importing pytables (3.1.1) in python 3.4.1 fails for me, complaining about a failed cPickle import
i try to use potables (3.1.1) with python (3.4.1)
In [1]: import tables
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-389ecae14f10> in <module>()
----> 1 import tables
/work/projects/vEnv/lib/python3.4/site-packages/tables/__init__.py in <module>()
80
81 # Necessary imports to get versions stored on the cython extension
---> 82 from tables.utilsextension import (
83 get_pytables_version, get_hdf5_version, blosc_compressor_list,
84 blosc_compcode_to_compname_ as blosc_compcode_to_compname,
/work/projects/vEnv/lib/python3.4/site-packages/tables/utilsextension.pyx in init tables.utilsextension (tables/utilsextension.c:15600)()
/work/projects/vEnv/lib/python3.4/site-packages/tables/description.py in <module>()
22 import numpy
23
---> 24 from tables import atom
25 from tables.path import check_name_validity
26
/work/projects/vEnv/lib/python3.4/site-packages/tables/atom.py in <module>()
18 import sys
19 import inspect
---> 20 import cPickle
21
22 import numpy
As i understand cPickle is only used instead of pickle in python2.
As of PyTable 3.x it should work fine with python3.x. How can there be a cPickle import than?
What do i have to do to use pytables with python3?
The error was produced most likely due to a problem with my vEnv. Uninstalling the package and reinstalling it fix the problem.
See github issue
Related
When trying to load BERT QA I get the following ImportError:
"Cannot import name 'network' from 'tensorflow.python.keras.engine'"
The full error log follows below
Following this post,
ImportError: cannot import name 'network' from 'tensorflow.python.keras.engine'
I have tried the following steps,
pip uninstall tf-agents
pip install tf-agents-nightly
and then in Python,
from tf_agents.environments import suite_gym
However, this did not resolve the problem. Any suggestions would be very welcome!
In case it is helpful, I'm running TensorFlow version 2.3.0. Also, the script init.py referred to below does exist, however the file is empty, i.e. 0 bytes.
ImportError Traceback (most recent call last)
<ipython-input-2-323bac0cb5ba> in <module>
----> 1 from bert_qa import squad
~/anaconda3/lib/python3.8/site-packages/bert_qa/squad.py in <module>
34 from . import model_training_utils
35 from . import bert_modeling as modeling
---> 36 from . import bert_models
37 from . import optimization
38 from . import input_pipeline
~/anaconda3/lib/python3.8/site-packages/bert_qa/bert_models.py in <module>
25 from . import bert_modeling
26 from . import weighted_sparse_categorical_crossentropy
---> 27 from . transformer_encoder import TransformerEncoder
28 from . albert_transformer_encoder import AlbertTransformerEncoder
29 from . import bert_classifier
~/anaconda3/lib/python3.8/site-packages/bert_qa/transformer_encoder.py in <module>
22 import tensorflow as tf
23
---> 24 from tensorflow.python.keras.engine import network # pylint: disable=g-direct-tensorflow-import
25
26 from . import activations
ImportError: cannot import name 'network' from 'tensorflow.python.keras.engine' (/home/user810643/anaconda3/lib/python3.8/site-packages/tensorflow/python/keras/engine/__init__.py)
Install tf-agents 0.6.0 version for Tebsorflow 2.3.
pip install tf-agents==0.6.0
Looks like the issue was caused due to TF-Agents and Tensorflow version incompatibility. For more information, please take a look at this release notes. Thanks!
I'm trying to import sklearn model_selection but I'm getting the following error:
ImportError Traceback (most recent call last)
<ipython-input-219-6bc6f0a77ca9> in <module>()
----> 1 import sklearn.model_selection
~/anaconda3/lib/python3.6/site-packages/sklearn/model_selection/__init__.py in <module>()
----> 1 from ._split import BaseCrossValidator
2 from ._split import KFold
3 from ._split import GroupKFold
4 from ._split import StratifiedKFold
5 from ._split import TimeSeriesSplit
~/anaconda3/lib/python3.6/site-packages/sklearn/model_selection/_split.py in <module>()
21
22 from ..utils import indexable, check_random_state, safe_indexing
---> 23 from ..utils import _approximate_mode
24 from ..utils.validation import _num_samples, column_or_1d
25 from ..utils.validation import check_array
ImportError: cannot import name '_approximate_mode'
I tried uninstalling scikit-learn and reinstalling it but I get the same error. My current version of scikit-learn is 0.21.2.
