I am attempting to run R in Jupyter notebook. I tried almost everything what I have found, but without results. So I tried to reinstall Anaconda (Python 2.7.13, Anaconda 4.3.0, IPython 5.1.0) and R (version 3.3.2) to have the latest versions.
Afterwards, I ran
conda install -c r r-essentials
But If I open Jupyter notebook and create a new file with R kernel, the kernel dies immediately and I get long error, see the full version here. The last line:
WindowsError: [Error 2] The system cannot find the file specified
Any suggestions will be very appreciated.
Related
I am trying to use GitHub Codespace with R + Jupyter Notebook setting. However, the notebooks on the codespace do not locate a correct kernel for R.
Here are the steps I went through:
I created a Codespace for my repo.
I clicked on 'Configure Dev Container' and selected "Jupyter Data Science Notebooks", which is supposed to support Python, R, and Julia.
After rebuild, I installed "R" VS code extension and checked that R codes on .r script run fine.
I executed R on Bash, and then installed packages "languageserver" and "IRkernel". IRkernel was already installed.
Then, I executed IRkernel::installspec().
I checked using jupyter kernelspec list that there is a Jupyter kernel for R:
Jupyter kernel list on Bash
However, I don't see a correct R kernel on Jupyter notebook, but instead there is a kernel named "R" with a path to Python:
Jupyter kernel list on notebook
What should I do to have the correct R kernel show up on Jupyter notebook?
I am running Drake on Ubuntu 20.04 using WSL2.
I use python3.8.10 and Drake1.2.0.
I tried running the "Mathematical Program Tutorial" obtained from deepnote on my PC, but the behavior of the ipopt solver is unnatural and does not give the expected results.
The 1st error is occurred in the section using ipopt solver.
All components of the solution is printed as "nan"
The 2nd error is below about "get_solver_details().status"
RuntimeError: The solver_details has not been set yet.
I can see both errors in "Demo on manually choosing a solver" in the tutorial.
The result is following
SolutionResult.kUnknownError
x* = [nan nan]
Solver is IPOPT
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
<ipython-input-12-2d1b3835c54a> in <module>
25 print("x* = ", result.GetSolution(x))
26 print("Solver is ", result.get_solver_id().name())
---> 27 print("Ipopt solver status: ", result.get_solver_details().status,
28 ", meaning ", result.get_solver_details().ConvertStatusToString())
RuntimeError: The solver_details has not been set yet.
Thank you in advance.
P.S.
I installed pydrake for venv by pip commands
python3 -m venv env
env/bin/pip install --upgrade pip
env/bin/pip install drake
sudo apt-get install --no-install-recommends \
libpython3.8 libx11-6 libsm6 libxt6 libglib2.0-0
source env/bin/activate
I just download the folder "Tutorial" from deepnote and put it under env.
Then, I run it by Jupyter Notebook as
jupyter notebook
and open env/Tutorials/mathematical_program.ipynb
It turns out that the pip drake == 1.2.0 version has a bug in the IpoptSolver compilation.
As a work-around, you can use SnoptSolver instead, or else use the https://drake.mit.edu/from_binary.html release (unpacking a zipped binary, instead of using pip).
It's possible that the pydrake.solvers.ipopt.IpoptSolver class (which is a wrapper around the https://coin-or.github.io/Ipopt/ library) does not run correctly under WSL2, due to using some odd libc API which doesn't work on Windows. We will need more information to reproduce the problem and try to debug.
Can you state exactly how you installed pydrake (i.e., show us the command lines you used). Was it via pip (https://drake.mit.edu/pip.html) or just via binary (https://drake.mit.edu/from_binary.html)?
Can you state exactly how you ran Jupyter (the command line) to launch the notebook? Was it python3 -m pydrake.tutorials or something else?
Looks like this may not be tied to WSL, but instead pip build (or just binary build). Ran into this on Ubuntu 20.04 (no WSL). Per Drake Slack, filed issue:
https://github.com/RobotLocomotion/drake/issues/17162
Background: I am new to the Python world and am using Plotly for creating basic graphs in Python. I am using AWS Sagemaker's JupyterLab for creating the python scripts.
Issue: I have been trying to run the basic codes mentioned on Plotly's website however even those are returning blank graphs.
Issue Resolution Tried by myself:
pip installed plotly version 4.6.0
Steps mentioned on https://plotly.com/python/getting-started/ for JupyterLab support have already been executed
Code Example:
import plotly.graph_objects as go
fig = go.Figure(data=go.Bar(y=[2, 3, 1]))
fig.show()
I recently had the same issue. Simple change suggested here helped me. I know this is a temporary workaround until a proper fix is found.
