Could not install pomegranate package for python 3.13

Question

I've tried to install pomegranate using pip for a while now, but it seems like it can't. All it did was giving me this output.

Collecting pomegranate
  Downloading pomegranate-1.1.1-py3-none-any.whl.metadata (467 bytes)
Collecting numpy>=1.22.2 (from pomegranate)
  Downloading numpy-2.1.2-cp313-cp313-win_amd64.whl.metadata (59 kB)
Collecting scipy>=1.6.2 (from pomegranate)
  Downloading scipy-1.14.1-cp313-cp313-win_amd64.whl.metadata (60 kB)
Collecting scikit-learn>=1.0.2 (from pomegranate)
  Downloading scikit_learn-1.5.2-cp313-cp313-win_amd64.whl.metadata (13 kB)
INFO: pip is looking at multiple versions of pomegranate to determine which version is compatible with other requirements. This could take a while.
Collecting pomegranate
  Downloading pomegranate-1.1.0-py3-none-any.whl.metadata (467 bytes)
  Downloading pomegranate-1.0.4-py3-none-any.whl.metadata (467 bytes)
  Downloading pomegranate-1.0.3-py3-none-any.whl.metadata (479 bytes)
  Downloading pomegranate-1.0.2-py3-none-any.whl.metadata (479 bytes)
  Downloading pomegranate-1.0.0-py3-none-any.whl.metadata (479 bytes)
  Downloading pomegranate-0.15.0.tar.gz (5.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.9/5.9 MB 11.5 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 3221225477
  ╰─> [23 lines of output]
      C:\Users\net15\AppData\Local\Temp\pip-build-env-kdrb5fma\overlay\Lib\site-packages\setuptools\_distutils\dist.py:261: UserWarning: Unknown distribution option: 'test_suite'       
        warnings.warn(msg)
      running dist_info
      creating C:\Users\net15\AppData\Local\Temp\pip-modern-metadata-sf6hlq8p\pomegranate.egg-info
      writing C:\Users\net15\AppData\Local\Temp\pip-modern-metadata-sf6hlq8p\pomegranate.egg-info\PKG-INFO
      writing dependency_links to C:\Users\net15\AppData\Local\Temp\pip-modern-metadata-sf6hlq8p\pomegranate.egg-info\dependency_links.txt
      writing requirements to C:\Users\net15\AppData\Local\Temp\pip-modern-metadata-sf6hlq8p\pomegranate.egg-info\requires.txt
      writing top-level names to C:\Users\net15\AppData\Local\Temp\pip-modern-metadata-sf6hlq8p\pomegranate.egg-info\top_level.txt
      writing manifest file 'C:\Users\net15\AppData\Local\Temp\pip-modern-metadata-sf6hlq8p\pomegranate.egg-info\SOURCES.txt'
      <frozen importlib._bootstrap>:488: Warning: Numpy built with MINGW-W64 on Windows 64 bits is experimental, and only available for
      testing. You are advised not to use it for production.

      CRASHES ARE TO BE EXPECTED - PLEASE REPORT THEM TO NUMPY DEVELOPERS
      C:\Users\net15\AppData\Local\Temp\pip-build-env-kdrb5fma\overlay\Lib\site-packages\numpy\core\getlimits.py:225: RuntimeWarning: invalid value encountered in exp2
        epsneg_f128 = exp2(ld(-113))
      C:\Users\net15\AppData\Local\Temp\pip-build-env-kdrb5fma\overlay\Lib\site-packages\numpy\core\getlimits.py:226: RuntimeWarning: invalid value encountered in exp2
        tiny_f128 = exp2(ld(-16382))
      C:\Users\net15\AppData\Local\Temp\pip-build-env-kdrb5fma\overlay\Lib\site-packages\numpy\core\getlimits.py:240: RuntimeWarning: invalid value encountered in exp2
        eps=exp2(ld(-112)),
      C:\Users\net15\AppData\Local\Temp\pip-build-env-kdrb5fma\overlay\Lib\site-packages\numpy\core\getlimits.py:41: RuntimeWarning: invalid value encountered in nextafter
        self._smallest_subnormal = nextafter(
      C:\Users\net15\AppData\Local\Temp\pip-build-env-kdrb5fma\overlay\Lib\site-packages\numpy\core\getlimits.py:52: RuntimeWarning: invalid value encountered in log10
        self.precision = int(-log10(self.eps))
      [end of output]

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

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

Does anyone have a solution for this?

I have installed Cython before this through it as well. I've also installed pytorch using .whl filetype. It seems like this package could not be installed.

Some guy on the internet told me to install VS C++ Build Tools, but it says "A setup package is either missing or damaged". Do I need to find a solution to this as well?

Answer 1

Your main problem might be related to building wheels for pomegranate with Python 3.13 which is a very recent Python version. There may be compatibility issues.

You can try the following:

1. Install with an earlier Python version since Python 3.13 is very new and many packages haven't been updated for full compatibility yet. Python 3.11 or 3.12 would be more stable choices

# Create a new environment with Python 3.11
conda create -n pomenv python=3.11
conda activate pomenv

# Then try installing pomegranate
pip install pomegranate

2. If you have to stick with 3.13 try installing from source with specific dependencies:

# First install build dependencies
pip install --upgrade pip wheel setuptools
pip install numpy scipy scikit-learn cython

# Then try pomegranate
pip install pomegranate --no-binary :all:

Regarding the Visual C++ Build Tools error ("A setup package is either missing or damaged"), this is a separate but related issue. You'll need this to compile some Python packages.

Here's how to fix it:

a. Download the Visual Studio Build Tools installer directly from Microsoft's official site

b. Run the installer as administrator

c. Select "Desktop development with C++" workload

d. Make sure to include "Windows 10/11 SDK" and "MSVC C++ Build Tools" in the installation