I am trying to import library COVSIRPHY to jupyter notebook following two steps:
pip install --upgrade covsirphy (I installed it using terminal in specific environment created in anaconda navigator)
It was installed successfully
import covsirphy as cs
I typed in directly in jupyter notebook, but it occured an error:
OSError: dlopen(/opt/anaconda3/envs/test/lib/python3.9/site-packages/lightgbm/lib_lightgbm.so, 0x0006): Library not loaded: /usr/local/opt/libomp/lib/libomp.dylib
Referenced from: /opt/anaconda3/envs/test/lib/python3.9/site-packages/lightgbm/lib_lightgbm.so
Reason: tried: '/usr/local/opt/libomp/lib/libomp.dylib' (no such file), '/usr/local/lib/libomp.dylib' (no such file), '/usr/lib/libomp.dylib' (no such file)
It is trying to search a path which does not exists, but physically the file libomp.dylib is located in other path, but I have no idea why it is seeking in this path.
I am wondering whether this library is possible to install on Mac with chip M1.
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Please re-install libomp to save 'libomp.dylib' file at '/usr/lib/libomp.dylib' or update PATH to include the current path.
An alternative:
Because the latest development version of covsirphy does not depend on lightgbm, try to reinstall the latest version (>= 3.0.0.dev7).
pip install --upgrade "git+https://github.com/lisphilar/covid19-sir.git#egg=covsirphy"
Related
I installed psycopg2 using pip but when I import psycopg2 I get this error
ImportError: dlopen(/Users/lce21/Documents/GitHub/hazen-web-
app/hazen-web-app/lib/python3.8/site-
packages/psycopg2/_psycopg.cpython-38-darwin.so, 0x0002): Library
not loaded: /usr/local/opt/postgresql/lib/libpq.5.dylib
Referenced from: /Users/lce21/Documents/GitHub/hazen-web-
app/hazen-web-app/lib/python3.8/site-
packages/psycopg2/_psycopg.cpython-38-darwin.so
Reason: tried: '/usr/local/opt/postgresql/lib/libpq.5.dylib'
(no such file), '/usr/local/lib/libpq.5.dylib' (no such file),
'/usr/lib/libpq.5.dylib' (no such file),
'/usr/local/Cellar/postgresql#14/14.6/lib/libpq.5.dylib' (no such
file), '/usr/local/lib/libpq.5.dylib' (no such file),
'/usr/lib/libpq.5.dylib' (no such file)
Things tried:
pip install psycopg2-binary
MacOS pip install psycopg2 with sudo and in the venv. No errors when I installed. Postgres installed.
I might need to change location of files but I don't know how to do that
I found the problem was that I had installed in my system a different version of postgresql than the version on my virtual env.
So I had to unistall from the system postgresql and then reinstall it.
I am using lazypredict to try to find good algorithms (source: here). The command pip install yields no error, and I have also done the upgrade of the package, yet when I use from lazypredict.Supervised import LazyRegressor (which should work according to the documentation) I end up with the following error:
OSError: dlopen(/Users/gaetanlefloch/opt/anaconda3/lib/python3.9/site-packages/lightgbm/lib_lightgbm.so, 0x0006): Library not loaded: /usr/local/opt/libomp/lib/libomp.dylib
Referenced from: /Users/gaetanlefloch/opt/anaconda3/lib/python3.9/site-packages/lightgbm/lib_lightgbm.so
Reason: tried: '/usr/local/opt/libomp/lib/libomp.dylib' (no such file), '/usr/local/lib/libomp.dylib' (no such file), '/usr/lib/libomp.dylib' (no such file)
Did someone have the same issue (with lazypredict or another package), and how can I overcome it without eventually doing a manual installation ?
Based on the presence of a /Users/... path in the logs you shared, I'm assuming you are on macOS.
LightGBM requires OpenMP by default, and links to it dynamically. That means that it expects to find it installed on your system at runtime.
Use Homebrew (link) to install OpenMP.
brew install libomp
If you are using lightgbm < 4.0 and Homebrew gives you libomp>=15.0, you may need to help Python find that library.
