EasyPQP couldn't import PyOpenMS package

[actopossum]

Hi,

I am running Fragpipe22 and it was working fine but I upgraded to easypqp v.1.5.0 and it seems to now have issues. I tried looking for the pyOpenMS libraries but I couldn't find the pyopenms*.so file within the directory as suggested in the dependency walker debug comment.

I had recently installed a standalone DIA-nn which messed up the skyline document functionality in Fragpipe22 but I think that's a separate issue.

Thanks for your help!

log_2024-10-22_11-37-21.txt

[fcyu]

Could you run the following to uninstall and install some Python packages in command line interface?

uninstall easypqp pyopenms -y
install easypqp

Thanks,

Fengchao

[actopossum]

Hi Fengchao!
Thanks for the quick response. Is this a cmd prompt or python prompt? I tried both and it's not working. Is 'uninstall.exe' in a fragpipe directory?

[fcyu]

Ah, I am sorry. I guess my head was not clear when I was typing. The commands should be

pip uninstall easypqp pyopenms -y
pip install easypqp

Is this a cmd prompt or python prompt?

Should be the cmd prompt that with pip (and Python) in the PATH.

Best,

Fengchao

[actopossum]

Ok I was able to uninstall and reinstall but I still get the same error as before. I did notice it seemed to not install in the site-packages folder so I tried adding that to PATH but it didn't help.

last few lines of the output from install command.

Installing collected packages: pyopenms, easypqp
WARNING: The script easypqp.exe is installed in 'C:\Users\shaoen\AppData\Roaming\Python\Python311\Scripts' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed easypqp-0.1.50 pyopenms-3.2.0

[guoci]

@actopossum
Please do:

C:\ProgramData\anaconda3\pip uninstall easypqp pyopenms -y
C:\ProgramData\anaconda3\pip install easypqp

[actopossum]

I did do that but it seems to not make a difference. Not sure it matters but this is on a Windows Server 2019 box.

[guoci]

@actopossum
I would suggest you try on a new install of Python. Using an existing installation may be causing the problem.
Can you install a new Python using Miniconda? https://docs.anaconda.com/miniconda/miniconda-install/
Please use Python 3.11 https://repo.anaconda.com/miniconda/Miniconda3-py311_24.7.1-0-Windows-x86_64.exe
Then, change the FragPipe Python path to the newly installed Python.

[actopossum]

Thanks Fengchao!
That seems to have done the trick. Didn't solve the Skyline document issue but maybe I should open a new thread for that.

[poshul]

Hi all,
we traced the issue down to python not reloading a newer visual C++ redistributable if it's already loaded an earlier version from another package (in this case pyarrow). Unfortunately between 3.1.0 and 3.2.0 Microsoft updated the mutex constructor, which led to code built with newer versions of MSVC being incompatible by default with earlier library versions (microsoft/STL#4730). We've released a fix, which is live in PYPI under version 3.2.0.1, and reached out to the pyarrow folks to see if they can update the redistributable that they ship. Please let me know if any of you have issues with the new version.

Sam

[fcyu]

Fixed in OpenMS/OpenMS#7699