title | titleSuffix | description | author | ms.author | ms.topic | ms.service | ms.subservice | ms.date | ms.custom |
---|---|---|---|---|---|---|---|---|---|
Known issue - Compute instance | Jupyter R Kernel doesn't start in new compute instance images |
Azure Machine Learning |
When trying to launch an R kernel in JupyterLab or a notebook in a new compute instance, the kernel fails to start |
s-polly |
scottpolly |
troubleshooting |
machine-learning |
core |
08/14/2023 |
known-issue |
[!INCLUDE dev v2]
When trying to launch an R kernel in JupyterLab or a notebook in a new compute instance, the kernel fails to start with Error: .onLoad failed in loadNamespace()
.
Status: Open
Problem area: Compute
After creating a new compute instance, try to launch R kernel in JupyterLab or a Jupyter notebook. The kernel fails to launch. You'll see the following messages in the Jupyter logs:
Aug 01 14:18:48 august-compute2Q6DP2A jupyter[11568]: Error: .onLoad failed in loadNamespace() for 'pbdZMQ', details:
Aug 01 14:18:48 august-compute2Q6DP2A jupyter[11568]: call: dyn.load(file, DLLpath = DLLpath, ...)
Aug 01 14:18:48 august-compute2Q6DP2A jupyter[11568]: error: unable to load shared object '/usr/local/lib/R/site-library/pbdZMQ/libs/pbdZMQ.so':
Aug 01 14:18:48 august-compute2Q6DP2A jupyter[11568]: libzmq.so.5: cannot open shared object file: No such file or directory
Aug 01 14:18:48 august-compute2Q6DP2A jupyter[11568]: Execution halted
To work around this issue, run this code in the compute instance terminal:
jupyter kernelspec list
sudo rm -r <path/to/kernel/directory>
conda create -n r -y -c conda-forge r-irkernel jupyter_client
conda run -n r bash -c 'Rscript <(echo "IRkernel::installspec()")'
jupyter kernelspec list