You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Looks like hdbscan (and possibly a related core dependency) is in need of upgrading. It appears 0.8.28 is no longer installable. See also scikit-learn-contrib/hdbscan#607
Building wheel for hdbscan (pyproject.toml): started
Building wheel for hdbscan (pyproject.toml): finished with status 'error'
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-39
creating build/lib.linux-x86_64-cpython-39/hdbscan
copying hdbscan/hdbscan_.py -> build/lib.linux-x86_64-cpython-39/hdbscan
copying hdbscan/prediction.py -> build/lib.linux-x86_64-cpython-39/hdbscan
copying hdbscan/__init__.py -> build/lib.linux-x86_64-cpython-39/hdbscan
copying hdbscan/plots.py -> build/lib.linux-x86_64-cpython-39/hdbscan
copying hdbscan/validity.py -> build/lib.linux-x86_64-cpython-39/hdbscan
copying hdbscan/flat.py -> build/lib.linux-x86_64-cpython-39/hdbscan
copying hdbscan/robust_single_linkage_.py -> build/lib.linux-x86_64-cpython-39/hdbscan
creating 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/__init__.py -> 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_flat.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
running build_ext
Wcpp]
17 |#warning "Using deprecated NumPy API, disable it with " \| ^~~~~~~
gcc -shared build/temp.linux-x86_64-cpython-39/hdbscan/_hdbscan_tree.o -L/usr/local/lib -o build/lib.linux-x86_64-cpython-39/hdbscan/_hdbscan_tree.cpython-39-x86_64-linux-gnu.so
/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/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-enr2f3tg/hdbscan_a99876124ebb4a3ab09e2a271c6fe529/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 "/usr/local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in<module>main()
File "/usr/local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/usr/local/lib/python3.9/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-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 434, in build_wheel
return self._build_with_temp_dir(
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 419, in _build_with_temp_dir
self.run_setup()
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 507, in run_setup
super(_BuildMetaLegacyBackend, self).run_setup(setup_script=setup_script)
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 341, in run_setup
exec(code, locals())
File "<string>", line 96, in<module>
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 103, in setup
return distutils.core.setup(**attrs)
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 989, in run_command
super().run_command(command)
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/wheel/bdist_wheel.py", line 364, in run
self.run_command("build")
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 989, in run_command
super().run_command(command)
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build.py", line 131, in run
self.run_command(cmd_name)
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 989, in run_command
super().run_command(command)
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/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-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 345, in run
self.build_extensions()
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 467, in build_extensions
self._build_extensions_serial()
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 493, in _build_extensions_serial
self.build_extension(ext)
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/Cython/Distutils/build_ext.py", line 130, in build_extension
new_ext = cythonize(
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
cythonize_one(*args)
File "/tmp/pip-build-env-ovf1wt22/overlay/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1321, 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
Building wheel for pygtrie (setup.py): started
Building wheel for pygtrie (setup.py): finished with status 'done'
Created wheel for pygtrie: filename=pygtrie-2.4.2-py3-none-any.whl size=19062 sha256=5888f15ccf3da1ef7efc16017d2fbfc0023304f8d499356018df55544d3d8f63
Stored in directory: /root/.cache/pip/wheels/2e/5d/81/d6e52fec193180ffffef19b185ecf1d0a85d418808c20c09c9
Building wheel for seqmagick (setup.py): started
Building wheel for seqmagick (setup.py): finished with status 'done'
Created wheel for seqmagick: filename=seqmagick-0.8.4-py3-none-any.whl size=54813 sha256=a2b58cfd5bbefb534003facb4e79527e305ae56c990cba409adc9459706d6ba8
Stored in directory: /root/.cache/pip/wheels/ce/c8/48/e042cac1778252d8a45da24ee09b17a463ba097cc21ba15fc0
Building wheel for taxtastic (setup.py): started
Building wheel for taxtastic (setup.py): finished with status 'done'
Created wheel for taxtastic: filename=taxtastic-0.9.2-py3-none-any.whl size=90017 sha256=00f0a0370b4f6761022f2904fe08149fc44e7ad4d90adc28683a40e9bf1ebabb
Stored in directory: /root/.cache/pip/wheels/98/cf/f0/7808e274808a0485f9e52a3e5a760b51dcb3256e26b2b2205f
Successfully built DendroPy fastalite pygtrie seqmagick taxtastic
Failed to build hdbscan
The text was updated successfully, but these errors were encountered:
Looks like hdbscan (and possibly a related core dependency) is in need of upgrading. It appears 0.8.28 is no longer installable. See also scikit-learn-contrib/hdbscan#607
/cc @crosenth
The text was updated successfully, but these errors were encountered: