RStudio not starting: "404 : Not Found .. You are requesting a page that does not exist!"

RenkuLab
1

I’m having trouble setting up a Docker environment that still allows RStudio to run. The JupyterLab part seems still fine.

Basically, I have 2 renkulab projects that are almost identical … one has an extra few lines in the Dockerfile to compile a piece of software from source:

# install packages manually 
RUN wget -O /tmp/samtools-1.11.tar.bz2 https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2
RUN tar xvfj /tmp/samtools-1.11.tar.bz2 --directory=/tmp && /bin/rm /tmp/samtools-1.11.tar.bz2
WORKDIR "/tmp/samtools-1.11"
RUN ./configure --prefix=/opt/sw && make && make install && /bin/rm -r /tmp/samtools-1.11

… and this somehow messes up the ability of RStudio to start/be seen.

The two projects are this:
Reproducible Data Science | Open Research | Renku (with the extra lines)
Reproducible Data Science | Open Research | Renku (extra lines commented out)
… in either case, the Docker images build fine.

From scanning the logs of the 2 sessions, I’ve somewhat narrowed it down to a version conflict between nbconvert or mistune, but I so far have not been able to find a workaround. Here some details …

2022-11-06T09:33:30.302221522Z [W 09:33:30.298 NotebookApp] Error loading server extension jupyter_server_proxy 
2022-11-06T09:33:30.302275428Z Traceback (most recent call last): 
2022-11-06T09:33:30.302288375Z File "/opt/conda/lib/python3.9/site-packages/notebook/notebookapp.py", line 2028, in init_server_extensions 
2022-11-06T09:33:30.302300419Z func(self) 
2022-11-06T09:33:30.302310306Z File "/opt/conda/lib/python3.9/site-packages/jupyter_server_proxy/__init__.py", line 30, in _load_jupyter_server_extension

2022-11-06T09:33:30.302413546Z raise VersionConflict(dist, req).with_context(dependent_req) 
2022-11-06T09:33:30.302425091Z pkg_resources.ContextualVersionConflict: (mistune 0.8.4 (/opt/conda/lib/python3.9/site-packages), Requirement.parse('mistune<3,>=2.0.3'), {'nbconvert'})

Can anyone suggest a solution?

Thanks in advance, Mark

2

We solved this off-line, but I wanted to document the solution here in case someone else comes across it. There seemed to be two problems:

  1. the user was set to root for installation of system packages, but not set back to NB_USER afterwards, which meant that packages were likely installed in the wrong environment
  2. the WORKDIR was not reset to /home/rstudio

After these changes were made, we were able to start an RStudio session normally :crossed_fingers: