Python Troubleshooting [21-40]
Higher category : 【Python】 Python Table of Contents
21. rpy2.rinterface_lib.embedded.RRuntimeError: Error in library(ggplot2) : there is no package called ‘ggplot2’
⑴ (package) Solution: Connect to R and then install.packages('ggplot2')
22. ERROR: pip’s dependency resolver does not currently take into account all the packages that are installed. This behavior is the source of the following dependency conflicts. stlearn 0.4.5 requires scikit-image>=0.19.2, but you have scikit-image 0.18.3 which is incompatible.
⑴ (package) Issue: Occurs when executing pip install stlearn==0.4.5
⑵ (package) Solution : pip install stlearn==0.4.5 --no-deps
⑶ Reference: https://stackoverflow.com/questions/12759761/pip-force-install-ignoring-dependencies/12759996#12759996
23. ImportError: cannot import name ‘_tsne_fix’ from ‘scanpy.tools’
⑴ (package) Solution: Downgrade scanpy==1.9.1 to scanpy==1.7.2
24. ValueError: m has more than 2 dimensions
⑴ (grammar) Issue: Occurs when using numpy.corrcoef and the elements in the input vector arguments are np.ndarray
⑵ (grammar) Solution: Convert all elements in the input vector arguments to scalars. Use ~.item()
25. TypeError: Descriptors cannot not be created directly. If this call came from a _pb2.py file, your generated code is out of date and must be regenerated with protoc >= 3.19.0. If you cannot immediately regenerate your protos, some other possible workarounds are: 1. Downgrade the protobuf package to 3.20.x or lower. 2. Set PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python (but this will use pure-Python parsing and will be much slower).
⑴ (package) Solution: Downgrade protobuf==3.19.1, then turn off and on anaconda before running again
⑵ Additional information: https://developers.google.com/protocol-buffers/docs/news/2022-05-06#python-updates%EF%BB%BF
26. TypeError: only length-1 arrays can be converted to Python scalars
⑴ (grammar) Issue: Function expects a specific value but an array is passed as an argument
⑵ (grammar) Solution: Use the function for each element in the array
⑶ Solution example
for i in range(len(top)):
top[i] = -math.log10(top[i])
27. UnicodeDecodeError: ‘cp949’ codec can’t decode bytes in position : illegal multibyte sequence
⑴ (grammar) Issue : f = open("example.txt", 'r')
⑵ Cause: Starting from Python 3, only files encoded in ANSI can be read without specifying a separate encoding method for UTF-8
⑶ (grammar) Solution : f = open("example.txt", 'r', encoding = 'utf-8')
28. TypeError: can only concatenate str (not “int”) to str
⑴ (grammar) Issue: Trying to concatenate an int variable to a str variable
⑵ Issue example : a = 3; print('a = ' + a)
⑶ (grammar) Solution: Convert the int variable to str using the str() function
⑷ Solution example : a = 3; print('a = ' + str(a))
29. _csv.Error: field larger than field limit (131072)
⑴ (grammar) Solution
import sys
import csv
csv.field_size_limit(sys.maxsize)
⑵ Reference: https://stackoverflow.com/questions/15063936/csv-error-field-larger-than-field-limit-131072
30. AttributeError: type object ‘scipy.spatial.transform.rotation.Rotation’ has no attribute ‘from_dcm’
⑴ (package) Solution: Downgrade to scipy==1.5.2
⑵ Reference: https://github.com/benjiebob/SMALify/issues/22
31. ERROR: Could not install packages due to an OSError: [WinError 225] Operation did not complete successfully because the file contains a virus or potentially unwanted software … ERROR: Could not install packages due to an OSError: [WinError 225] Operation did not complete successfully because the file contains a virus or potentially unwanted software
⑴ (others) Cause: Package installation is blocked by security software
⑵ (others) Solution 1: Disable the problematic security program as shown in this link
⑶ (others) Solution 2: Download the package on a different computer and transfer it directly to the computer where the package installation fails
32. error: OpenCV(4.6.0) D:\a\opencv-python\opencv-python\opencv\modules\imgproc\src\color.cpp:182: error: (-215:Assertion failed) !_src.empty() in function ‘cv::cvtColor’
⑴ (grammar) Issue: Incorrectly entered directory, failing to properly input the image with cv2.imread
33. ERROR: Could not find a version that satisfies the requirement git (from versions: none). ERROR: No matching distribution found for git
⑴ (package) Issue: git is not installed
⑵ (package) Solution: conda install git
conda install git
34. AttributeError: ‘dict’ object has no attribute ‘iteritems’, ‘iterkeys’ or ‘itervalues’
⑴ (grammar) Issue: Starting from Python3, .iteritems(), .iterkeys(), and .itervalues() functions have been removed, causing this error
⑵ (grammar) Solution: Use the .items() function instead
35. The current PyTorch install supports CUDA capabilities sm_37 sm_50 sm_60 sm_70. If you want to use the NVIDIA GeForce RTX 3090 GPU with PyTorch, please check the instruction.
