WIP: Build from an R base image

[cookpa]

Replaces the old Ubuntu docker file with one based on the rocker project image. This has R pre-installed and avoids having to deal with installing custom keys. It makes it easier to get a specific R version and have some dependencies (eg, devtools) pre-installed.

This is a WIP, it builds with minimal dependencies

[cookpa]

@ntustison @stnava is there an updated list of recommended dependencies for full functionality? The list here

https://github.com/ANTsX/ANTsR/wiki/ANTsR-Dependencies-for-(close-to)-full-functionality

is from a couple of years ago. R CMD INSTALL doesn't install most dependencies, but I can install in the dockerfile via install.packages.

devtools tries to install all dependencies from the DESCRIPTION file, but I can't get devtools install to work (#377)

[ntustison]

That's a good question, @cookpa . Perhaps @stnava has more concrete knowledge (I certainly don't) but I'm guessing we might have to figure it out for the current set-up.

[stnava]

https://remotes.r-lib.org/reference/package_deps.html tool above might help ... the wiki list is probably not too far off ... brian

…

On Thu, May 11, 2023 at 12:26 PM Nick Tustison ***@***.***> wrote: That's a good question, @cookpa <https://github.com/cookpa> . Perhaps @stnava <https://github.com/stnava> has more concrete knowledge (I certainly don't) but I'm guessing we might have to figure it out for the current set-up. — Reply to this email directly, view it on GitHub <#384 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACPE7TWTUIQVMVICN3XDSDXFUHJXANCNFSM6AAAAAAX6KTCUE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[cookpa]

Thanks @stnava the remotes method works. I was trying to do something similar with pak but my mistake was not calling the "local" version.

BTW, pak also has local_system_requirements which will print out an apt command to install system dependencies. Quite useful on certain systems.

[cookpa]

ENH: Update docker file

Multiple improvements:

• Use rocker base image with R pre-installed, saves time and effort dealing with manual install
• Follow Dockerfile convention for placement of file, uses local source to build
• Switch to R CMD INSTALL, because devtools install is not working on recent versions