pythonpippackageconsolepysam

How do I fix the error when installing the pysam package?

I decided to install the gemini package via pip install gemini in the console, an error was issued when installing pysam, I already installed cython, added it to the PATH, but the error still persists, help solve the problem, below I attach messages from the console in text and as a screenshot. The text version:

C:\Users\1>pip install pysam
Collecting pysam
  Downloading pysam-0.22.0.tar.gz (4.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 2.9 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
  ╰─> [40 lines of output]
      # pysam: cython is available - using cythonize if necessary
      # pysam: htslib mode is shared
      # pysam: HTSLIB_CONFIGURE_OPTIONS=None
      "." Ґ пў«пҐвбп ўгв॥© Ё«Ё ўҐиҐ©
      Є®¬ ¤®©, ЁбЇ®«пҐ¬®© Їа®Ја ¬¬®© Ё«Ё Ї ЄҐвл¬ д ©«®¬.
      "." Ґ пў«пҐвбп ўгв॥© Ё«Ё ўҐиҐ©
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      # pysam: htslib configure options: None
      Traceback (most recent call last):
        File "C:\Users\1\AppData\Local\Programs\Python\Python312\Lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 353, in <module>
          main()
        File "C:\Users\1\AppData\Local\Programs\Python\Python312\Lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "C:\Users\1\AppData\Local\Programs\Python\Python312\Lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 118, in get_requires_for_build_wheel
          return hook(config_settings)
                 ^^^^^^^^^^^^^^^^^^^^^
        File "C:\Users\1\AppData\Local\Temp\pip-build-env-ub99jpmq\overlay\Lib\site-packages\setuptools\build_meta.py", line 325, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=['wheel'])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "C:\Users\1\AppData\Local\Temp\pip-build-env-ub99jpmq\overlay\Lib\site-packages\setuptools\build_meta.py", line 295, in _get_build_requires
          self.run_setup()
        File "C:\Users\1\AppData\Local\Temp\pip-build-env-ub99jpmq\overlay\Lib\site-packages\setuptools\build_meta.py", line 480, in run_setup
          super(_BuildMetaLegacyBackend, self).run_setup(setup_script=setup_script)
        File "C:\Users\1\AppData\Local\Temp\pip-build-env-ub99jpmq\overlay\Lib\site-packages\setuptools\build_meta.py", line 311, in run_setup
          exec(code, locals())
        File "<string>", line 442, in <module>
        File "<string>", line 82, in run_make_print_config
        File "C:\Users\1\AppData\Local\Programs\Python\Python312\Lib\subprocess.py", line 466, in check_output
          return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "C:\Users\1\AppData\Local\Programs\Python\Python312\Lib\subprocess.py", line 548, in run
          with Popen(*popenargs, **kwargs) as process:
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "C:\Users\1\AppData\Local\Programs\Python\Python312\Lib\subprocess.py", line 1026, in __init__
          self._execute_child(args, executable, preexec_fn, close_fds,
        File "C:\Users\1\AppData\Local\Programs\Python\Python312\Lib\subprocess.py", line 1538, in _execute_child
          hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      FileNotFoundError: [WinError 2] Не удается найти указанный файл
      [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.

Screenshot: Screenshot of console

I tried to use the restriction when installing gemini (Cython version < 3.0), added it to the PATH, but the error is still there and I don't understand how to get rid of it, the Python version is 64-bit

Solution

  • You seem to be trying to install pysam package on windows however according to PyPi, pysam is only available on the following Operating Systems:

    See https://pypi.org/project/pysam/ for more information.