cannnot install - Githubissues

stanfordmlgroup / chexpert-labeler

CheXpert NLP tool to extract observations from radiology reports.

MIT License

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cannnot install #14

Closed kekeke29341 closed 4 years ago

kekeke29341 commented 4 years ago

I got an error. Please help><

jirvin16 commented 4 years ago

If you haven't yet resolved this, this looks like an incorrect version of negbio. I'd suggest updating.

TheRedMoon commented 4 years ago

Do not use bioc==1.3 but instead use bioc==1.1.dev3. The 1.3 version is not compatible with netBio.

https://github.com/ncbi-nlp/NegBio/issues/32#issuecomment-502133836

You can look there for further information

jirvin16 commented 4 years ago

It looks like it is compatible with their Python 3.7 environment:

https://github.com/ncbi-nlp/NegBio/blob/master/environment3.7.yml#L18

Have you tested this with the packages in the CheXpert labeler environment?

TheRedMoon commented 4 years ago

Yes, I have. Ran against the same problem even after installing all the packages correctly. Downgrading from 1.3 to 1.1 fixed it for me (even though like you said it said it should work). I think negbio hasn't been upgraded to deal with the bioc 1.3 yet (correct me if I am wrong).

jirvin16 commented 4 years ago

Got it, thanks for explaining. I'm not sure what's going on, but it may be a Python 3.6 vs. 3.7 issue. It seems like the current packages specified in the CheXpert labeler environment.yml are correct though. Did installing the conda environment from the environment.yml fail for you?

TheRedMoon commented 4 years ago

Could surely be the case. I think i was running on python 3.6. Yes, the environment installed correctly. I will try to use the project soon on a new clean pc and see if I will run against the same problem again.

jirvin16 commented 4 years ago

Great, thanks. In that case going to close this issue for now.