Installation problems

[EfraMP]

Hi,

I'm a MacOS user facing some problems.

First, I tried to install cnvkit via conda, but I was unable and got the next output:

Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides bioconductor-dnacopy needed by cnvkit-0.9.10-pyhdfd78af_0

Could not solve for environment specs
The following package could not be installed
└─ cnvkit is not installable because it requires
   └─ bioconductor-dnacopy, which does not exist (perhaps a missing channel).

Them I attempted to use pip, but got the next output:

Collecting cnvkit
  Downloading CNVkit-0.9.11.tar.gz (176 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 176.3/176.3 kB 1.9 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: biopython>=1.80 in /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages (from cnvkit) (1.81)
Requirement already satisfied: matplotlib>=3.5.2 in /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages (from cnvkit) (3.8.1)
Requirement already satisfied: numpy>=1.24.2 in /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages (from cnvkit) (1.26.1)
Requirement already satisfied: pandas>=1.5.3 in /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages (from cnvkit) (2.1.2)
Collecting pomegranate<=0.14.9,>=0.14.8 (from cnvkit)
  Downloading pomegranate-0.14.9.tar.gz (4.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.7/4.7 MB 5.5 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [75 lines of output]
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
      
      cpdef disable_gpu():
          global GPU
          GPU = False
      
      cdef ndarray_wrap_cpointer(void* data, numpy.npy_intp n):
          ^
      ------------------------------------------------------------
      
      pomegranate/utils.pyx:120:5: Function signature does not match previous declaration
      Compiling pomegranate/BayesClassifier.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/BayesianNetwork.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/FactorGraph.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/MarkovNetwork.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/NaiveBayes.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/base.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/bayes.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/gmm.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/hmm.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/kmeans.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/scipy/linalg/cython_blas.pxd.
      Compiling pomegranate/parallel.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/utils.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/scipy/linalg/cython_blas.pxd.
      Compiling pomegranate/distributions/BernoulliDistribution.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/BetaDistribution.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/ConditionalProbabilityTable.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/DirichletDistribution.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/DiscreteDistribution.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/ExponentialDistribution.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/GammaDistribution.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/IndependentComponentsDistribution.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/JointProbabilityTable.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/KernelDensities.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/LogNormalDistribution.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/MultivariateGaussianDistribution.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/scipy/linalg/cython_blas.pxd.
      Compiling pomegranate/distributions/NormalDistribution.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/PoissonDistribution.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/UniformDistribution.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/distributions.pyx because it depends on /private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      [ 1/28] Cythonizing pomegranate/BayesianNetwork.pyx
      [ 2/28] Cythonizing pomegranate/MarkovNetwork.pyx
      [ 3/28] Cythonizing pomegranate/distributions/ConditionalProbabilityTable.pyx
      [ 4/28] Cythonizing pomegranate/distributions/IndependentComponentsDistribution.pyx
      [ 5/28] Cythonizing pomegranate/distributions/JointProbabilityTable.pyx
      [ 6/28] Cythonizing pomegranate/distributions/MultivariateGaussianDistribution.pyx
      [ 7/28] Cythonizing pomegranate/hmm.pyx
      [ 8/28] Cythonizing pomegranate/kmeans.pyx
      [ 9/28] Cythonizing pomegranate/utils.pyx
      Traceback (most recent call last):
        File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
          return hook(config_settings)
                 ^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 327, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 297, in _get_build_requires
          self.run_setup()
        File "/private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 497, in run_setup
          super().run_setup(setup_script=setup_script)
        File "/private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 313, in run_setup
          exec(code, locals())
        File "<string>", line 61, in <module>
        File "/private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1115, in cythonize
          cythonize_one(*args)
        File "/private/var/folders/zy/5y2l_rkj4f32jtwxywyysp2m0000gn/T/pip-build-env-p3fet7vd/overlay/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1238, in cythonize_one
          raise CompileError(None, pyx_file)
      Cython.Compiler.Errors.CompileError: pomegranate/utils.pyx
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

[ningbioinfo]

Hi, I'm getting the same error in a linux environement within a clean conda environment.

