Getting Wheel error for command pip install vcf2fhir

[pankajsurti]

Prerequisites

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• I am running the latest version
• I checked the documentation and found no answer
• I checked to make sure that this issue has not already been filed

Context

Please provide any relevant information about your setup. This is important in case the issue is not reproducible except for under certain conditions.

• Package Version:
• Operating System:

Expected Behavior

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Current Behavior

What is the current behavior?

Failure Information (for bugs)

C:\SRC\vcf2fhir\vcf2fhir\test>pip install vcf2fhir
Collecting vcf2fhir
Using cached vcf2fhir-0.1.1-py3-none-any.whl (26 kB)
Collecting PyVCF3>=1.0.3
Using cached PyVCF3-1.0.3.tar.gz (977 kB)
Preparing metadata (setup.py) ... done
Requirement already satisfied: Cython>=0.29.21 in c:\users\XYZUser\appdata\local\programs\python\python310\lib\site-packages (from vcf2fhir) (0.29.34)
Collecting pyranges>=0.0.96
Using cached pyranges-0.0.120.tar.gz (687 kB)
Preparing metadata (setup.py) ... done
Collecting pandas
Using cached pandas-2.0.0-cp310-cp310-win_amd64.whl (11.2 MB)
Collecting pysam
Using cached pysam-0.21.0.tar.gz (4.1 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
╰─> [34 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\XYZUser\AppData\Local\Programs\Python\Python310\lib\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 353, in
main()
File "C:\Users\XYZUser\AppData\Local\Programs\Python\Python310\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\XYZUser\AppData\Local\Programs\Python\Python310\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\XYZUser\AppData\Local\Temp\pip-build-env-s85ck20c\overlay\Lib\site-packages\setuptools\build_meta.py", line 338, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=['wheel'])
File "C:\Users\XYZUser\AppData\Local\Temp\pip-build-env-s85ck20c\overlay\Lib\site-packages\setuptools\build_meta.py", line 320, in _get_build_requires
self.run_setup()
File "C:\Users\XYZUser\AppData\Local\Temp\pip-build-env-s85ck20c\overlay\Lib\site-packages\setuptools\build_meta.py", line 484, in run_setup
super(_BuildMetaLegacyBackend,
File "C:\Users\XYZUser\AppData\Local\Temp\pip-build-env-s85ck20c\overlay\Lib\site-packages\setuptools\build_meta.py", line 335, in run_setup
exec(code, locals())
File "", line 383, in
File "", line 79, in run_make_print_config
File "C:\Users\XYZUser\AppData\Local\Programs\Python\Python310\lib\subprocess.py", line 420, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "C:\Users\XYZUser\AppData\Local\Programs\Python\Python310\lib\subprocess.py", line 501, in run
with Popen(*popenargs, **kwargs) as process:
File "C:\Users\XYZUser\AppData\Local\Programs\Python\Python310\lib\subprocess.py", line 966, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "C:\Users\XYZUser\AppData\Local\Programs\Python\Python310\lib\subprocess.py", line 1435, 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.

C:\SRC\vcf2fhir\vcf2fhir\test>

Please help provide information about the failure if this is a bug. If it is not a bug, please remove the rest of this template.

Steps to Reproduce

Please provide detailed steps for reproducing the issue.

1. Did "pip install cython wheel"
2. failed on vcf2fhir pip install

Failure Logs

Please include any relevant log snippets or files here.

[rhdolin]

Hi @pankajsurti , can you please take a look at #70 and see if that answers your issue? Are you running on Windows? If so, can you try running on Ubuntu?

[pankajsurti]

Ok, Thank you. I ran it on windows. I will try on Ubuntu and report.

[pankajsurti]

I used the link below to run Ubuntu on Windows and got both the first two install commands working. Thank you @rhdolin.

https://pbpython.com/wsl-python.html