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PyProphet / pyprophet

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
http://www.openswath.org
BSD 3-Clause "New" or "Revised" License
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sqlite3.OperationalError:database is locked #119

Open yuz2011 opened 1 year ago

yuz2011 commented 1 year ago

I have meet an error when I run my code as follows: error

Besides, I meet continuous problems when I install pyprophet. For now, the environment has python of 3.9.13, numpy 1.24.3, the installation is through pip install git+https://github.com/PyProphet/pyprophet (with installation warning WARNING: Ignoring invalid distribution -ip (e:\tools\gprodia\gprodia-main\data\result\syn\cleanenv\lib\site-packages) WARNING: You are using pip version 22.0.4; however, version 23.1.2 is available.) Besides, I have installed visual studio, with MSVC v140, MSVC v143, and Windows 10 SDK, windows 11 SDK, C++ CMake installed. Is that anything wrong with my installation?

Thank you very much. Looking forward to your reply.

singjc commented 1 year ago

Hi,

It's a little hard to say what the issue might be. The error indicates that one of the OSW files is currently being operated on (i.e. database is locked). Is anything else operating on the OSW files? If you files are small enough, I could test to see if I run into the same error.

As for installation, your python environment seems fine. I just tested installing via pip install pyprophet on a windows machine with a conda environment (python 3.9.13 and numpy 1.21), and I didn't run into any warnings or errors.

Best,

Justin

yuz2011 commented 1 year ago

Thank you very much for your answer! I re-downloaded the software again and solved the problem. However, the software developed by other developers conflicts with the current version, and errors still occur in later operations (TrpeError: PyProphet () missing 6 required positional arguments: " ss score filter','color palette，'main score_selection report,'outfile', 'level', and ' ss use dynamic main score"). May I ask how to download PyProphet version 2.1.5?

singjc commented 1 year ago

I would suggest downloading via PyPi, using pip install pyprophet. This will contain the most recent updates of PyProphet which is inline with this repository.