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Bokeh cannot find NodeJS when executed in Jupyter Notebook

NumesSanguisMar 26, 2019 #1

Hello,

I’m trying to get the spectrogram example (https://github.com/bokeh/bokeh/tree/master/examples/app/spectrogram) to work in Jupyter Notebook on Ubuntu 18.04. It works for me in the terminal, but not when executing the Python code in a Notebook using the same conda environment.

The following code will result in a: RuntimeError: node.js v6.10.0 or higher is needed to allow compilation of custom models ("conda install nodejs" or follow https://nodejs.org/en/download/)

from bokeh.io import output_notebook, show
from bokeh.core.properties import Color, Float, Int, Override, Seq
from bokeh.models import Renderer

class WaterfallRenderer(Renderer):
implementation = “waterfall.ts”

output_notebook()

!node --version

/bin/sh: 1: node: not found


See for all details this GitHub issue: [https://github.com/bokeh/bokeh/issues/8790](https://github.com/bokeh/bokeh/issues/8790)

Based on the comments I tried the following:
So indeed it cannot find NodeJS.
In the GitHub issue it was suggested to set `BOKEH_NODEJS_PATH`. However, how do I do this?
I have found a node installation here: /home/*username*/anaconda3/envs/bokeh/bin

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BryanMar 26, 2019 #2

Hi,

Setting environment variables is platform- and even shell-specific. Assuming you are on linux with a bash like shell, you can set the variable when you start the notebook:

BOKEH_NODEJS_PATH="path/to/node" ipython notebook

or to set it permanently for a shell session use export:

export BOKEH_NODEJS_PATH="path/to/node"

If you are one a different shell you will have to do a web search since I am only immediately familiar with Bash-like shells.

That said, it still seems like the most likely explanation is that somehow the notebook is installed and running out of a different conda environment, one that does not have node installed.

Thanks,

Bryan

···

On Mar 26, 2019, at 12:44 AM, NumesSanguis <numessanguis@gmail.com> wrote:

Hello,

I'm trying to get the spectrogram example (https://github.com/bokeh/bokeh/tree/master/examples/app/spectrogram\) to work in Jupyter Notebook on Ubuntu 18.04. It works for me in the terminal, but not when executing the Python code in a Notebook using the same conda environment.

The following code will result in a: `RuntimeError: node.js v6.10.0 or higher is needed to allow compilation of custom models ("conda install nodejs" or follow https://nodejs.org/en/download/\)`
from bokeh.io import output_notebook, show
from bokeh.core.properties import Color, Float, Int, Override, Seq
from bokeh.models import Renderer

class WaterfallRenderer(Renderer):
__implementation__ = "waterfall.ts"

output_notebook()

See for all details this GitHub issue: Bokeh v1.1.0dev11 WaterfallRenderer (spectrogram example) RuntimeError in notebook (.ts not supported?) · Issue #8790 · bokeh/bokeh · GitHub

Based on the comments I tried the following:
!node --version
# /bin/sh: 1: node: not found

So indeed it cannot find NodeJS.
In the GitHub issue it was suggested to set `BOKEH_NODEJS_PATH`. However, how do I do this?
I have found a node installation here: /home/*username*/anaconda3/envs/bokeh/bin

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NumesSanguisMar 27, 2019 #3

Hi,

I’ve identified the issue!

My kernel were both the same in the terminal and Jupyter Notebook, but I executed jupyter notebook in a terminal without the environment activated.

Both of these worked:

BOKEH_NODEJS_PATH=“/home/user/anaconda3/envs/bokeh/bin/node” ipython notebook
export BOKEH_NODEJS_PATH=“/home/user/anaconda3/envs/bokeh/bin/node”

At this point, BOKEH could use Node, but it was still not in the environment? Because the output was still:

!node --version

/bin/sh: 1: node: not found

!which node

empty

Also I got:

from bokeh.util.compiler import nodejs_version, npmjs_version

print(“node.js version : %s” % nodejs_version())

node.js version : v10.13.0

print(“npm version : %s” % npmjs_version())

npm version : None

Executing the following code with BOKEH_NODEJS_PATH set, just executing jupyter notebook and in terminal (with env active) all gave:

import sys
sys.executable

‘/home/user/anaconda3/envs/speechmod/bin/python’

So the Python kernel was from the same conda environment with everything I tried.

Conclusion

Even while the kernel that is used to execute Python code is the same, the environment is not if Jupyter Notebook is not called from the active conda environment matching the kernel.

Note: I don’t have Node installed in a conda environment (or system itself) besides speechmod.

Next up: Getting the Spectrogram example to work in a Jupyter Notebook.

···

On Wednesday, 27 March 2019 08:52:32 UTC+9, Bryan Van de ven wrote:

Hi,

Setting environment variables is platform- and even shell-specific. Assuming you are on linux with a bash like shell, you can set the variable when you start the notebook:
    BOKEH_NODEJS_PATH="path/to/node" ipython notebook
or to set it permanently for a shell session use export:
    export BOKEH_NODEJS_PATH="path/to/node"
If you are one a different shell you will have to do a web search since I am only immediately familiar with Bash-like shells.

That said, it still seems like the most likely explanation is that somehow the notebook is installed and running out of a different conda environment, one that does not have node installed.

Thanks,

Bryan

On Mar 26, 2019, at 12:44 AM, NumesSanguis numess...@gmail.com wrote:

Hello,

I’m trying to get the spectrogram example (https://github.com/bokeh/bokeh/tree/master/examples/app/spectrogram) to work in Jupyter Notebook on Ubuntu 18.04. It works for me in the terminal, but not when executing the Python code in a Notebook using the same conda environment.

The following code will result in a: RuntimeError: node.js v6.10.0 or higher is needed to allow compilation of custom models ("conda install nodejs" or follow [https://nodejs.org/en/download/)](Node.js — Download Node.js®))

from bokeh.io import output_notebook, show

from bokeh.core.properties import Color, Float, Int, Override, Seq

from bokeh.models import Renderer

class WaterfallRenderer(Renderer):

implementation = “waterfall.ts”

output_notebook()

See for all details this GitHub issue: https://github.com/bokeh/bokeh/issues/8790

Based on the comments I tried the following:
!node --version

/bin/sh: 1: node: not found

So indeed it cannot find NodeJS.

In the GitHub issue it was suggested to set BOKEH_NODEJS_PATH. However, how do I do this?

I have found a node installation here: /home/username/anaconda3/envs/bokeh/bin

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systemJul 21, 2021 #4

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