DeepFoldRNA installation Errors

[kulkarnim_bii]

Hi,

I downloaded DeepFoldRNA from https://github.com/robpearc/DeepFoldRNA and tried to install all dependencies.

I am facing error at SPOT-RNA-1D installation (Numpy version conflict). Even though SPOT-RNA-1D installation was incomplete, I tried to test runDeepFoldRNA.py, but it also crashed with PyTorch issues.

Code: Select all

 File "runDeepFoldRNA.py", line 7, in <module>
    import torch
  File "/miniforge3/envs/deepfoldrna/lib/python3.7/site-packages/torch/__init__.py", line 197, in <module>
    from torch._C import *  # noqa: F403
ImportError: /miniforge3/envs/deepfoldrna/lib/python3.7/site-packages/torch/lib/libtorch_cpu.so: undefined symbol: iJIT_NotifyEvent

Could you please suggest if there is new version or updated set of packages for DeepFoldRNA?

Best,
Mandar

[XiZhang]

Dear user,

I'm not aware of a newer DeepFoldRNA release or an updated package set beyond what's currently on GitHub. The SPOT-RNA-1D issue looks like a NumPy version mismatch, and the iJIT_NotifyEvent error is probably a compatibility issue between the conda PyTorch build and the MKL version in your Miniforge environment. You could try installing SPOT-RNA-1D with its own requirements.txt and then either downgrading MKL (e.g. to 2024.0) or reinstalling PyTorch via pip in the deepfoldrna environment to see if that helps.

Best,
Xi