I created a new environment in jupyter called "rpy2" and try to use %%R magic but the installation is failed.
QN: How to use %%R magic in jupyter-notebook ?
Platform: MacOS High Sierra
Steps
jupyter kernelspec list
conda create -n rpy2 python=3.7
source activate rpy2
which pip
/Users/poudel/miniconda3/envs/rpy2/bin/pip install rpy2
conda install ipykernel
python -m ipykernel install --user --name rpy2 --display-name "Py37rpy2"
jupyter-notebook
Issues
# Now
import rpy2 shows no error
import rpy2.rinterface # gives error
Note
# I have checked all the files given in error log, all of them exist
492 ls /Users/poudel/miniconda3/lib/R/lib/libR.dylib
493 ls /usr/lib/libiconv.2.dylib
494 ls /Users/poudel/miniconda3/lib/R/lib/libR.dylib
495 /Users/poudel/miniconda3/lib/R/lib/libR.dylib
496 ls /Users/poudel/miniconda3/lib/R/lib/libR.dylib
All shows given file, and none is missing.
Error
OSError: cannot load library '/Users/poudel/miniconda3/lib/R/lib/libR.dylib': dlopen(/Users/poudel/miniconda3/lib/R/lib/libR.dylib, 2): Symbol not found: _libiconv
Referenced from: /Users/poudel/miniconda3/lib/R/lib/libR.dylib
Expected in: /usr/lib/libiconv.2.dylib
in /Users/poudel/miniconda3/lib/R/lib/libR.dylib
Update
As suggested by #akrun, I tried using pyper but it takes infinite time to load a libary and when stopped shows that it has broken pipe.
pip install pyper.
if you're still looking for a solution, here's what you need.
Start the notebook with
%load_ext rpy2.ipython
Then run R cells using the R magic function
%%R
library("tidyverse")
This works for the latest rpy2 version (3.4.5).
Related
While installing LabelImg in M1 Mac using below command
pip install pyqt5 lxml
This is the error I got
ERROR: pyqt5 from https://files.pythonhosted.org/packages/7c/5b/e760ec4f868cb77cee45b4554bf15d3fe6972176e89c4e3faac941213694/PyQt5-5.14.0.tar.gz#sha256=0145a6b7de15756366decb736c349a0cb510d706c83fda5b8cd9e0557bc1da72 has a pyproject.toml file that does not comply with PEP 518: 'build-system.requires' contains an invalid requirement: 'sip >=5.0.1 <6'
How to install lableImg annotation tool in M1 Mac?
I got it to work by using the following commands
brew install pyqt#5
pip install labelimg
And that's it, it just works
You just need to type labelimg in the Terminal and the app will start running
I don't know why they don't tell you this in the installation guide
Alrighty!
On MacOS Monterey, none of the other solutions posted here solved this problem for me. However, I managed to easily solve the issue, without a virtual environment or too much fiddling about like so:
Firstly, you have to download all labelImg packages from this link:
https://github.com/tzutalin/labelImg#macos
(You can download it as a .zip file or clone it)
Unzip and then in your terminal cd into whatever directory you downloaded the above files to.
Then run the following commands in order:
pyrcc5 -o libs/resources.py resources.qrc
Then,
pip3 install lxml
Finally,
python3 labelImg.py
It should run without an issue now.
You can go one of two ways:
Using brew:
You can use homebrew to install the dependencies - like qt and libxml2. This will let your package manager handle everything and generally should solve the problem with the . Then you can run
python3 labelimg.py
Using Virtual Environments:
This is the more recommended way to go about in such cases. You can use conda, pipenv or venv to create a virtual environment which is isolated from your system python installation. Then you can try to install it as explained in the README.rst in the root of the repository:
brew install python3
pip3 install pipenv
pipenv run pip install pyqt5==5.12.1 lxml
pipenv run make qt5py3
pipenv run python3 labelImg.py
[Optional] rm -rf build dist; python setup.py py2app -A;mv "dist/labelImg.app" /Applications
You can try the two methods and and get back with the errors if there are any.
This is my note.
I just succeed on my Mac M1 Chip
CHECK THIS OUT!
Installation of labelimg on mac m1 chip
my first reference
my second reference
First, you must use terminal with rosetta version
Then, you already have python3
Then...
[Done]
# check where python3 is
$ where python3
# create env
$ /usr/bin/python3 -m venv env
# check env is
$ where env
# activate env list
$ source env/bin/activate
# updated to the newest
$ pip install --upgrade pip
# installation of PyQt5
$ pip install PyQt5
# start to run labelImg.py
$ cd Documents/repos/labelImg
$ pip3 install pyqt5 lxml
$ make qt5py3
# [run ok!!]
$ python3 labelImg.py
Using Conda
Create a virtual environment in conda and activate it
conda create -n venv
conda activate venv
Install pyqt using conda
conda install pyqt
Install lxml using pip
pip install lxml
Change directory to the downloaded/cloned labelImg folder
cd path/to/labelImg/folder/
Make qt5py3
make qt5py3
Run LabelImg
python labelImg.py
I am using MacOS and try to use Stata in the jupyter notebook. I went over the following step to do so.
First, in the terminal:
pip install stata_kernel
python -m stata_kernel.install
conda install -c conda-forge nodejs -y
jupyter labextension install jupyterlab-stata-highlight
pip install ipystata
And then in my jupyter notebook:
import ipystata
from ipystata.config import config_stata
config_stata('/Macintosh HD/Applications/Stata/StataSE')
import ipystata
%%stata
display "Hello, I am printed in Stata."
