo1 commented Jul 17, 2023

hdbscan==0.8.31 does indeed fix the problem.

@Ricksanchez000
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I believe this is [a known issue with HDBSCAN for which a new version was released that hopefully resolved the issue. I also just checked Pypi and saw that a minute ago a new version of HDBSCAN was released. That might just solve the issue.

yeah, thank you so much, I just updated my scikit-learn along with HDBSCAN, and it works again,
so happy because it's one of the important topic modeling models I used for my dissertation :)

@Cezary-Kuik Cezary-Kuik mentioned this issue Jul 17, 2023
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@MaartenGr
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Glad to hear that it works again. If you run into any other issues, feel free to reach out!

@manjunath-hanmantgad
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Mine got fixed at 0.8.32 v.

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4 participants
@manjunath-hanmantgad @MaartenGr @Ricksanchez000 @jburdo1