Thanks for the help!
I shutdown the kernel and restarted it again. Now it's working fine! Thanks!!
You are using python notebook. I found that error once when I have installed the package before importing. I have tested this at Google AI notebook and worked well.
Save the notebook -> shutdown the kernel -> close and open the notebook again.
You can restart the kernel or use the importlib library
from importlib import reload
sklearn= reload(sklearn)
ModuleNotFoundError Traceback (most recent call last)
~\AppData\Roaming\Python\Python36\site-packages\sklearn\__check_build\__init__.py in <module>()
43 try:
---> 44 from ._check_build import check_build # noqa
45 except ImportError as e:
ModuleNotFoundError: No module named
'sklearn.__check_build._check_build'
During handling of the above exception, another exception occurred:
ImportError Traceback (most recent call last)
<ipython-input-1-f14d678f34eb> in <module>()
1 from keras.models import Sequential
2 from keras.layers import Dense, Dropout
----> 3 from sklearn.model_selection import train_test_split
4 import numpy
5 import pandas as pd
~\AppData\Roaming\Python\Python36\site-packages\sklearn\__init__.py in <module>()
61 # process, as it may not be compiled yet
62 else:
---> 63 from . import __check_build
64 from .base import clone
65 from .utils._show_versions import show_versions
~\AppData\Roaming\Python\Python36\site-packages\sklearn\__check_build\__init__.py in <module>()
44 from ._check_build import check_build # noqa
45 except ImportError as e:
---> 46 raise_build_error(e)
~\AppData\Roaming\Python\Python36\site-packages\sklearn\__check_build\__init__.py in raise_build_error(e)
39 to build the package before using it: run `python setup.py install` or
40 `make` in the source directory.
---> 41 %s""" % (e, local_dir, ''.join(dir_content).strip(), msg))
42
43 try:
ImportError: No module named 'sklearn.__check_build._check_build'
Contents of C:\Users\owaisaaa\AppData\Roaming\Python\Python36\site-packages\sklearn\__check_build:
setup.py _check_build.cp36-win32.pyd__init__.py
__pycache__
It seems that scikit-learn has not been built correctly.
If you have installed scikit-learn from source, please do not forget
to build the package before using it: run python setup.py install or
make in the source directory.
If you have used an installer, please check that it is suited for your
Python version, your operating system and your platform.
I recently used the pycharm on the same machine and downloaded the packages in it. From that moment onward I am getting the above mentioned error in my jupyter notebook.
Try installing scipy and restarting python shell
Upgrading scikit-learn worked for me:
$ pip install --upgrade scikit-learn
I have just installed gdal into my Python3 root environment using conda:
conda install -c conda-forge gdal
Installation went fine with the usual updates of some dependencies. Now returning to some of my scripts, both netCDF4 and mpl_toolkits.basemap have stopped working. These are the errors I get:
from netCDF4 import Dataset
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-7-09694a7f0e01> in <module>()
----> 1 from netCDF4 import Dataset
2 import numpy as np
3 import matplotlib.pyplot as plt
4 from scipy.interpolate import griddata
5 from mpl_toolkits.basemap import Basemap
/anaconda3/lib/python3.6/site-packages/netCDF4/__init__.py in <module>()
1 # init for netCDF4. package
2 # Docstring comes from extension module _netCDF4.