But I keep getting the error message
UsageError: Line magic function %%stata not found.
I am not sure if this is path problem or something else.
Could you help me to fix the problem?
I've installed Ipython 6.0.0 successfully using Pip3:
pip3 install IPython
but when tried to run the command
Ipython
I got this error:
bash: IPython: command not found
This is the pip list result:
ipykernel (5.1.3)
ipython (6.0.0)
ipython-genutils (0.2.0)
..
..
notebook (6.0.2)
and this is the result of pip3 show IPython
Name: ipython
Version: 6.0.0
Summary: IPython: Productive Interactive Computing
Home-page: https://ipython.org
Author: The IPython Development Team
Author-email: ipython-dev#python.org
License: BSD
Location: /home/pi/.local/lib/python3.5/site-packages
Requires: setuptools, traitlets, jedi, pexpect, pygments, pickleshare, simplegeneric, prompt-toolkit, decorator
This is a problem of case sensitivity...
The correct typography is IPython.
pip is not case sensitive, see Is PyPI case sensitive?
IPython is installed as ipython (lowercase), as shown in your pip3 show IPython
bash is case sensitive...
So, just enter ipython.
As you have specified pip3, I would also recommend to invoke ipython3 to avoid python2/3 confusions.
I am not able to link Jupyter kernels to their parent Conda environments. After creating a new kernel linked to Conda environment, I'm getting a different version of Python and its dependencies inside Jupyter lab.
Here are the steps I followed:
Created a conda environment using:
conda create -n nlp python=3.6
conda activate nlp
(nlp) ➜ ~ python --version
Python 3.6.9 :: Anaconda, Inc.
(nlp) ➜ ~ which python
/anaconda3/envs/nlp/bin/python
Inside the environment I created a Jupyter kernel with:
(nlp) ➜ ~ python -m ipykernel install --user --name=nlp
Installed kernelspec nlp in /Users//Library/Jupyter/kernels/nlp
Investigating the created json file for the kernel:
(nlp) ➜ ~ cat /Users/<username>/Library/Jupyter/kernels/nlp/kernel.json
{
"argv": [
"/anaconda3/envs/nlp/bin/python",
"-m",
"ipykernel_launcher",
"-f",
"{connection_file}"
],
"display_name": "nlp",
"language": "python"
}%
It seems to be pointing to the environment version of Python
But when I start Jupyter Lab and select the nlp kernel, I get a different version of Python and some dependencies are missing
!python --version
Python 3.5.6 :: Anaconda, Inc.
!which python
/anaconda3/bin/python
Could you please try the following steps:
conda activate nlp
conda install ipykernel
ipython kernel install --name nlp --user
After these steps please try changing the kernel again in jupyter lab to "nlp".
Thanks.
this behavior is actually normal in Jupyter lab.
If you run
import sys
print(sys.version)
!python --version
in a notebook, the print statement will give you the Python version of the conda env, while the second will give you the Python version of your base env.
The easiest workaround for this is to simply pip install jupyterlab in your conda env and then run jupyter lab in your conda env. Then, there will not be a mismatch in Python versions between the new "base" env and the conda env which will help clear up any DLL problems.
It's probably not best practice, but you do what you gotta do when working with legacy code, ig.
Can you try this :
# in base env
conda install nb_conda_kernels
conda activate nlp
conda install ipykernel
conda install ipywidgets
# install kernelspec
python -m ipykernel install --user --name nlp --display-name "nlp env"
When you run jupyter notebook, you will see 2 nlp kernels. Use the one with "Python [conda:env:nlp]"
After many different ways of trying to install jupyter, it does not seem to install correctly.
May be MacOS related based on how many MacOS system python issues I've been having recently
pip install jupyter --user
Seems to install correctly
But then jupyter is not found
where jupyter
jupyter not found
Not found
Trying another install method found on SO
pip install --upgrade notebook
Seems to install correctly
jupyter is still not found
where pip /usr/local/bin/pip
What can I do to get the command line jupyter notebook command working as in the first step here: https://jupyter.readthedocs.io/en/latest/running.html#running
Short answer: Use python -m notebook
After updating to OS Catalina, I installed a brewed python: brew install python.
It symlinks the Python3, but not the python command, so I added to my $PATH variable the following:
/usr/local/opt/python/libexec/bin
to make the brew python the default python command (don't use system python, and now python2.7 is deprecated). python -m pip install jupyter works, and I can find the jupyter files in ~/Library/Python/3.7/bin/, but the tutorial command of jupyter notebook doesn't work. Instead I just run python -m notebook.
My MacOS has python 2.7, I installed python3 with brew, then the following commands work for me
brew install python3
brew link --overwrite python
pip3 install ipython
python3 -m pip install jupyter
You need to add the local python install directory to your path. Apparently this is not done by default on MacOS.
Try:
export PATH="$HOME/Library/Python/<version number>/bin:$PATH"
and/or add it to your ~/.bashrc.
Try solving this with Conda or Poetry.
Poetry makes it a lot easier to manage Python dependencies (including Jupyter) and build a virtual environment.
Here are the steps to adding Jupyter to a project:
Run poetry add pandas jupyter ipykernel to add the dependency
Run poetry shell to create a shell within the virtual environment
Run jupyter notebook to to fire up a notebook with access to all the virtual environment dependencies
The other suggested solutions are just band-aids. Conda / Poetry can give you a sustainable solution that's easy to maintain and will shield you from constant Python dependency hell.