Issues with added on/committed to docker.io/bioconductor/bioconductor_docker images
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? Sincerely, Joh
Hi Joh, Thanks for reaching out. On Thu, Sep 1, 2022 at 4:08 PM Johannes Graumann via Podman < podman@lists.podman.io> wrote:
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 _______________________________________________ Podman mailing list -- podman@lists.podman.io To unsubscribe send an email to podman-leave@lists.podman.io
participants (2)
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Johannes Graumann -
Valentin Rothberg