search

fhcrc / deenurp

16S rRNA gene sequence curation and phylogenetic reference set creation
GNU General Public License v3.0
4 stars 3 forks source link

Docker build issue related to hbdscan #76

Closed dhoogest closed 10 months ago

dhoogest commented 11 months ago

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 https://github.com/scikit-learn-contrib/hdbscan/issues/607/

/cc @crosenth 

  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
crosenth commented 11 months ago

Is this from building a Docker image?

dhoogest commented 11 months ago

Yeah or just install from requirements.txt