----> 3 from ._netCDF4 import *
4 # Need explicit imports for names beginning with underscores
5 from ._netCDF4 import __doc__, __pdoc__
ImportError: dlopen(/anaconda3/lib/python3.6/site-packages/netCDF4/_netCDF4.cpython-36m-darwin.so, 2): Library not loaded: #rpath/libhdf5.101.dylib
Referenced from: /anaconda3/lib/python3.6/site-packages/netCDF4/_netCDF4.cpython-36m-darwin.so
Reason: image not found
from mpl_toolkits.basemap import Basemap
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-8-5fb601138328> in <module>()
3 import matplotlib.pyplot as plt
4 from scipy.interpolate import griddata
----> 5 from mpl_toolkits.basemap import Basemap
6 import numpy.ma as ma
7 import glob
/anaconda3/lib/python3.6/site-packages/mpl_toolkits/basemap/__init__.py in <module>()
35 import numpy as np
36 import numpy.ma as ma
---> 37 import _geoslib
38 import functools
39
ImportError: dlopen(/anaconda3/lib/python3.6/site-packages/_geoslib.so, 2): Library not loaded: #rpath/libgeos-3.5.0.dylib
Referenced from: /anaconda3/lib/python3.6/site-packages/_geoslib.so
Reason: image not found
I have no idea what these errors mean, since those paths do exist. What is most baffling is that the netCDF4 and mpl_toolkits modules did not change (i.e. were not updated/downgraded) with the installation of gdal, so why now are they failing?
I'm at the end of my tether with problems like this. Fortunately I made a copy of my Python root directory before attempting this installation so I can now revert back to it (I've been here many times before).
I know about working in separate conda environments, but am I seriously supposed to install a new environment every time I want to use a new Python module? This not only takes up a lot of harddrive space but most inconveniently means adding new functionality to old codes is impossible (I want to use GDAL to plot some geotiffs using Basemap, which now does not work!).
I cannot imagine proficient Python users battling with these issues - so what am I doing wrong?
I am very new to installing my own programs and packages on linux, so please be gentle ;)
I am working on Linux Mint 17.3 (Rosa) 64 bit (Ubuntu Trusty) and am trying to run through the scikitlearn tutorials located here:
https://github.com/savarin/pyconuk-introtutorial
I have installed all the relevant packages using:
pip install numpy pandas sklearn ipython
and everything looks great until I start trying to import some things from related packages i.e.
from scipy.stats import mode
I see the following error code:
sam#samputer ~/Desktop $ ipython
In [1]: from scipy.stats import mode
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-a8b1ace850b6> in <module>()
----> 1 from scipy.stats import mode
/home/sam/anaconda2/lib/python2.7/site-packages/scipy/stats/__init__.py in <module>()
336 from __future__ import division, print_function, absolute_import
337
--> 338 from .stats import *
339 from .distributions import *
340 from .morestats import *
/home/sam/anaconda2/lib/python2.7/site-packages/scipy/stats/stats.py in <module>()
178 from scipy._lib.six import callable, string_types
179 from numpy import array, asarray, ma, zeros
--> 180 import scipy.special as special
181 import scipy.linalg as linalg
182 import numpy as np
/home/sam/anaconda2/lib/python2.7/site-packages/scipy/special/__init__.py in <module>()
625 from __future__ import division, print_function, absolute_import
626
--> 627 from ._ufuncs import *
628
629 from .basic import *
ImportError: libgfortran.so.1: cannot open shared object file: No such file or directory
I'm also running into issues when I try to link through to R for visualisation. I add this as it may shed further light on the issue:
In [11]: %%R
....: library(ggplot2)
....:
/home/sam/anaconda2/lib/python2.7/site-packages/rpy2/robjects /functions.py:106: UserWarning: Error in library(ggplot2) : there is no package called ‘ggplot2’
res = super(Function, self).__call__(*new_args, **new_kwargs)
Error in library(ggplot2) : there is no package called ‘ggplot2’
If anyone can help me understand these issues and offer me some lines/links to fix them, I would be extremely grateful, as my googling hasn't made much progress.
Cheers!
If you're using Anaconda you should try installing packges with conda install first rather than pip install if you can — actually all of the the packages you installed come with the standard Anaconda distribution, so I would try reinstalling this first (did you install miniconda?)
For your second question I'm guessing you'll need to install ggplot in R, I think you do this by running install.packages("ggplot2") in R.