I just tried to use pd.HDFStore in IPython Notebook with a Python 3 kernel (Anaconda 2&3 on Ubuntu 14.04)
import pandas as pd
store = pd.HDFStore('/home/Jian/Downloads/test.h5')
but it throws the following error
ImportError: HDFStore requires PyTables, "libhdf5.so.9: cannot open shared object file: No such file or directory" problem importing
I initially thought it's because pytables is somehow missing, but when I check $source activate py34 and $conda list, pytables 3.2.0 is already installed under anaconda python3 environment.
Also, if I switch to Python 2, for example, $source activate py27 and start ipython notebook, it works properly and no import error is thrown.
I guess that I must miss something for configuring pytables under anaconda python 3 env, but I cannot figure it out. Any help is highly appreciated.
Update:
I just tried on a fresh install of Anaconda3-2.3.0-Linux-x86_64 from official website and it ends up with the same error. When I try $locate libhdf5.so.9 in command line, nothing shows up.
This is a known issue that we are working on. When it is fixed, conda update --all will update the libraries and fix the issue.
Related
I was able to install xgboost on my mac and have it so that I can import the module without any errors. However I cannot use it. When I try to import XGBRegressor. I get the following error :
cannot import name 'XGBRegressor' from 'xgboost' (unknown location).
Some of the support for this type of problem says that there may be more than one xgboost location, and that python is selecting the incorrect xgboost, however I have not been able to find how to fix this problem.
When I print the xgboost.__file__ location, it returns 'None'. However I know its in the site-packages folder in my python path.
I have python 3.9
Maybe this.
conda install -c conda-forge xgboost=0.6a2
Then, restart Spyder and re-run!
So basically I am using PyCharm with Anaconda env Python 3.6. I tried reinstalling everything, folder with my projects env contains the whole package for opencv, in Anaconda Navigator also and PyCharm recognises cv2 when I import (code) yet when i start my main.py it says that there is no cv2 module.
Anyone any ideas why the error occurs?
I suppose the first thing you should check is if your conda environment is configured to your project when you're using PyCharm. Have a look at this: https://docs.anaconda.com/anaconda/user-guide/tasks/pycharm/#:~:text=Configuring%20a%20conda%20environment%20in%20PyCharm,-In%20the%20Settings&text=Select%20Preferences.,dialog%20box%2C%20select%20Conda%20Environment.
I am trying to do the following in Python 3.7.1 on Windows
import sqlite3
but I get the following error message
Traceback (most recent call last):
File "<console>", line 1, in <module>
File "c:\programdata\anaconda3\lib\sqlite3\__init__.py", line 23, in <module>
from sqlite3.dbapi2 import *
File "c:\programdata\anaconda3\lib\sqlite3\dbapi2.py", line 27, in <module>
from _sqlite3 import *
ImportError: DLL load failed: The specified module could not be found.
I have searched for a solution to the problem for quite a while now to no avail. I have also successfully run pip install pysqlite3 on the Anaconda prompt, but the import still fails. What do?
I got this working on windows by downloading: the sqlite3 dll (find your system version)
And placing it into the folder: C:\Users\YOURUSER\Anaconda3\DLLs
(Depending on how you installed Anaconda, this may have to be placed into
the following folder: C:\ProgramData\Anaconda3\DLLs)
According to #alireza-taghdisian, you can locate the exact path of
your conda environments (where you need to copy the sqlite3 dll) by typing:
conda info --envs on your anaconda prompt.
Locate the sqlite3.dll file. In my case it was in following folder
C:\Users\Admin\anaconda3\Library\bin
where C:\Users\Admin\anaconda3 is the folder where Anaconda was installed
Add this to PATH in environment variables, and it should work then.
Try copying the sqlite3.dll from the
C:\Users\YOURUSER\anaconda3\Library\bin
folder to
C:\Users\YOURUSER\Anaconda3\DLLs
Please check https://github.com/jupyter/notebook/issues/4332
I added anaconda root/Library/bin to my PATH and now it works!
