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Known issue - Jupyter R Kernel doesn't start in new compute instance images

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APPLIES TO: Azure CLI ml extension v2 (current) Python SDK azure-ai-ml v2 (current)

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

Symptoms

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

Solutions and workarounds

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

Next steps