You can do that modifying environment variable LD_LIBRARY_PATH.
export LD_LIBRARY_PATH=/usr/local/opt/libomp/lib:"${LD_LIBRARY_PATH}"
Or by using brew link.
brew link --force libomp
When I install OpenCV, I get an error as shown below. What should I do?
ImportError: DLL load failed: The specified module could not be found.
Installing OpenCV
To install a package in Jupyter Notebook, you can use the magic %pip command.
%pip install opencv-python
If the above command doesn't work on IPython < 7.3, you can try this command instead.
!pip install --user opencv-python
Demonstration
Let's see it in action. First, you insert a new cell, type in either of the two commands above, and then execute the cell using the Ctrl + Enter shortcut.
You should now be able to import and use OpenCV without any errors.
This is usually a dependency issue. Just .pyd is not enough (all .DLLs are required).
On Windows add entries to .dll into PATH environment variable (not enough for Python 3.8 with updated security policies)
I installed Pillow, and after I want to do:
from PIL import Image
I get the following error:
Traceback (most recent call last):
File "<console>", line 1, in <module>
File "/usr/local/lib/python2.7/dist-packages/PIL/Image.py", line 61, in <module>
ImportError: cannot import name _imaging
However, if I import these separately, everything is fine, ie:
import _imaging
import Image
Do you know what the problem might be?
I had the same problem and I solved that by upgrading this package using the command below:
pip install -U Pillow
This also happens if you built Pillow in one OS and then copied the contents of site-packages to another one. For example, if you are creating AWS Lambda deployment package, that's the error you will face when running the Lambda function. If that's the case, then Pillow needs to be installed in a Amazon Linux instance and you have to use the resulting site-packages in your deployment package. See instructions and details here:
http://docs.aws.amazon.com/lambda/latest/dg/with-s3-example-deployment-pkg.html
I ran into this problem as well. It can happen if you have PIL installed, then install Pillow on top of it.
Go to /usr/local/lib/python2.7/dist-packages/ and delete anything with "PIL" in the name (including directories). If the Pillow .egg file is there you might as well delete that too.
Then re-install Pillow.
substitute "python2.7" for the version of python you're using.
What is your version of pillow?
Pillow >= 2.1.0 no longer supports import _imaging. Please use from PIL.Image import core as _imaging instead. Here's the official documentation.
I have got the same error with Python 3.6. Upgrading Pillow did the job for me.
sudo python3.6 -m pip install Pillow --upgrade
Probably for other python versions use your version instead of 3.6.
This can happen if you're trying to run Pillow installed on a Mac in a Linux environment (for example, e.g. building an AWS Lambda on a Mac then deploying it to a Linux runtime).
To make sure you're installing it for the right platform do the following:
pip3 install --platform manylinux1_x86_64 --only-binary=:all:
The --only-binary=:all: is required when specifying --platform and the platform itself can be found by looking at https://pypi.org/project/Pillow/7.2.0/#files (for example) - the platform is the last part of the filename e.g. win32, manylinux1_x86_64, manylinux1_i686 etc.
This avoids the need to be running Linux to install the Linux build of Pillow.
This may be a niche solution but I was able to fix this problem on Pycharm by going to file->settings->python interpreter and clicking the upgrade symbol next to the pillow package.
For pillow to work PIL must be in /usr/local/lib/python2.7 or3/dist-packages/PIL.py.
In dist-packages PIL.py should have a folder.
sudo apt-get update
pip install Pillow
PIL != PiL
I had the same problem when it tried to deploy a lambda package, the thing is that you have to precompile the package emulating the lambda architecture/runtime that you are going to use, otherwise you'll get cannot import name _imaging. 2 ways of solving this:
1 - spin up an EC2 Amazon Linux instance.( i will only cover this part)
2 - Use dockers.
Short solution
Install Python 3 in Amazon Linux 2 intance. (Must be python3.X you plan to use in lambda)
Install a virtual environment under the ec2-user home directory.
Activate the environment, and then install Boto 3.
Install Pillow
Create a ZIP archive with the contents of the library(PIL and Pillow.libs)
Add your function code to the archive.
Update your the lambda.(AWS CLI)
Long solution
If Python 3 isn't already installed, then install the package using the yum package manager.
