Thanks for reaching out.
Hi,
In a bit for reproducible/revisitable data analysis I have been
operating as follows for a while (first with docker, now with podman):
1) Get the bioconductor-provided image providing an RStudio Server
installation and all OS-level libraries potentially required to install
any R packages from CRAN & bioconductor:
> podman pull docker.io/bioconductor/bioconductor_docker
2) Work:
2.a) > podman run -d -p 127.0.0.1:8787:8787 -v /tmp:/tmp -e ROOT=TRUE
-e DISABLE_AUTH=TRUE docker.io/bioconductor/bioconductor_docker
2.b) open browser, log onto 127.0.0.1:8787 and analyze data using
RStudio/bioconductor, etc.
3) After finishing: (attempt to) save the entire toolchain:
3.a) > podman commit <CONTAINER ID> <PIRVATEREGISTRY/PROJECTID:latest>
3.b) > podman push <PIRVATEREGISTRY/PROJECTID:latest>
This has served me extremely well. In my field people frequently come
back with minor adaptation requests YEARS after the original analysis
(usually plotting prior to publication) and I can just pull the image
and provide them with those edits in the context of EXACTLY the same
tool chain irrespective of where Linux, Libraries, R, R packages, my
own in house code etc. meanwhile has moved.
Recently, however, I have had issues with not being able to connect to
the RStudio server in containers from images retrieved from our private
registry. The container will start fine, but No matter what I do, no
RStudio ever starts/is accessible and I have not succeeded in debugging
this behavior.
When going through step 3.a) today, I noted the following warnings and
was wondering whether I may have overlooked them and they might be at
the base of my issues to access RStudio after a comitt/push/pull cycle:
> podman push WARN[0024] archive: skipping
> "/home/user/.local/share/containers/storage/overlay/a1785f29a13373408
> 1f82f42b53ba8e20a7b0e2d8d2fd3cdc69303d4c681aa96/merged/run/rstudio-
> server/rstudio-rserver/session-server-rpc.socket" since it is a
> socket
> WARN[0024] archive: skipping
> "/home/user/.local/share/containers/storage/overlay/a1785f29a13373408
> 1f82f42b53ba8e20a7b0e2d8d2fd3cdc69303d4c681aa96/merged/run/rstudio-
> server/rstudio-rsession/rstudio-d" since it is a socket
Is this likely at the basis of my woes and how might it be fixed?
I would be surprised if that was the source of your problem. Sockets are ignored when creating images as they are tied to the current kernel. They'll be created on access.
Any chance you can get logs from RStudio? Did you try running a specific tag of the image (e.g., RELEASE_3_15). Maybe the "latest" tag is currently broken?
Kind regards,
Valentin
Sincerely, Joh
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