Error when running pip install

[shaf8906]

Medaka is a Research Release.

Research releases are provided as technology demonstrators to provide early access to features or stimulate Community development of tools. Support for this software will be minimal and is only provided directly by the developers. Feature requests, improvements, and discussions are welcome and can be implemented by forking and pull requests. However much as we would like to rectify every issue and piece of feedback users may have, the developers may have limited resource for support of this software. Research releases may be unstable and subject to rapid iteration by Oxford Nanopore Technologies.

Please ensure that you are using the most recent version of medaka before filing a bug report. The most recent version can be found on the release page. If you are not using the most recent release, and file a issue regardless the most likely response from our developers will be to ask you to first upgrade.

Please ensure also to provide the information below, not doing so will likely result in a request for the information.

Describe the bug When I use my command prompt to install medaka (pip install medaka) it gets hung up on getting requirements to build wheel. I cannot successfully install medaka with pip. I have a Windows system with WSL installed.

Logging Please attach any relevant logging messages. (Use ``` before and after code blocks).

C:\Users\721588>pip install medaka Defaulting to user installation because normal site-packages is not writeable Collecting medaka Using cached medaka-2.0.1.tar.gz (9.6 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 ╰─> [35 lines of output] Cannot import pyabpoa, some features may not be available. Cannot import wurlitzer, some features may not be available. Bundling models: ['r103_fast_g507', 'r103_fast_snp_g507', 'r103_fast_variant_g507', 'r103_hac_g507', 'r103_hac_snp_g507', 'r103_hac_variant_g507', 'r103_sup_g507', 'r103_sup_snp_g507', 'r103_sup_variant_g507', 'r1041_e82_260bps_fast_g632', 'r1041_e82_260bps_fast_variant_g632', 'r1041_e82_260bps_hac_g632', 'r1041_e82_260bps_hac_v4.0.0', 'r1041_e82_260bps_hac_v4.1.0', 'r1041_e82_260bps_hac_variant_g632', 'r1041_e82_260bps_hac_variant_v4.1.0', 'r1041_e82_260bps_joint_apk_ulk_v5.0.0', 'r1041_e82_260bps_sup_g632', 'r1041_e82_260bps_sup_v4.0.0', 'r1041_e82_260bps_sup_v4.1.0', 'r1041_e82_260bps_sup_variant_g632', 'r1041_e82_260bps_sup_variant_v4.1.0', 'r1041_e82_400bps_bacterial_methylation', 'r1041_e82_400bps_fast_g615', 'r1041_e82_400bps_fast_g632', 'r1041_e82_400bps_fast_variant_g615', 'r1041_e82_400bps_fast_variant_g632', 'r1041_e82_400bps_hac_g615', 'r1041_e82_400bps_hac_g632', 'r1041_e82_400bps_hac_v4.0.0', 'r1041_e82_400bps_hac_v4.1.0', 'r1041_e82_400bps_hac_v4.2.0', 'r1041_e82_400bps_hac_v4.3.0', 'r1041_e82_400bps_hac_v5.0.0', 'r1041_e82_400bps_hac_variant_g615', 'r1041_e82_400bps_hac_variant_g632', 'r1041_e82_400bps_hac_variant_v4.1.0', 'r1041_e82_400bps_hac_variant_v4.2.0', 'r1041_e82_400bps_hac_variant_v4.3.0', 'r1041_e82_400bps_hac_variant_v5.0.0', 'r1041_e82_400bps_sup_g615', 'r1041_e82_400bps_sup_v4.0.0', 'r1041_e82_400bps_sup_v4.1.0', 'r1041_e82_400bps_sup_v4.2.0', 'r1041_e82_400bps_sup_v4.3.0', 'r1041_e82_400bps_sup_v5.0.0', 'r1041_e82_400bps_sup_variant_g615', 'r1041_e82_400bps_sup_variant_v4.1.0', 'r1041_e82_400bps_sup_variant_v4.2.0', 'r1041_e82_400bps_sup_variant_v4.3.0', 'r1041_e82_400bps_sup_variant_v5.0.0', 'r104_e81_fast_g5015', 'r104_e81_fast_variant_g5015', 'r104_e81_hac_g5015', 'r104_e81_hac_variant_g5015', 'r104_e81_sup_g5015', 'r104_e81_sup_g610', 'r104_e81_sup_variant_g610', 