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.

[bioruffo]

@andhena try installing specifically pomegranate 0.15.0 and then cnvkit 0.9.10. I get your same error with cnvkit 0.9.11.

pip install pomegranate==0.15.0
pip install cnvkit==0.9.10

[etal]

Packaging has been updated and the tricky pomegranate version range is gone. It should go smoothly with conda now.

Installation with pip might be fine, too, but pytorch/torch sometimes needs special care.

I see bioconductor-dnacopy is in the bioconda repo, so I'd guess the problem is that it hasn't been compiled for your specific architecture (CPU or operating system). In that case, you could try running the docker container (safest, recommended) or installing the R package directly from within R, which should fetch the source and compile it on your machine.