I took this example to run interactive Bokeh (in this case with sliders) in Jupyter Notebook: How to get interactive bokeh in Jupyter notebook
That works fine.
But when I start the notebook with voila on the command line ("voila bokeh_jupyter.ipynb") than the only output I see is "BokehJS 2.4.2 successfully loaded."
Why does it not work with Voila and what can I do about it?
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Summary
Installed R kernel in Anaconda environment
Works with Anaconda's browser Jupyter notebook, but not VS Code.
Details
I am trying to set up VS Code to recognize my R kernel for use with Jupyter Notebooks. The steps I have followed are as follows:
Create a new R environment (via the Anaconda interface... Rstudio works just fine).
Using the command line interface with the above environment activated, ensure Jupyter is installed: conda install jupyter
Install irkernel: conda install -c r r-irkernel
Run R from command line and initialize irkernel:
R
> IRkernel::installspec()
Open VS Code and create a new notebook. Select the R kernel that appears, and run a basic commannd in the first cell: file.path(getwd())
These follow the steps here, and in other Stackoverflow posts (here and here).
Unfortunately, I cannot get the kernel to work. The above code in item 5 results in the following error:
Failed to start the Kernel.
The kernel died. Error: ... View Jupyter log for further details.
There is a copy of the log available here (should be visible to everyone). The notebook is available here (but is literally just the one line of code mentioned above).
My hypothesis is that IRkernel::installspec() installs the kernel in a different location than the conda environment. The kernel is installed in C:\Users\aaron\AppData\Roaming\jupyter\kernels\ir, while in VS Code the kernel selected is in C:\Users\aaron\.conda\envs\rstudio\lib\R\bin\x64\R (the environment name is rstudio).
However, when I open Jupyter notebook via the Anaconda interface (not VS Code... i.e. the browser version), everything works just fine. The same code (file.path(getwd())) returns the appropriate 'C:/Users/aaron'.
I am sure I have done something silly wrong, and appreciate your help in advance!
I wanted to ask how to repair kernel connection for R in jupyter notebook,
I am able to run R in Rstudio and python in jupyter notebook, I used to write R in jupyter notebook but after some updates(I dont know what updates) R stop working in jupyter notebook.
I would like to ask for some advices - I would like to run it without reinstalling it
I also folled some question on stackoverflow and on google but it was not helpfull.
I attached images of what errors it returns
I did try: $ conda install -c r r-irkernel
I am looking for a way to get the path of current working notebook on jupyter notebook irkernel in order to do setwd() easier.
Using reticulate and call python os does not work. Although it works in a python notebook.
library(reticulate)
os <- import("os")
os$listdir(".")
I have jupyter notebook installed, I also have R installed. Both work fine independently.
When I run jupyter with jupyter notebook, then try to open an ipynb file, I see
The only option in the dropdown is Python 3 (R is not an option).
Question
How do you open a jupyter notebook with an R kernel (on mac)?
Note
I tried jupyter notebook --runtime-dir /usr/local/bin/R but that was just guessing
Looks like the R kernel could be installed via pip?
Open any R session (e.g. in RStudio is fine, or open terminal/bash and type R to start an R session).
Install the kernel with:
install.packages("devtools")
devtools::install_github("IRkernel/IRkernel")
IRkernel::installspec()
Close and reopen the notebook and the R kernel will now be available.
If the R kernel does not appear as an option within a Jupyter notebook even after installing R, and one is using Anaconda, bringing up the conda prompt from the Start menu (Windows 10), and running the following commands may do the trick:
conda config --add channels r
conda install --yes r-irkernel
Credit to this post.
I am using Jupyter on Linux, Jupyter itself is working fine, I need to download my notebook to pdf through the Jupyter menu. I tried following the error message to install pandoc, ...., just not successful, still error out like below:
nbconvert failed: pandoc wasn't found.
I already installed both nbconvert and pandoc though.
Thanks.