Pip failed when using environment.yml

TIO-IKIM / CellViT

CellViT: Vision Transformers for Precise Cell Segmentation and Classification

https://doi.org/10.1016/j.media.2024.103143

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Pip failed when using environment.yml #64

Closed linatakemaru closed 1 month ago

linatakemaru commented 1 month ago

Hi, I'm having issues creating a conda environment from the provided environment.yml file. The command I used is conda env create -f environment.yml. I believe the issue is encountered during installation of the open slide dependencies. Below are screenshots of the output.

I appreciate the help! This error is reproducible on multiple machines and users. Thank you!

lisafournier commented 1 month ago

Hello! I had the same error and copied /usr/include/crypt.h to /anaconda3/envs/cellvit_env/include and it did the job, similar to this issue.

linatakemaru commented 1 month ago

Hi, I really appreciate your response! I did see that thread, but I don't have the crypt.h file in my anaconda3/include folder

lisafournier commented 1 month ago

Yes but do you have it in /usr/include? If yes then you can copy it where you need (in the /include folder of your anaconda env)

linatakemaru commented 1 month ago

Fixed by running module load gcc/10.2.0