s6-mkfifo Error

[AndrewSkelton]

Hi,

After slimming my image, when I try to start it up, I get the following error:

s6-mkfifo: fatal: unable to mkfifo /var/run/s6/services/s6-fdholderd/supervise/control: No such file or directory

Any suggestions on a way to resolve this?

To reproduce:

docker pull bioconductor/bioconductor_docker:devel
./docker-slim build bioconductor/bioconductor_docker:devel
docker run \                                                                                            
        -e PASSWORD=bioc \
        -p 8787:8787 \
        bioconductor/bioconductor_docker.slim
# s6-mkfifo: fatal: unable to mkfifo /var/run/s6/services/s6-fdholderd/supervise/control: No such file or directory

[kcq]

adding a few links for context...

The container image info:

• https://hub.docker.com/r/bioconductor/bioconductor_docker
• https://github.com/Bioconductor/bioconductor_docker
• https://github.com/Bioconductor/bioconductor_docker/blob/master/Dockerfile - the Dockerfile for the image

[kcq]

Looks like there's a lot of stuff in that image and it's more like a base image and an IDE rolled into one :-) This means that they'll be lots of extra packages there intentionally because it's meant to be used as a tool to build new applications...

The error itself is probably related to the s6-overlay init system and how it's designed. Need to investigate more...

[AndrewSkelton]

Interestingly, (and something I should have included in the original post) is that /var/run/s6/services/s6-fdholderd/supervise/control doesn't seem to exist when starting the un-slimmed image with bash, but could be something that is created when starting the web service to serve the IDE.

This image is built from rocker/rstudio:4.0.2, which stems from debian:buster. Essentially contains the following:

• Base language R
• IDE RStudio which is served through a web interface (port 8787)
• Base set of packages (Bioconductor)

Happy to test any hypotheses, as the slimming procedure drastically reduces the size burden of this image, and makes it much more workable!