Keep system library clean

[hturner]

Currently the Dockerfile installs the languageserver package in the system library: https://github.com/r-devel/r-dev-env/blob/dev-container/Dockerfile#L18

On Slack I suggested that we manage without the languageserver package to avoid any conflict with base packages or any behaviour that is not reproducible with vanilla R. On reflection, I think it is okay to have it installed as people can always choose to use vanilla R by starting R in the bash terminal.

However, we should install the languageserver package into a separate library from the main system library. Otherwise when we rebuild R and overwrite the system install of R this means we have R 4.4 in the system, but still a lot of packages built under R 4.1 in the system library. We might do this by running some R code once the container has started. There are some pointers here: https://jozef.io/r300-language-server-setup/. I am not sure we will want to use their languageserversetup package directly as we will want to incorporate this in the container set up/start up, but I think we want to follow their general approach (maybe look inside their functions to see what the code does).

[hturner]

Thinking some more, a separate library doesn't completely solve the issue as the package build should match the R version. So we would need to at least reinstall languageserver when we build R-devel for the first time and the package or its dependencies may need rebuilding when R-devel is re-built, depending what people modify in base R. This could get messy as it won't be handled by make and slow down iterative development. So let's try not using languageserver at all and see how we get on.

[hturner]

I've had a closer look at the R extension settings (https://github.com/REditorSupport/vscode-R/wiki/Extension-settings) and it actually allows us to define two versions of R: r.rpath.linux for running background processes and r.rterm.linux for using in R terminals. I think this solves our issue here: we can set r.rpath.linux to a stable version of R, with languageserver installed and then set r.rterm.linux to the version that we have built (either relying on the PATH or by editing the settings.json file, see also discussion #50).

[jamestripp]

@StarTrooper08 These options can be changed in the container.dev file (for example, see 877bfd6 ). It might be cleaner to make the modifications in the 25-keep-system-library-clean branch and then merge these using a PR request. Thanks!

[jamestripp]

@StarTrooper08 , thanks for fixing this in 412b31d and suggesting I look at the change.

I had not realised that the user is now unable to open R via the R plugin (either via the not attached button at the bottom toolbar or via the command pallette). This could be disorientating for the user so I suggest we leave this issue open and discuss this as a group.

One possible workaround is to syslink the R version in the OS to the new path. The command can be run after the devcontainer starts (or within the image itself)

mkdir -p /workspaces/r-dev-env/bin/R/bin/ && ln -s /usr/bin/R /workspaces/r-dev-env/bin/R/bin/R

[hturner]

Fixed in #68: can now build R and switch to it before opening a new terminal. Only the default version of R has languageserver installed so the built R has a clean library, but it is still possible to use basic VS code/R extension interactions, e.g. sending code from .R files to the R terminal with Ctrl/Cmd + Enter.