`$ sudo yum install python3 -y`
Create a virtual environment under the ec2-user home directory
The following command creates the app directory with the virtual environment inside of it. You can change my_app to another name. If you change my_app, make sure that you reference the new name in the remaining resolution steps.
`$ python3 -m venv my_app/env`
Activate the virtual environment and install Boto 3
Attach an AWS Identity and Access Management (IAM) role to your EC2 instance with the proper permissions policies so that Boto 3 can interact with the AWS APIs. For other authentication methods....For a quick use you can set your credential using $ aws confifure see documentation ( you will need this in step 7)
3.1 Activate the environment by sourcing the activate file in the bin directory under your project directory.
`$ source ~/my_app/env/bin/activate`
3.2. Make sure that you have the latest pip module installed within your environment.
$ pip install pip --upgrade
3.3 Use the pip command to install the Boto 3 library within our virtual environment.
`pip install boto3`
Install libraries with pip.
$ pip install Pillow
4.1 Deactivate the virtual environment.
`$ deactivate`
Create a ZIP archive with the contents of the library.
change directory to where pip is installes. it should be something like /my_app/env/lib/python3.x/site-packages.
IMPORTANT: the key here is to zip the file inside site-packages into
your lambda.(i only used PIL and Pillow.libs to save space but you can
zip everything)
5.1 ZIP everything thats inside the PIL folder.
`zip -r9 PIL.zip ./PIL/`
add the Pillow.libs to your ZIP
`zip -gr PIL.zip Pillow.libs`
Add your function code to the archive.
you can do this in the console if it just on file of code, but i recomend doing it in this step.If you don't have your code,just create a file using vi or nano and save it with the name that your lambda handler will use (in this case will use lambda_function.py).
`zip -g PIL.zip lambda_function.py`
Update your the lambda.(AWS CLI)
if you haven't create a lambda function,do it now before updating the function from the aws cli, make sure that you have the right permission to update lambda from the aws cli.
change LAMBDAFUNCTIONNAME for your function name
aws lambda update-function-code --function-name LAMBDAFUNCTIONNAME P --zip-file fileb://PIL.zip
Getting out of the first loop of hell
go to your lambda console and test your code, make sure you use the same runtime/python version you used in the EC2 instance
Quick solution - import PyQt5 as well,
you will not get that error message.
import PyQt5
from PIL import ImageGrab
As some other answers have alluded to, this can happen when you build Pillow on MacOS and try to import PIL in another OS like some Amazon Linux flavor.
My exact use-case was to package imagehash as a Lambda layer which includes pillow as a dependency. The following guideline has worked great for me for all python packages.
Install the SAM CLI SAM Installation
Create your python script with the lambda handler defined
Create your template.yml file with your Lambda function defined. Your CodeUri should be the relative path to your python script.
Add the package you are trying to create a layer for to your requirements.txt.
Run the following SAM command sam build -t path_to_template
You will now have the following directory .aws-sam/build/{Logical ID Of Lambda Function}. Inside you will see that your python packages and their dependencies have been installed just as if you ran pip download package and unzipped the wheel files.
Now, the python files have been prepped by SAM specifically for Lambda and you can continue with creating your Lambda Layer as desired. Configuring Lambda Layers
Since I use AWS SAM CLI already for running Lambda functions locally, this has been the easiest method for me to create my layers.
Just uninstall pillow:
pip uninstall pillow
then install pillow again:
pip install pillow
works great
I'm using Flask with Google App Engine. I have the module Pillow installed via this command:
pip install -t lib pillow
I fixed this error by defined PIL in my app.yaml file:
libraries:
- name: PIL
version: latest
Solution
pip uninstall PIL
pip uninstall Pillow
pip install Pillow
I'm trying to install Pandas using pip, but I'm having a bit of trouble. I just ran sudo pip install pandas which successfully downloaded pandas. However, it did not get downloaded to the location that I wanted. Here's what I see when I use pip show pandas:
---
Name: pandas
Version: 0.14.0
Location: /Library/Python/2.7/site-packages/pandas-0.14.0-py2.7-macosx-10.9-intel.egg
Requires: python-dateutil, pytz, numpy
So it is installed. But I was confused when I created a new Python Project and searched under System Libs/lib/python for pandas, because it didn't show up. Some of the other packages that I've downloaded in the past did show up, however, so I tried to take a look at where those were. Running pip show numpy (which I can import with no problem) yielded:
---
Name: numpy
Version: 1.6.2
Location: /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python
Requires:
Which is in a completely different directory. For the sake of confirming my error, I ran pip install pyquery to see where it would be downloaded to, and got:
Name: pyquery
Version: 1.2.8
Location: /Library/Python/2.7/site-packages
Requires: lxml, cssselect
So the same place as pandas...
