Renku base R upgrade causes Jupyter 404 error

I renku team,

I recently upgraded the R base image of a project (4.0 to 4.2.0), and installed the 3.16 version of bioconductor (though I doubt that would be the issue). Everyting installed just fine, I can launch sessions, but when connecting, I get “404 : Not Found You are requesting a page that does not exist!” from Jupyter. Any idea how to solve that issue ?

I suspect it may be because I’m forcing the use of Renku v. 1.6.0 through


in the dockerfile, but I’m not sure.

Thanks in advance for your help !

Cyril Pulver

Hi @bopekno are you using the renku/renkulab-r:4.2.0-0.15.0 image? If so, please revert to 0.14.0 for the time being, there is an incompatibility with the latest jupyter that we are working to resolve, which unfortunately went undetected until we tagged the new images.

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It looks like renku/renkulab-r:4.2.0-0.14.0 is based on R 4.3, not 4.2…

I’d need 4.2 due to the bioconductor version, trying to downgrade to 0.13.0

> BiocManager::install(version = BIOCONDUCTOR_VERSION, update = TRUE, ask = FALSE, quiet = TRUE) Error: Bioconductor version '3.16' requires R version '4.2'; use BiocManager::install(version = ‘3.17’) with R version 4.3; see Execution halted The command '/bin/bash -c -o pipefail R -f /tmp/install.R' returned a non-zero code: 1 Cleaning up project directory and file based variables 00:02 ERROR: Job failed: exit code 1

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Indeed something is weird with that image. In any case, if the base image for bioconductor 3.16 exists, I will add that to our build matrix so you don’t have to install it on top of a plain R image.

In the meantime, I just opened a PR to fix the issue you encountered - this is the resulting R 4.2 image: renku/renkulab-r:4.2.0-d9f45b5. Not fully vetted yet, but you can give it a shot :slight_smile:

I tried using the latest renku-bioc 3.16 image ( renku/renkulab-bioc:RELEASE_3_16-e4bbebc), the 404 error is back again…

The images with a commit sha in the tag should not be considered stable - they might be pushed from a branch that does not have all the changes incorporated etc. You should try the ones tagged with 0.15.1, that’s what we just pushed yesterday and it should have the correct behavior. So in this case it would be renku/renkulab-bioc:RELEASE_3_16-0.15.1.

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Using this stable image, I can’t launch notebooks (either R or python)


@bopekno I am not exactly sure what you are trying to do.

If I create an empty file and give it a .ipynb extension then that does not work anywhere. But if I go through jupyterlab, create a new notebook through File->New->Notebook then that notebook works fine in jupyterlab.

In rstudio I do not see any way through the Menus to create a jupyter notebook. Also when I create a valid notebook through the jupyter interface and then open this in Rstudio all I see in Rstudio is the json contents of the notebook - not the actual notebook.

And this behaviour seems to be there in our older images too.

But perhaps I am missing something and your experience with older or different images was different and better?


It seems like all notebooks operations are broken, I can’t duplicate, rename, create or open existing notebooks. It’s the first time I’ve encountered that issue with renku. Any idea what may be causing the issue ?

e.g trying to open an existing notebook by double clicking on the .ipynb file:

@bopekno you are trying to do these things from the jupyterlab interface, that looks like this?

yes, for example

Also do you see anything more about the error other than that modal that you posted? It seems like there is some text related to the error in the background of the modal - perhaps in the terminal? Or is this unrelated?

I’ve also seen some strange jupyterlab errors when trying an image with a new jupyter version. Could you restarting the browser and open a private browser window and try again?

It’s unrelated to the statusbar of the terminal, which was just caused by an untracked text file in git.

I’ve found that thread about these types of error, and how to get a log, but I dont know where the corresponing dir is in the renku dir architecture. python - IPython Notebook error: Error loading notebook - Stack Overflow

I did that, cleared the cache and cookies. The private window does not help:

@bopekno I think this is potentially the result of some incompatibilities between jupyter or notebook versions.

Can you run jupyter --version in a terminal in your session where you see the problems and post the output here.

jupyter --version
Selected Jupyter core packages…
IPython : 8.11.0
ipykernel : 6.21.3
ipywidgets : not installed
jupyter_client : 8.0.3
jupyter_core : 5.3.0
jupyter_server : 2.5.0
jupyterlab : 3.6.1
nbclient : 0.7.2
nbconvert : 7.2.9
nbformat : 5.7.3
notebook : 6.5.3
qtconsole : not installed
traitlets : 5.9.0

any chance you can share the project? or push a version that reproduces the problem to one that we could access? I can’t reproduce this using the 0.15.1 bioc image

Sure thing, I’ve changed the visibility to public: Reproducible Data Science | Open Research | Renku