'r941_e81_fast_g514', 'r941_e81_fast_variant_g514', 'r941_e81_hac_g514', 'r941_e81_hac_variant_g514', 'r941_e81_sup_g514', 'r941_e81_sup_variant_g514', 'r941_min_fast_g507', 'r941_min_fast_snp_g507', 'r941_min_fast_variant_g507', 'r941_min_hac_g507', 'r941_min_hac_snp_g507', 'r941_min_hac_variant_g507', 'r941_min_sup_g507', 'r941_min_sup_snp_g507', 'r941_min_sup_variant_g507', 'r941_prom_fast_g507', 'r941_prom_fast_snp_g507', 'r941_prom_fast_variant_g507', 'r941_prom_hac_g507', 'r941_prom_hac_snp_g507', 'r941_prom_hac_variant_g507', 'r941_prom_sup_g507', 'r941_prom_sup_snp_g507', 'r941_prom_sup_variant_g507', 'r941_sup_plant_g610', 'r941_sup_plant_variant_g610'] Traceback (most recent call last): File "C:\Users\721588\AppData\Roaming\Python\Python311\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 389, in main() File "C:\Users\721588\AppData\Roaming\Python\Python311\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 373, in main json_out["return_val"] = hook(**hook_input["kwargs"]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\721588\AppData\Roaming\Python\Python311\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 143, in get_requires_for_build_wheel return hook(config_settings) ^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\721588\AppData\Local\Temp\1\pip-build-env-u3mlm648\overlay\Lib\site-packages\setuptools\build_meta.py", line 334, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=[]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\721588\AppData\Local\Temp\1\pip-build-env-u3mlm648\overlay\Lib\site-packages\setuptools\build_meta.py", line 304, in _get_build_requires self.run_setup() File "C:\Users\721588\AppData\Local\Temp\1\pip-build-env-u3mlm648\overlay\Lib\site-packages\setuptools\build_meta.py", line 522, in run_setup super().run_setup(setup_script=setup_script) File "C:\Users\721588\AppData\Local\Temp\1\pip-build-env-u3mlm648\overlay\Lib\site-packages\setuptools\build_meta.py", line 320, in run_setup exec(code, locals()) File "", line 114, in File "", line 52, in check_model_lfs File "C:\Program Files\Python311\Lib\subprocess.py", line 466, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\Python311\Lib\subprocess.py", line 548, in run with Popen(*popenargs, **kwargs) as process: ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\Python311\Lib\subprocess.py", line 1024, in init self._execute_child(args, executable, preexec_fn, close_fds, File "C:\Program Files\Python311\Lib\subprocess.py", line 1493, 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.

**Environment (if you do not have a GPU, write No GPU): No GPU

• Installation method: pip install
• OS: Microsoft Windows 10 Enterprise version 10.0.19045 Build 19045
• medaka version: I can't install it, no version
• GPU model: No GPU
• Nvidia driver version: N/A
• CUDA version: N/A
• cuDNN version N/A

Additional context I am having the same issue across several systems, and when I run the command prompt as administrator.

[alisamatisse]

I think it is an issue with python, I had to downgrade to python=3.9 for my environment. Hope that helps.

@cjw85 are you planning to upgrade for python>3.9 or is it another issue here?

[cjw85]

Python is well supported on python 3.9 and 3.10. There are binary packages on PYPI: https://pypi.org/project/medaka/#files

@shaf8906 The above log suggested that you are installing into your Windows environment, not your WSL environment.

[asan-emirsaleh]

Hello! I have similar message while installing on my Linux machine. Downgrading python to 3.10 resolved the problem. On v3.13, installation is currently broken.

Best regards Asan