Problem with singularity/docker?

[ltosti]

Hi there,

I installed the package as recommended and I opted for singularity. When I run dynwrap::test_singularity_installation(detailed = TRUE), I get

✔ Singularity is installed
✔ Singularity is at correct version (>=3.0): 3.3.0-1 is installed
✔ Singularity can pull and run a container from Dockerhub
✔ Singularity can mount temporary volumes
✔ Singularity test successful ------------------------------------------------------------
[1] TRUE

However, when I run model <- infer_trajectory(dataset, ti_comp1()) as in the user guide I get now the following error

Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Get http://%2Fvar%2Frun%2Fdocker.sock/v1.40/version: dial unix /var/run/docker.sock: connect: permission denied
Error in processx::run("docker", c("images", paste0("--format=", format),  : 
  System command error

Any idea of what's happening?

[zouter]

Hi!

Most probably it's still trying to run docker, because it detects that it is installed. You can set the default container environment using babelwhale::set_default_config(create_singularity_config()).

Hope that helps :slightly_smiling_face:

[rlorenzc]

Hi!

I'm also actually trying to run this as well. When I do run: babelwhale::set_default_config(create_singularity_config()).

I get an error: Error in save(config, file = config_file, compress = "gz") : 'compress = "gz"' is invalid

Should this be "gzip" instead of "gz" like in the R base::save function?

[ltosti]

I had the same problem as @rlorenzc but we solved it by using dynwrap::set_default_config(dynwrap::create_singularity_config(cache_dir = ""),permanent = FALSE)

Hope this helps!

[whatever60]

@ltosti

Hi!

Most probably it's still trying to run docker, because it detects that it is installed. You can set the default container environment using babelwhale::set_default_config(create_singularity_config()).

Hope that helps 🙂

This should be put into a conspicuous place in the documentation.

[XMUwsa]

Hi there,

I installed the package as recommended and I opted for Docker. When I run dynwrap::test_docker_installation(detailed = TRUE), I get Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Get "http://%2Fvar%2Frun%2Fdocker.sock/v1.24/version": dial unix /var/run/docker.sock: connect: permission denied and Error in dynwrap::test_docker_installation(detailed = TRUE) : Hope for helps @zouter

[feanaros]

Same of @XMUwsa please help