⑴ (package) Issue: Currently, RTX 3090 requires CUDA 11 or higher
⑵ (package) Solution: pip install torch==1.7.1+cu110 torchvision==0.8.2+cu110 -f https://download.pytorch.org/whl/torch_stable.html
pip install torch==1.7.1+cu110 torchvision==0.8.2+cu110 -f https://download.pytorch.org/whl/torch_stable.html
36. ImportError: DLL load failed while importing utilsextension: The specified module could not be found.
⑴ (package) Issue: There is an issue with the pytables section connected to scanpy in Python 3.8
⑵ (package) Solution
conda install -c conda-forge pytables
37. AttributeError: module ‘tensorflow.keras.layers’ has no attribute ‘RandomContrast’
⑴ (grammar) Issue: tensorflow version 2.11.0 uses tf.keras.layers.RandomContrast, while tensorflow version 2.4 uses tf.keras.layers.experimental.preprocessing.RandomContrast
38. NotImplementedError: Cannot convert a symbolic Tensor
⑴ (package) Solution: Downgrade to numpy==1.19.5
39. ModuleNotFoundError: No module named ‘pydatset’
⑴ (grammar) Issue: Error occurs when executing the following code:
from pydatset.cifar10 import get_CIFAR10_data
⑵ (grammar) Solution: Instead, directly run the following code (source)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import cPickle as pickle
import numpy as np
import os
def get_CIFAR10_data(cifar10_dir, num_training=49000, num_validation=1000, num_test=1000):
'''
Load the CIFAR-10 dataset from disk and perform preprocessing to prepare
it for the neural net classifier.
'''
# Load the raw CIFAR-10 data
X_train, y_train, X_test, y_test = load(cifar10_dir)
# Subsample the data
mask = range(num_training, num_training + num_validation)
X_val = X_train[mask]
y_val = y_train[mask]
mask = range(num_training)
X_train = X_train[mask]
y_train = y_train[mask]
mask = range(num_test)
X_test = X_test[mask]
y_test = y_test[mask]
X_train = X_train.astype(np.float64)
X_val = X_val.astype(np.float64)
X_test = X_test.astype(np.float64)
# Transpose so that channels come first
X_train = X_train.transpose(0, 3, 1, 2)
X_val = X_val.transpose(0, 3, 1, 2)
X_test = X_test.transpose(0, 3, 1, 2)
mean_image = np.mean(X_train, axis=0)
std = np.std(X_train)
X_train -= mean_image
X_val -= mean_image
X_test -= mean_image
X_train /= std
X_val /= std
X_test /= std
return {
'X_train': X_train, 'y_train': y_train,
'X_val': X_val, 'y_val': y_val,
'X_test': X_test, 'y_test': y_test,
'mean': mean_image, 'std': std
}
def load_CIFAR_batch(filename):
''' load single batch of cifar '''
with open(filename, 'r') as f:
datadict = pickle.load(f)
X = datadict['data']
Y = datadict['labels']
X = X.reshape(10000, 3, 32, 32).transpose(0, 2, 3, 1).astype("float")
Y = np.array(Y)
return X, Y
def load(ROOT):
''' load all of cifar '''
xs = []
ys = []
for b in range(1, 6):
f = os.path.join(ROOT, 'data_batch_%d' % (b, ))
X, Y = load_CIFAR_batch(f)
xs.append(X)
ys.append(Y)
Xtr = np.concatenate(xs)
Ytr = np.concatenate(ys)
del X, Y
Xte, Yte = load_CIFAR_batch(os.path.join(ROOT, 'test_batch'))
return Xtr, Ytr, Xte, Yte
40. ModuleNotFoundError: No module named ‘cPickle’
⑴ (grammar) Issue: In Python 3, it has been changed to ‘pickle’
⑵ (grammar) Solution
pip install pickle
Input : 2022-05-09 22:23