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mmzdouc / FERMO

Dashboard for analysis of liquid chromatography (tandem) mass spectrometry data.
https://fermo.bioinformatics.nl/example
MIT License
28 stars 2 forks source link

Installation Problem on version 0.8.8 - ModuleNotFoundError: No module named 'matchms.metadata_utils' #5

Closed andrekind17 closed 1 year ago

andrekind17 commented 1 year ago

Ciao Mitja, thanks for sharing FERMO! I'm having a problem during the installation procedure of the 0.8.8 version. I have tried to install both via script and manually but I keep getting the error (see log below). I went back to install the 0.5 version and everything goes smooth via script (see attachment). Marianna and Matteo are facing the same problem both on Mac and Windows.

Thanks for the help! Andrea

Looking for miniconda3 in C:\Users\Dell-NAI-3\ or anaconda3 in C:\Users\Dell-NAI-3\ was successful. Proceeding ... Attempting to activate conda environment FERMO FERMO successfully activated. Traceback (most recent call last): File "src\fermo\app.py", line 45, in from app_utils.FERMO_peaktable_processing import ( File "C:\Users\Dell-NAI-3\Desktop\FERMO-main\src\fermo\app_utils\FERMO_peaktable_processing.py", line 17, in from processing.ms2query_search import ms2query_search File "C:\Users\Dell-NAI-3\Desktop\FERMO-main\src\fermo\processing\ms2query_search.py", line 1, in from ms2query.run_ms2query import download_zenodo_files File "C:\Users\Dell-NAI-3\miniconda3\envs\FERMO\lib\site-packages\ms2query__init__.py", line 3, in from .library_files_creator import LibraryFilesCreator File "C:\Users\Dell-NAI-3\miniconda3\envs\FERMO\lib\site-packages\ms2query\library_files_creator.py", line 8, in from matchmsextras.pubchem_lookup import pubchem_metadata_lookup File "C:\Users\Dell-NAI-3\miniconda3\envs\FERMO\lib\site-packages\matchmsextras\pubchem_lookup.py", line 5, in from matchms.metadata_utils import is_valid_inchikey ModuleNotFoundError: No module named 'matchms.metadata_utils' Press any key to continue . . .

FERMO

mmzdouc commented 1 year ago

Hi Andrea,

thank you for bringing this to our attention.

We found that the error was caused by the recent update of the package matchmsextras that the ms2query package relies upon. FERMO 0.5.0 used an earlier version of ms2query which did not need the matchmsextras package, therefore it still works. We fixed this error and released a new version of FERMO (0.8.9).

Please let me know if that fixes the problem for you.

Kind regards,

Mitja

mariannaiorio commented 1 year ago

Thank you Mitjia! Now it works!

andrekind17 commented 1 year ago

Thanks Mitja! It works!