Add CONDA_DLL_SEARCH_MODIFICATION_ENABLE=1 to your environment variables.
before executing the program, enter conda activate in your shell.
I had tried all above solutions But for me and my system I got to know that
I downloaded Python in C:\Python27 hence there is dll folder in python C:\Python27\DLLs
I installed Sqlite3.dll in my above dll folder
May be this solution will help you because it completely depends on where do you install your python
Happy coding :)
I put the sqlite3.dll in the path folder of my Python venv and still wont work. I suspected it is a path problem.
(In my case: E:\Virtual_Env\mini_zinc\env\Scripts)
I found in my case I messed up installation in a virtual evn, somehow using an anaconda python kernel within a Python venv.
I reinstall the Python Venv and check the python version after installed Env is correct (not the Anaconda python), then proceed with Jupyter Notebook (or Juyterlab) and works fine.
I was able to resolve this issue by putting sqlite3.dll file in the C:\Users<USERID>\AppData\Local\conda\conda\envs<ENV NAME>\DLLs.
Download sqlite3.dll file from https://www.sqlite.org/download.html
or copy it from C:\ProgramData\Anaconda3\DLLs\
I found the #elgsantos useful. But for those who are new to Python and Conda like me, I would like to add a little bit of details.
1- I use miniconda3 for creating new environment.
2- interestingly, I got two installation path on my computer for conda: the first one (the obvious) is located on "C:\Users\taghdisian\miniconda3". The second one is on "C:\Users\taghdisian\AppData\Local\r-miniconda". The latter is the primary path that you need to copy your sqlite3 files into the envs folder. I copy them in the "C:\Users\taghdisian\AppData\Local\r-miniconda\envs\sdr3.9\DLLs" in which the sdr3.9 is one of my virtual Condo environment.
you can locate the exact path of your conda environments (where you need to copy sqlite3) by typing the conda info --envs on your anaconda prompt.
I hope this help.
got the same error while loading the jupyter notebook from other conda prompt than "base" environment.
[1]: https://i.stack.imgur.com/2DW7E.png
Resolved by installing sqlite package
(nlpenv) C:\Users\arunk>conda install sqlite
launching
*
(nlpenv) C:\Users\arunk>jupyter notebook
After installing miniconda with python 3.7 I do the following:
conda create --name opencv_test python=3.7
conda activate opencv_test
conda install -c anaconda opencv
Then to test the environement I do:
python
>>> import cv2
>>> exit()
Everything goes according to plan
Then if I launch PyCharm or vs code, set my new environment as the interpreter and create a simple file that contains only
import cv2
On launch I get:
ImportError: DLL load failed: The specified module could not be found.
What I learned from the internets:
This, this and this, all those posts refer to a problem that seems similar, the difference being that the issue for me only happens when using IDEs
What I tried before posting here:
Recreating the environment multiple times switching channels.
As it seemed to be a path issue, I added the paths which contained opencv dll to the environment paths in PyCharm settings one at a time
What I just tried after spending a considerable amount of time creating this post:
conda update conda
This weirdly downgrades python to 3.6
conda create --name opencv_test_2 python=3.6
conda activate opencv_test_2
conda install -c anaconda opencv
This seems to fix all the issues but:
I don't know what just happened and why the issue only appeared on IDEs
I'd like to use python 3.7
So in short, why when using python 3.7 and PyCharm I seem to be unable to import opencv even if it works on command line?
Thanks in advance.
Happy October everyone,
I've successfully downloaded modules before using either the pycharm installer or pip through the command screen, but for some reason when installing matplotlib pycharm cannot recognize it. I've uninstalled and reinstalled, I've installed through both methods, I've followed past similar questions asked on this site which make sure that you have the same interpreter and that it was installed in the right folder (pycharm error while importing, even though it works in the terminal).