// fig = go.Figure()
fig = go.FigureWidget() // replace with this
// fig.show()
fig // remove .show()
Sagemaker notebook instances are using (As of Jan 2022), for some reason, jupyterlab==1.2.21. You can verify that by running pip freeze | grep lab from the terminal or !pip freeze | grep lab from a notebook.
According to the documentation, you'll need to install the following jupyterlab extensions (which are not needed if sagemaker was running jupyterlab 3):
jupyterlab-plotly
jupyter-widgets/jupyterlab-manager
You can install those on a up-and-running instance by running
jupyter labextension install jupyterlab-plotly#5.5.0 #jupyter-widgets/jupyterlab-manager in the terminal or notebook (using ! if you are running on the notebook ofcourse). Notice that the jupyterlab-plotly extension version (here 5.5.0) should match the plotly version you are installing. Mismatches my cause issues. In this case by plotly version is 5.5.0 and thus that's also the jupyterlab-plotly version I've installed.
If you need, like I did, to have it ready upon spinning up a notebook instance, you'll need to:
Create a lifecycle script
To it, add:
PATH=$PATH:/home/ec2-user/anaconda3/envs/JupyterSystemEnv/bin - To ensure nodejs path which is needed for the extension installation
pip install plotly==5.5.0 - To ensure a specific version
jupyter labextension install jupyterlab-plotly#5.5.0 #jupyter-widgets/jupyterlab-manager - To ensure same version
of coures, you can change the version according to the most up to date.
I think that documentation is not on par. You now need to install jupyterlab-plotly extension.
jupyter labextension install jupyterlab-plotly
UPDATE
I followed a mix of instructions here and here.
First Enable Extention manager from jupyter-lab
then from terminal
conda install -c conda-forge "nbformat" "ipywidgets>=7.5" -y
jupyter labextension install jupyterlab-plotly
jupyter labextension install #jupyter-widgets/jupyterlab-manager plotlywidget
And within your environment
conda install nbformat
I tried installing the datascience jupyter docker image (tag 45b8529a6bfc, last update Feb 14, 2019) from docker stacks. My entire dockerfile:
FROM jupyter/datascience-notebook:45b8529a6bfc
USER $NB_UID
When I open a new Jupyter notebook with an R kernel, the notebook works fine. When I try a %%R cell magic in an ipython notebook, it doesn't work:
%%R
3+4
UsageError: Cell magic `%%R` not found.
I wandered around various stackoverflow answers and internet searches, tried installing rpy2 (it was already installed). Didn't work.
Suggestions?
Load the jupyter extension before you try to use it:
%load_ext rpy2.ipython
I tried %load_ext rpy2.ipython as suggested by #lgautier, and got the error message No module named 'simplegeneric'. Once I pip installed simplegeneric, everything works and I don't need the load_ext statement.
Not sure why the dockerfile doesn't install simplegeneric, but there you have it.
I'm trying to learn Pytorch, but whenever I seem to try any online tutorial (https://pytorch.org/tutorials/beginner/blitz/tensor_tutorial.html#sphx-glr-beginner-blitz-tensor-tutorial-py), I get errors when trying to run certain functions, but only in Jupyter Notebook.
When running
x = torch.empty(5, 3)
I get an error:
module 'torch' has no attribute 'empty'
Furthermore, when running
x = torch.zeros(5, 3, dtype=torch.long)
I get the error:
module 'torch' has no attribute 'long'
Some other functions work fine like:
x = torch.rand(5, 3)
But generally, most code I try to run seems to run into an error really quickly. I couldn't find any resolution online.
When I go into my docker container and simply run python in the shell, I can run these lines just fine with no errors.
I'm running pytorch in a Docker image that I extended from a fastai image, as it already included things like jupyter notebook and pytorch. I used anaconda to update everything, and committed it to a new image for myself.
I have absolutely no idea what the issue could be. I've tried updating packages through anaconda, pip, aptitude in my docker container, and making sure to commit my changes, but nothing seems to work. I also tried creating a new kernel with python 3.7 as I noticed that my Jupyter Notebook only runs in 3.6.4, and when I run python in the shell it is at 3.7.
I've also tried getting different docker images and extending them with what I need, but all images that I've tried have had errors with anaconda where it gets stuck on "Solving environment" step.
Ok, so the fix for me was to either update pytorch through conda using the following command
conda update pytorch
If it's not installed yet, I've gotten it to work in other environments by simply installing it through conda
conda install pytorch
Kind of stupid that I didn't try this earlier, but I was confused on the difference between conda and pip.