(cnvkit) [a1692215@p2-log-1 LPWGS_Karyotyping]$ pip install cnvkit
Defaulting to user installation because normal site-packages is not writeable
Collecting cnvkit
  Using cached CNVkit-0.9.11.tar.gz (176 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting biopython>=1.80 (from cnvkit)
  Using cached biopython-1.84-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
Requirement already satisfied: matplotlib>=3.5.2 in /gpfs/apps/icl/software/Anaconda3/2024.06-1/lib/python3.12/site-packages (from cnvkit) (3.8.4)
Requirement already satisfied: numpy>=1.24.2 in /gpfs/apps/icl/software/Anaconda3/2024.06-1/lib/python3.12/site-packages (from cnvkit) (1.26.4)
Requirement already satisfied: pandas>=1.5.3 in /gpfs/apps/icl/software/Anaconda3/2024.06-1/lib/python3.12/site-packages (from cnvkit) (2.2.2)
Collecting pomegranate<=0.14.9,>=0.14.8 (from cnvkit)
  Using cached pomegranate-0.14.9.tar.gz (4.7 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [69 lines of output]
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
      
      cpdef disable_gpu():
          global GPU
          GPU = False
      
      cdef ndarray_wrap_cpointer(void* data, numpy.npy_intp n):
          ^
      ------------------------------------------------------------
      
      pomegranate/utils.pyx:120:5: Function signature does not match previous declaration
      Compiling pomegranate/BayesClassifier.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/BayesianNetwork.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/FactorGraph.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/MarkovNetwork.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/NaiveBayes.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/base.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/bayes.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/gmm.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/hmm.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/kmeans.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/scipy/linalg/cython_blas.pxd.
      Compiling pomegranate/parallel.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/utils.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/scipy/linalg/cython_blas.pxd.
      Compiling pomegranate/distributions/BernoulliDistribution.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/distributions/BetaDistribution.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/distributions/ConditionalProbabilityTable.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/distributions/DirichletDistribution.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/distributions/DiscreteDistribution.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/distributions/ExponentialDistribution.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/distributions/GammaDistribution.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/distributions/IndependentComponentsDistribution.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/distributions/JointProbabilityTable.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/distributions/KernelDensities.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/distributions/LogNormalDistribution.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/distributions/MultivariateGaussianDistribution.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/scipy/linalg/cython_blas.pxd.
      Compiling pomegranate/distributions/NormalDistribution.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/distributions/PoissonDistribution.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/distributions/UniformDistribution.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      Compiling pomegranate/distributions/distributions.pyx because it depends on /tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Includes/cpython/object.pxd.
      [ 1/28] Cythonizing pomegranate/distributions/MultivariateGaussianDistribution.pyx
      [ 2/28] Cythonizing pomegranate/kmeans.pyx
      [ 3/28] Cythonizing pomegranate/utils.pyx
      Traceback (most recent call last):
        File "/gpfs/apps/icl/software/Anaconda3/2024.06-1/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/gpfs/apps/icl/software/Anaconda3/2024.06-1/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/gpfs/apps/icl/software/Anaconda3/2024.06-1/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
          return hook(config_settings)
                 ^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 327, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 297, in _get_build_requires
          self.run_setup()
        File "/tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 497, in run_setup
          super().run_setup(setup_script=setup_script)
        File "/tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 313, in run_setup
          exec(code, locals())
        File "<string>", line 61, in <module>
        File "/tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1115, in cythonize
          cythonize_one(*args)
        File "/tmp/pip-build-env-xl71obkd/overlay/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1238, in cythonize_one
          raise CompileError(None, pyx_file)
      Cython.Compiler.Errors.CompileError: pomegranate/utils.pyx
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

[Stikus]

Looks like duplicate of #890 - workaround there

[etal]

Fixed here: #911

Does installation work for you now?

[andhena]

Hi,

I am facing a similar problem from my new work computer (I have been using cnvkit without any issues in the past but I am now working from a Mac).
Here is the details of the error with conda:

conda create -n mycnvkit cnvkit
Channels:
- bioconda
- conda-forge
- andhena
- defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides bioconductor-dnacopy needed by cnvkit-0.9.10-pyhdfd78af_0

Could not solve for environment specs
The following package could not be installed
└─ cnvkit is not installable because it requires
   └─ bioconductor-dnacopy, which does not exist (perhaps a missing channel).

