thebioengineer/dockyard

Tools for building and working with docker containers in R

dockyard's Issues

Docker needs sudo on Unices

Hi, I found your package from the rockerverse paper. Nice work!

One thing though: running docker typically requires sudo on Unix-based OSes, including Linux and Mac. I'll make a PR for this.

> list_images()
WARNING: Error loading config file: /home/hongo/.docker/config.json: stat /home/hongo/.docker/config.json: permission denied
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/images/json: dial unix /var/run/docker.sock: connect: permission denied
Error in gregexpr(pattern = "\\s\\s\\w", header)[[1]] :
  subscript out of bounds
In addition: Warning message:
running command 'docker image ls ' had status 1

Namespace collisions: consider R6 instead of S3

Just as a matter of design: convenience functions like run, install, copy_from_url etc are good to have, but also highly generic. Because of this, there's a good chance that they will collide with exported functions in other packages. In fact update already collides with the function from stats.

Instead of S3, perhaps consider using R6 to define your dockerfile class. Then you can expose these functions as class methods without having to worry about namespace collisions.

How it would look:

shiny_dockerfile <- Dockerfile$
    new()$
    from("rocker/r-ver:devel")$
    update()$
    install("...")$
    ...

instead of magrittr pipes, you use method chaining, which is basically the same idea expressed in OOP syntax.