How do I change the default download location for pip so that these packages are downloaded to the same location that numpy is in?
Note: There were a few similar questions that I saw when searching for a solution, but I didn't see anything that mentioned permanently changing the default location.
According to pip documentation at
http://pip.readthedocs.org/en/stable/user_guide/#configuration
You will need to specify the default install location within a pip.ini file, which, also according to the website above is usually located as follows
On Unix and Mac OS X the configuration file is: $HOME/.pip/pip.conf
On Windows, the configuration file is: %HOME%\pip\pip.ini
The %HOME% is located in C:\Users\Bob on windows assuming your name is Bob
On linux the $HOME directory can be located by using cd ~
You may have to create the pip.ini file when you find your pip directory. Within your pip.ini or pip.config you will then need to put (assuming your on windows) something like
[global]
target=C:\Users\Bob\Desktop
Except that you would replace C:\Users\Bob\Desktop with whatever path you desire. If you are on Linux you would replace it with something like /usr/local/your/path
After saving the command would then be
pip install pandas
However, the program you install might assume it will be installed in a certain directory and might not work as a result of being installed elsewhere.
You can set the following environment variable:
PIP_TARGET=/path/to/pip/dir
https://pip.pypa.io/en/stable/user_guide/#environment-variables
Open Terminal and type:
pip config set global.target /Users/Bob/Library/Python/3.8/lib/python/site-packages
except instead of
/Users/Bob/Library/Python/3.8/lib/python/site-packages
you would use whatever directory you want.
Follow these steps
pip config set global.target D:\site-packages to change install path
or py -m pip config --user --editor notepad edit
[global]
target = D:\site-packages
set environment variable to use download import xxx
PIP_TARGET=site-packages
PYTHONPATH=site-packages
3.pip config unset global.target, to upgrade pip py -m pip install --upgrade pip
#Austin's answer is outdated, here for more up-to-date solution:
According to pip documentation at
https://pip.pypa.io/en/stable/topics/configuration/
You will need to specify the default install location within a configuration file, which, also according to the website above is usually located as follows
Mac OS
$HOME/Library/Application Support/pip/pip.conf if directory $HOME/Library/Application Support/pip exists else $HOME/.config/pip/pip.conf.
The legacy “per-user” configuration file is also loaded, if it exists: $HOME/.pip/pip.conf.
The $HOME folder can be located by navigating to ~/ (cmd+shift+G in Finder; cmd+shift+. to show hidden files).
Windows
%APPDATA%\pip\pip.ini
The legacy “per-user” configuration file is also loaded, if it exists: %HOME%\pip\pip.ini
The %HOME% is located in C:\Users\Bob on windows assuming your username is Bob
Unix
$HOME/.config/pip/pip.conf, which respects the XDG_CONFIG_HOME environment variable.
The legacy “per-user” configuration file is also loaded, if it exists: $HOME/.pip/pip.conf.
On linux the $HOME directory can be located by using cd ~
You may have to create the configuration file when you find your pip directory. Put something like
[global]
target = /Library/Frameworks/Python.framework/Versions/Current/lib/python3.10/site-packages/
if you are on a Mac. Except that you would replace /Library/Frameworks/Python.framework/Versions/Current/lib/python3.10/site-packages/ with whatever path you desire. If you are on Linux you would replace it with something like /usr/local/your/path
After saving the command would then be
pip install pandas
However, the program you install might assume it will be installed in a certain directory and might not work as a result of being installed elsewhere.
Please note that
pip3 install pandas
might be the solution if your packages gets installed in the Python2 folder vs Python3.