Then I tried with pip:

pip install cnvkit
Collecting cnvkit
  Downloading CNVkit-0.9.11.tar.gz (176 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting biopython>=1.80 (from cnvkit)
  Downloading biopython-1.84-cp312-cp312-macosx_11_0_arm64.whl.metadata (12 kB)
Collecting matplotlib>=3.5.2 (from cnvkit)
  Downloading matplotlib-3.9.2-cp312-cp312-macosx_11_0_arm64.whl.metadata (11 kB)
Collecting numpy>=1.24.2 (from cnvkit)
  Downloading numpy-2.1.1-cp312-cp312-macosx_14_0_arm64.whl.metadata (60 kB)
Collecting pandas>=1.5.3 (from cnvkit)
  Downloading pandas-2.2.2-cp312-cp312-macosx_11_0_arm64.whl.metadata (19 kB)
Collecting pomegranate<=0.14.9,>=0.14.8 (from cnvkit)
  Downloading pomegranate-0.14.9.tar.gz (4.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.7/4.7 MB 17.2 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error

  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [75 lines of output]

      Error compiling Cython file:
      ------------------------------------------------------------
      ...

      cpdef disable_gpu():
          global GPU
          GPU = False

      cdef ndarray_wrap_cpointer(void* data, numpy.npy_intp n):
          ^
      ------------------------------------------------------------

      pomegranate/utils.pyx:120:5: Function signature does not match previous declaration
      Compiling pomegranate/BayesClassifier.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/BayesianNetwork.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/FactorGraph.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/MarkovNetwork.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/NaiveBayes.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/base.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/bayes.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/gmm.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/hmm.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/kmeans.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/scipy/linalg/cython_blas.pxd.
      Compiling pomegranate/parallel.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/utils.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/scipy/linalg/cython_blas.pxd.
      Compiling pomegranate/distributions/BernoulliDistribution.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/BetaDistribution.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/ConditionalProbabilityTable.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/DirichletDistribution.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/DiscreteDistribution.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/ExponentialDistribution.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/GammaDistribution.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/IndependentComponentsDistribution.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/JointProbabilityTable.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/KernelDensities.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/LogNormalDistribution.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/MultivariateGaussianDistribution.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/scipy/linalg/cython_blas.pxd.
      Compiling pomegranate/distributions/NormalDistribution.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/PoissonDistribution.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/UniformDistribution.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      Compiling pomegranate/distributions/distributions.pyx because it depends on /private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Includes/libc/string.pxd.
      [ 1/28] Cythonizing pomegranate/BayesianNetwork.pyx
      [ 2/28] Cythonizing pomegranate/MarkovNetwork.pyx
      [ 3/28] Cythonizing pomegranate/distributions/ConditionalProbabilityTable.pyx
      [ 4/28] Cythonizing pomegranate/distributions/IndependentComponentsDistribution.pyx
      [ 5/28] Cythonizing pomegranate/distributions/JointProbabilityTable.pyx
      [ 6/28] Cythonizing pomegranate/distributions/MultivariateGaussianDistribution.pyx
      [ 7/28] Cythonizing pomegranate/hmm.pyx
      [ 8/28] Cythonizing pomegranate/kmeans.pyx
      [ 9/28] Cythonizing pomegranate/utils.pyx
      Traceback (most recent call last):
        File "/Users/miniconda3/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/Users/miniconda3/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/Users/miniconda3/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
          return hook(config_settings)
                 ^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 332, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 302, in _get_build_requires
          self.run_setup()
        File "/private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 503, in run_setup
          super().run_setup(setup_script=setup_script)
        File "/private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 318, in run_setup
          exec(code, locals())
        File "<string>", line 61, in <module>
        File "/private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1115, in cythonize
          cythonize_one(*args)
        File "/private/var/folders/qp/4y1f5v415gx8k4b6p3c4rb2w0000gp/T/pip-build-env-0226pxll/overlay/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1238, in cythonize_one
          raise CompileError(None, pyx_file)
      Cython.Compiler.Errors.CompileError: pomegranate/utils.pyx
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Any help would be greatly appreciated.
Let me know if you need more infos,

Thank you for your help

[EfraMP]

Hi @andhena,

I haven't tried yet. I was able to install CNVkit on a LInux server so I stopped trying on MacOS.