search

GreatChenLab / Deep-B3

A multi-model framework for blood-brain barrier permeability discovery
14 stars 3 forks source link

i have configed the environment, but the model can't be trained, i don't know why, #2

Open songyu2022 opened 1 year ago

songyu2022 commented 1 year ago

python train.py train --feature train_feature.csv --epoch 50 --bs 64 Traceback (most recent call last): File "train.py", line 3, in from fastai.text import File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/fastai/text/init.py", line 3, in from .learner import File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/fastai/text/learner.py", line 11, in from .models import File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/fastai/text/models/init.py", line 1, in from .awd_lstm import File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/fastai/text/models/awd_lstm.py", line 6, in from ..data import TextClasDataBunch File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/fastai/text/data.py", line 3, in from .transform import * File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/fastai/text/transform.py", line 4, in import spacy File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/init.py", line 14, in from . import pipeline # noqa: F401 File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/pipeline/init.py", line 1, in from .attributeruler import AttributeRuler File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/pipeline/attributeruler.py", line 6, in from .pipe import Pipe File "spacy/pipeline/pipe.pyx", line 8, in init spacy.pipeline.pipe File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/training/init.py", line 11, in from .callbacks import create_copy_from_base_model # noqa: F401 File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/training/callbacks.py", line 3, in from ..language import Language File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/language.py", line 25, in from .training.initialize import init_vocab, init_tok2vec File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/training/initialize.py", line 14, in from .pretrain import get_tok2vec_ref File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/training/pretrain.py", line 16, in from ..schemas import ConfigSchemaPretrain File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/schemas.py", line 216, in class TokenPattern(BaseModel): File "pydantic/main.py", line 299, in pydantic.main.ModelMetaclass.new File "pydantic/fields.py", line 411, in pydantic.fields.ModelField.infer File "pydantic/fields.py", line 342, in pydantic.fields.ModelField.init File "pydantic/fields.py", line 451, in pydantic.fields.ModelField.prepare File "pydantic/fields.py", line 545, in pydantic.fields.ModelField._type_analysis File "pydantic/fields.py", line 550, in pydantic.fields.ModelField._type_analysis File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/typing.py", line 774, in subclasscheck return issubclass(cls, self.origin) TypeError: issubclass() arg 1 must be a class

songyu2022 commented 1 year ago

import fastai,torch,torchvision,pandas,numpy,rdkit print(fastai.version,torch.version,torchvision.version) 1.0.61 1.9.0 0.10.0a0 print(pandas.version,numpy.version,rdkit.version) 1.4.2 1.22.3 2020.09.1 these are version of my softwares

BioTKang commented 1 year ago

python train.py train --feature train_feature.csv --epoch 50 --bs 64 Traceback (most recent call last): File "train.py", line 3, in from fastai.text import File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/fastai/text/init.py", line 3, in from .learner import File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/fastai/text/learner.py", line 11, in from .models import File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/fastai/text/models/init.py", line 1, in from .awd_lstm import File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/fastai/text/models/awd_lstm.py", line 6, in from ..data import TextClasDataBunch File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/fastai/text/data.py", line 3, in from .transform import * File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/fastai/text/transform.py", line 4, in import spacy File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/init.py", line 14, in from . import pipeline # noqa: F401 File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/pipeline/init.py", line 1, in from .attributeruler import AttributeRuler File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/pipeline/attributeruler.py", line 6, in from .pipe import Pipe File "spacy/pipeline/pipe.pyx", line 8, in init spacy.pipeline.pipe File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/training/init.py", line 11, in from .callbacks import create_copy_from_base_model # noqa: F401 File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/training/callbacks.py", line 3, in from ..language import Language File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/language.py", line 25, in from .training.initialize import init_vocab, init_tok2vec File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/training/initialize.py", line 14, in from .pretrain import get_tok2vec_ref File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/training/pretrain.py", line 16, in from ..schemas import ConfigSchemaPretrain File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/site-packages/spacy/schemas.py", line 216, in class TokenPattern(BaseModel): File "pydantic/main.py", line 299, in pydantic.main.ModelMetaclass.new File "pydantic/fields.py", line 411, in pydantic.fields.ModelField.infer File "pydantic/fields.py", line 342, in pydantic.fields.ModelField.init File "pydantic/fields.py", line 451, in pydantic.fields.ModelField.prepare File "pydantic/fields.py", line 545, in pydantic.fields.ModelField._type_analysis File "pydantic/fields.py", line 550, in pydantic.fields.ModelField._type_analysis File "/data/songyu/softwareInstall/Anaconda3/envs/Deep-B3/lib/python3.8/typing.py", line 774, in subclasscheck return issubclass(cls, self.origin) TypeError: issubclass() arg 1 must be a class

It looks like there's a conflict between the version of pydantic and spacy.

songyu2022 commented 1 year ago

i installed them by default, so what're the right version about two packages?