So, here's the whole problem. Here's is the simple code, submitted into both pycharm and IDLE:
import matplotlib.pyplot as plt
plt.plot([1,2,3],[2,1,3])
plt.show()
When submitted into IDLE, my plot appears. When submitted into pycharm, the following error appears:
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:/PythonProject/matplotlib.py", line 1, in <module>
import matplotlib.pyplot as plt
File "C:\PythonProject\matplotlib.py", line 1, in <module>
import matplotlib.pyplot as plt
ImportError: No module named 'matplotlib.pyplot'; 'matplotlib' is not a package
I am currently running Python 3.4, PyCharm 2016.2.3, and my matplotlib folders are indeed in my site-packages folder inside my Python34 folder. Also for further verification:
PyCharm installation
Please help I've become frustrated since this is the only module I've run into trouble with. I've scoured StackOverflow and related websites to help, I've made sure I have all the requirements, etc.
I guess if you named your current writing python module as matplotlib.py.That cause the python load your current writing module instead of the actual matplotlib.py, which triggers an error.
I recommend you to use virtualenv. Is not strictly necessary but is good for dividing your project environments.
This is how I tested matplotlib on my Windows 10 installation, hope it helps.
Be sure that you have the python 3 installation folder listed in your Windows PATH environment variable, should be already listed if you checked "Add Python 3.5 to PATH":
You need also to set the Scripts folder in your PATH environment variable usually should be this path:
C:\Users\<your username>\AppData\Local\Programs\Python\Python35\Scripts
If you don't do that you have to prepend python -m to every command below like this: python -m <command>, so the command below would be python -m pip install virtualenv. I prefer the first solution.
To test matplotlib on Pycharm I've used virtualenv, here is how; first install virtualenv:
pip install virtualenv
Then you create your virtual environment in a folder of your choice, in my case I used python_3_env_00:
virtualenv python_3_env_00
After that you can activate you python 3 virtual environment:
python_3_env_00/Scripts/activate.bat
Now you should see in your command line the active virtual environment (python_3_venv_00), like this:
Now you can install matplotlib:
pip install matplotlib
Fire up PyCharm and add your virtual environment as you project interpreter, go to File->Settings search for Project Interpreter click on the gear icon and Add Local and set the path of your virtual environment, should look like something like this:
Test it:
import sys
print(sys.path)
run this code in where the import worked, and run it in the Pycharm project. Compare the lists. Find out which path that is not present in Pycharm sys.path.
Before importing pyplot, append the missing path to sys.path.
import sys
sys.path.append("the path")
import matplotlib.pyplot as plt
Does this work?
Please follow below steps if you are still getting an error:
If you are using PyCharm, it automatically create virtualenv.
Ensure Scripts path is set into PATH
C:\Users\<Username>\AppData\Local\Programs\Python\Python37-32
Then open PyCharm and go to File-> settings. Search for Project Interpreter. You will see window like this
sample image
Click on setting icon -> Existing Environment -> click on ... give below path
C:\Users\Krunal\AppData\Local\Programs\Python\Python37-32\python.exe
Click on Apply -> ok and you are good to go.
After installing matplotlib When I was trying to use matplotlib.pyplot it was giving error module not found.
I browsed some white papers and found out that we also need to install scipy library to use the matplotlib so I used the below in my command prompt
python -mpip install scipy
Restarted my kernel session.
It worked!!!
I was also facing issue while importing matplotlib but it got resolved and now I am able to use it from pycharm as well.
Please make sure you should have visual c++ 14 installed in your system.
2.If you have more than two python version installed on your system then please install matplotlib from both the version.
Eg. pip install matplotlib
pip3 install matplotlib
If matplotlib is working from python idle then please check whether you are using correct interpreter in pycharm or not and try to choose pythonw.exe path from your installed location.
Hope this will help, Please do let me know if you are still facing issue.
I had similar issue but I solved it very easily on pycharm 2019.3.2. In case anyone looking for an easier solution:
I just opened the terminal window on pycharm and typed pip install matplotlib and it was all good to go. Every project has its own virtual environment. Opening terminal window of IDE cds to project directory by default. So the installing command was enough.