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katzlabbrandeis / blech_clust

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Issues with xgboost #179

Closed Mraymon5 closed 4 months ago

Mraymon5 commented 4 months ago

Having trouble running bash blech_run_process.sh

Trying to take it in steps, and running into an issue with blech_process.py:

Traceback (most recent call last): File "blech_process.py", line 152, in classifier_handler.load_pipelines() File "/home/ramartin/blech_clust/utils/blech_process_utils.py", line 588, in load_pipelines self.pred_pipeline = load(self.pred_pipeline_path) File "/home/ramartin/anaconda3/envs/blech_clust/lib/python3.8/site-packages/joblib/numpy_pickle.py", line 587, in load obj = _unpickle(fobj, filename, mmap_mode) File "/home/ramartin/anaconda3/envs/blech_clust/lib/python3.8/site-packages/joblib/numpy_pickle.py", line 506, in _unpickle obj = unpickler.load() File "/home/ramartin/anaconda3/envs/blech_clust/lib/python3.8/pickle.py", line 1212, in load dispatchkey[0] File "/home/ramartin/anaconda3/envs/blech_clust/lib/python3.8/pickle.py", line 1528, in load_global klass = self.find_class(module, name) File "/home/ramartin/anaconda3/envs/blech_clust/lib/python3.8/pickle.py", line 1583, in find_class return getattr(sys.modules[module], name) AttributeError: module 'xgboost.compat' has no attribute 'XGBoostLabelEncoder'

It looks like maybe the people running XGBoost just totally nixed that whole function: https://github.com/dmlc/xgboost/issues/6209

I'll try to work through the problem and see if I can figure it out, but yeah, I think there's a compatibility issue with the newest version of xgboost.

abuzarmahmood commented 4 months ago

That's weird because we use a specific version of xgboost. Could you check that the version you have in your environment is the same version specificied in the requirements (1.5.0)? https://github.com/abuzarmahmood/neuRecommend/blob/master/requirements.txt

Mraymon5 commented 4 months ago

It is definitely not! Oops. I uninstalled and reinstalled it at some point to try and do... something (don't remember), so that's the issue. I'll re-run the compatibility stuff.

Mraymon5 commented 4 months ago

Yeah, reran the requirements downloads, and that fixed the xgboost issue.

abuzarmahmood commented 4 months ago

Glad to hear it :)