`runDLKcat()`: _pickle.UnpicklingError: invalid load key, 'v'.

edkerk commented 1 month ago

Description of the bug:

When running runDLKcat(); the following error is thrown:~

Traceback (most recent call last):
  File "//DLKcat.py", line 26, in <module>
    fingerprint_dict = load_pickle('input/fingerprint_dict.pickle')
  File "//DLKcat.py", line 24, in load_pickle
    return pickle.load(f)
_pickle.UnpicklingError: invalid load key, 'v'.

Reproducing these results:

Probably only occurs if GECKO is cloned as git repository, not when downloaded as zip or installed as MATLAB Add-On.

However, the problem is not reproducible.

Solution:

~The error suggests that something is wrong with the file, but the underlying problem might be git lfs.~

~What solved this for me was to:~ ~1. Delete the src/dlkcat_gecko/input/fingerprint_dict.pickle file.~ ~2. Run git restore . (or actually, I did "Discard changes ..." in my git GUI client), to bring back the file.~ ~3. There was no need to (re)install git lfs or re-clone the repository.~

System information

Operating system: Windows 10
MATLAB version: 2024a (probably irrelevant)
GECKO version: 3.2.2
RAVEN version: 2.10.1 (probably irrelevant)

I hereby confirm that:

[x] My GECKO installation met all requirements.
[x] This bug occurs in the main branch of the repository.
[x] A similar issue does not already exist.

edkerk commented 1 month ago

Probably related to #393, will include there.

mihai-sysbio commented 3 weeks ago

Hmm @edkerk are we leaving the ARM64 issue open then - or is this issue more general, applicable to all new Docker images?

edit: I'm wondering if it could have something to do with the new packages that are used in obtaining the new image.

edkerk commented 3 weeks ago

The ARM64 issue should remain open.

The problem described here is a consequence of the 0.1-multiarch container, so it makes sense to keep the discussion of this in #393.
The solution I initially thought I had found, as mentioned in the first post of this Issue, did not work. So IMHO this Issues should remain closed and inactive.

SysBioChalmers / GECKO