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ANTsX / ANTsR

R interface to the ANTs biomedical image processing library
https://antsx.github.io/ANTsR
Apache License 2.0
127 stars 35 forks source link

WIP: Build from an R base image #384

Closed cookpa closed 1 year ago

cookpa commented 1 year ago

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 commented 1 year ago

@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 commented 1 year ago

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 commented 1 year ago

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 https://github.com/ANTsX/ANTsR/pull/384#issuecomment-1544300998, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACPE7TWTUIQVMVICN3XDSDXFUHJXANCNFSM6AAAAAAX6KTCUE . You are receiving this because you were mentioned.Message ID: @.***>

cookpa commented 1 year ago

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 commented 1 year ago

ENH: Update docker file

Multiple improvements: