Issue while doing pip install pybedtools

[sungwookm]

Hi I'm using Python 3.12.2 and have encountered this issue: PS C:\Users\sungw> pip install pandas Collecting pandas Downloading pandas-2.2.1-cp312-cp312-win_amd64.whl.metadata (19 kB) Requirement already satisfied: numpy<2,>=1.26.0 in c:\users\sungw\appdata\local\programs\python\python312\lib\site-packages (from pandas) (1.26.4) Requirement already satisfied: python-dateutil>=2.8.2 in c:\users\sungw\appdata\roaming\python\python312\site-packages (from pandas) (2.9.0) Collecting pytz>=2020.1 (from pandas) Downloading pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB) Collecting tzdata>=2022.7 (from pandas) Downloading tzdata-2024.1-py2.py3-none-any.whl.metadata (1.4 kB) Requirement already satisfied: six>=1.5 in c:\users\sungw\appdata\roaming\python\python312\site-packages (from python-dateutil>=2.8.2->pandas) (1.16.0) Downloading pandas-2.2.1-cp312-cp312-win_amd64.whl (11.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.5/11.5 MB 40.9 MB/s eta 0:00:00 Downloading pytz-2024.1-py2.py3-none-any.whl (505 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 505.5/505.5 kB 31.0 MB/s eta 0:00:00 Downloading tzdata-2024.1-py2.py3-none-any.whl (345 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 345.4/345.4 kB ? eta 0:00:00 Installing collected packages: pytz, tzdata, pandas Successfully installed pandas-2.2.1 pytz-2024.1 tzdata-2024.1 PS C:\Users\sungw> pip install numpy Requirement already satisfied: numpy in c:\users\sungw\appdata\local\programs\python\python312\lib\site-packages (1.26.4) PS C:\Users\sungw> pip install pybedtools Collecting pybedtools Using cached pybedtools-0.9.1.tar.gz (12.5 MB) Preparing metadata (setup.py) ... done Requirement already satisfied: six in c:\users\sungw\appdata\roaming\python\python312\site-packages (from pybedtools) (1.16.0) Collecting pysam (from pybedtools) Using cached pysam-0.22.0.tar.gz (4.6 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 ╰─> [40 lines of output]

pysam: cython is available - using cythonize if necessary

  # pysam: htslib mode is shared
  # pysam: HTSLIB_CONFIGURE_OPTIONS=None
  '.' is not recognized as an internal or external command,
  operable program or batch file.
  '.' is not recognized as an internal or external command,
  operable program or batch file.
  # pysam: htslib configure options: None
  Traceback (most recent call last):
    File "C:\Users\sungw\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\sungw\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\sungw\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\sungw\AppData\Local\Temp\pip-build-env-28rlphez\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\sungw\AppData\Local\Temp\pip-build-env-28rlphez\overlay\Lib\site-packages\setuptools\build_meta.py", line 295, in _get_build_requires
      self.run_setup()
    File "C:\Users\sungw\AppData\Local\Temp\pip-build-env-28rlphez\overlay\Lib\site-packages\setuptools\build_meta.py", line 487, in run_setup
      super().run_setup(setup_script=setup_script)
    File "C:\Users\sungw\AppData\Local\Temp\pip-build-env-28rlphez\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\sungw\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\sungw\AppData\Local\Programs\Python\Python312\Lib\subprocess.py", line 548, in run
      with Popen(*popenargs, **kwargs) as process:
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "C:\Users\sungw\AppData\Local\Programs\Python\Python312\Lib\subprocess.py", line 1026, in __init__
      self._execute_child(args, executable, preexec_fn, close_fds,
    File "C:\Users\sungw\AppData\Local\Programs\Python\Python312\Lib\subprocess.py", line 1538, in _execute_child
      hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  FileNotFoundError: [WinError 2] The system cannot find the file specified
  [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.

[daler]

This looks to be a problem with installing the pysam dependency. Are you able to pip install pysam?

[dbolser]

Close as can't reproduce?

[daler]

@sungwookm please reopen if this is still an issue.