R kernel fails to start (stringi.so / libicui18n.so.58 not found)

[jburos]

What docker image you are using?

I am running jupyter/datascience-notebook

Output from docker images | grep datascience-notebook:

jupyter/datascience-notebook            latest                     0bd200f283cb        2 days ago          5.719 GB

What complete docker command do you run to launch the container (omitting sensitive values)?

docker run -d -p 8889:8888 --name jacki-datascience jupyter/datascience-notebook start-notebook.sh --NotebookApp.token=''

What steps do you take once the container is running to reproduce the issue?

1. Visit http://localhost:8889
2. Start a new R notebook
3. .. Wait ~ 3 seconds

What do you expect to happen?

I expect to see "connected" in the top right-hand corner. I also expect to be able to create and execute R code in cells in the notebook.

What actually happens?

I see the message (in status area): kernel starting .. please wait
I see the message (in status area): Connected

Then immediately it turns to Dead & I see a popup.

Finally the status reads No kernel & the popup is as follows:

The kernel has died, and the automatic restart has failed. It is possible the kernel cannot be restarted. If you are not able to restart the kernel, you will still be able to save the notebook, but running code will no longer work until the notebook is reopened.

At this point, my docker log reads as follows:

[I 19:42:25.745 NotebookApp] Kernel started: 083d4f7f-f13d-42bd-8530-6aab7e9a2834
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/opt/conda/lib/R/library/stringi/libs/stringi.so':
  libicui18n.so.58: cannot open shared object file: No such file or directory
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
[I 19:42:28.742 NotebookApp] KernelRestarter: restarting kernel (1/5)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/opt/conda/lib/R/library/stringi/libs/stringi.so':
  libicui18n.so.58: cannot open shared object file: No such file or directory
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
[I 19:42:31.753 NotebookApp] KernelRestarter: restarting kernel (2/5)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/opt/conda/lib/R/library/stringi/libs/stringi.so':
  libicui18n.so.58: cannot open shared object file: No such file or directory
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
[I 19:42:34.763 NotebookApp] KernelRestarter: restarting kernel (3/5)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/opt/conda/lib/R/library/stringi/libs/stringi.so':
  libicui18n.so.58: cannot open shared object file: No such file or directory
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
[W 19:42:35.785 NotebookApp] Timeout waiting for kernel_info reply from 083d4f7f-f13d-42bd-8530-6aab7e9a2834
[I 19:42:37.773 NotebookApp] KernelRestarter: restarting kernel (4/5)
kernel 083d4f7f-f13d-42bd-8530-6aab7e9a2834 restarted
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/opt/conda/lib/R/library/stringi/libs/stringi.so':
  libicui18n.so.58: cannot open shared object file: No such file or directory
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
[W 19:42:40.786 NotebookApp] KernelRestarter: restart failed
[W 19:42:40.786 NotebookApp] Kernel 083d4f7f-f13d-42bd-8530-6aab7e9a2834 died, removing from map.
kernel 083d4f7f-f13d-42bd-8530-6aab7e9a2834 restarted failed!
[W 19:42:40.858 NotebookApp] 410 DELETE /api/sessions/395a52bf-c697-40e6-8eb5-2575e49c5979 (172.17.0.1): Kernel deleted before session
[W 19:42:40.858 NotebookApp] Kernel deleted before session
[W 19:42:40.859 NotebookApp] 410 DELETE /api/sessions/395a52bf-c697-40e6-8eb5-2575e49c5979 (172.17.0.1) 3.84ms referer=http://localhost:8889/notebooks/work/Untitled.ipynb?kernel_name=ir

And, if I try to confirm the status of the docker image:

burosj01@demeter-csmaz11-18:~/projects/rcc-analyses3/docker$ docker pull jupyter/datascience-notebook
Using default tag: latest
latest: Pulling from jupyter/datascience-notebook
Digest: sha256:3cfab0d1ab6ab927e5961db18f056cb3417c8e229c9778ffe6101977430a54fa
Status: Image is up to date for jupyter/datascience-notebook:latest

Some intermediate googling around led to the following related conda issues:

• Unable to load R kernel in Jupyter notebook ContinuumIO/anaconda-issues#1133 & specifically Unable to load R kernel in Jupyter notebook ContinuumIO/anaconda-issues#1133 (comment)

[maximz]

I was able to reproduce this on my machine following those instructions.

[parente]

Regression in the latest build. I believe all of the R packages are now coming from conda-forge, however.

[parente]

Possibly fixed by #499.

[parente]

@jburos Can you try pulling the latest r-notebook and see if @minrk's fix has resolved the problem?

[jburos]

@parente Looking into this now

[jburos]

@parente Yes, I can confirm that this works using the latest images.

I have tested on:

• jupyter/r-notebook
• jupyter/datascience-notebook

Here's the clean log:

Execute the command: jupyter notebook --NotebookApp.token=
[I 19:28:15.376 NotebookApp] Writing notebook server cookie secret to /home/jovyan/.local/share/jupyter/runtime/notebook_cookie_secret
[W 19:28:16.290 NotebookApp] WARNING: The notebook server is listening on all IP addresses and not using encryption. This is not recommended.
[W 19:28:16.290 NotebookApp] WARNING: The notebook server is listening on all IP addresses and not using authentication. This is highly insecure and not recommended.
[I 19:28:16.351 NotebookApp] JupyterLab alpha preview extension loaded from /opt/conda/lib/python3.6/site-packages/jupyterlab
[I 19:28:16.377 NotebookApp] Serving notebooks from local directory: /home/jovyan
[I 19:28:16.377 NotebookApp] 0 active kernels
[I 19:28:16.377 NotebookApp] The Jupyter Notebook is running at:
[I 19:28:16.377 NotebookApp] http://[all ip addresses on your system]:8888/
[I 19:28:16.377 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[I 19:28:25.343 NotebookApp] Creating new notebook in
[I 19:28:25.478 NotebookApp] Writing notebook-signing key to /home/jovyan/.local/share/jupyter/notebook_secret
[I 19:28:26.541 NotebookApp] Kernel started: 0cf290cb-b991-4492-89e1-0d5fce0ca30f
[I 19:28:27.811 NotebookApp] Adapting to protocol v5.0 for kernel 0cf290cb-b991-4492-89e1-0d5fce0ca30f
[I 19:28:40.454 NotebookApp] Creating new notebook in
[I 19:28:41.831 NotebookApp] Kernel started: 650d4c0e-4ec9-4f71-b39b-95dcecadf5fa
[I 19:28:43.041 NotebookApp] Adapting to protocol v5.1 for kernel 650d4c0e-4ec9-4f71-b39b-95dcecadf5fa

🙏 for your help & the rapid turnaround.

[parente]

Passing the 🙏 thanks on to @minrk and closing this out. Cheers!