Monthly - May, 2025 - Links and notes

Monthly Shaarli

All links of one month in a single page.

May, 2025

I just realized why my plays keep re-running roles when running a certain role.
It is because I have dutifully replicated the same parameters used in the play for each role in the dependencies list, which includes the tags parameter.

So when I call the play with --tags R, the R role (which is tagged eponymously) triggers, but also any role in the play which lists R in its dependencies, because I tagged the dependencies!

The solution is obvious and I am embarrassed it has taking me so long to realize: do not tag roles in the dependencies list!

ansible sysadmin Linux

A rudimentary direnv example with per-project R versions

Considered because I was trying to answer the question:

Can we use a different R version per directory/project?

With my R role it has been easy to maintain multiple different R versions on a server. But I have not really been able to pick-and-choose which R version to use with any particular project since there was only one version symlinked globally (/usr/local/bin/R -> ...).

Could we not set a different version locally, in a particular R project?

https://github.com/r-lib/rig - this would do it, but does much more than I want, would interfere with my Ansible role
https://www.monicathieu.com/posts/2024-05-21-multiple-r-versions.html
https://support.posit.co/hc/en-us/articles/200486138-Changing-R-versions-for-the-RStudio-Desktop-IDE - export RSTUDIO_WHICH_R=/usr/local/bin/R
https://github.com/vubiostat/Renv - good, but last commit 13 yrs ago
https://direnv.net - this probably fits the bill
https://github.com/hyperupcall/autoenv - similar to direnv but smaller in scope
https://github.com/jdx/mise - direnv, make and asdf all in one tool https://news.ycombinator.com/item?id=34583080
https://github.com/untitaker/quickenv - like direnv but less intrusive, more light-weight
https://asdf-vm.com
https://modules.sourceforge.net - Environment Modules, the OG in this space apt install modules
https://github.com/TACC/Lmod - LMod, this is what's used by UPPMAX

asdf

After reading about it a little, I get the feeling it would be more cumbersome than direnv.
I am not sure I understood correctly, but sounds like the R plugin actually wants to manage the
entire R installation (essentially what rig does).

https://github.com/asdf-vm/asdf
https://asdf-vm.com/guide/introduction.html
https://github.com/asdf-community/asdf-r - community plugin for R

direnv

I cannot find anyone talking about direnv with R on the web. Weird.

[So what I want] is a "shim" binary that dispatch to the desired binary
https://mise.jdx.dev/dev-tools/shims.html

The .envrc file is treated like a shell script, where you can also list arbitrary
shell commands that you want to be executed when you enter a project directory.
http://rednafi.com/misc/direnv/#why-envrc-file-and-not-just-a-plain-env-file

My direnv example

Machine in question is Ubuntu 22.04 x64.

$ apt install direnv
$ printf 'if hash direnv >/dev/null 2>&1; then\n   eval \"$(direnv hook bash)\"\nfi' >> ~/.bashrc

In the R project directory, I created a subdirectory bin (for convenience) and created a symlink to the R binary I wanted, naming it R. Also added this subdirectory to .gitignore (and .Rbuildignore if it's an R package).

In the package directory I created .envrc containing simply:

PATH_add bin

And enabled with direnv allow the first time I cd into the directory.
Now the R command defined in bin successfully overrides the system-wide command:

$ ls -l `which R`
lrwxrwxrwx 1 taha taha 18 maj  3 21:47 /media/bay/R/periodicdata/bin/R -> /opt/R/4.5.0/bin/R

Note that this works in the terminal. I am pretty sure we will need to do more to have IDEs such as RStudio Server or Codium Server take heed on a per-directory basis. Will investigate further as time permits.

Support for direnv in RStudio Server

In RStudio Server the built-in terminal behaves like any terminal and respects our direnv config, but the built-in "R Console" does not, and neither do the other built-in buttons, Knit, etc. So a lot of stuff will use the wrong R version. Unfortunately Posit still to this day lock their "multiple versions of R" functionality behind a "Pro" license, so that cannot help us.

I guess one (really ugly) work-around would be to run multiple RStudio Server instances, each with a different hard-coded R version: export RSTUDIO_WHICH_R=.... For R package development it's primarily R-release and R-devel that matters, so it's not unworkable. And I have been known to run multiple instances anyway (one per LXC container).

Support for direnv in VSCodium or Code Server

You must install the direnv extension.
In addition, I recommend you reset r.rpath.linux setting in the workspace to:

{ "settings": { "r.rpath.linux": "R" } }

because otherwise VSCodium will use the default R version during startup (before direnv takes effect) which causes lots of warnings about missing packages such as jsonlite or languageserver.

This works not only in code-server but also in VSCodium on the desktop (assuming you have installed direnv on the system) and when using VSCodium with the Remote SSH extension.

https://github.com/direnv/direnv/wiki/VSCode recommends https://open-vsx.org/extension/mkhl/direnv
https://github.com/direnv/direnv-vscode (source code of mkhl/direnv, also on https://codeberg.org/mkhl/vscode-direnv although slightly outdated compared to github)
https://github.com/cab404/vscode-direnv - another VSCode extension, but explicitly superseded by mkhl version above
https://mtlynch.io/notes/zig-vscode-nix
https://github.com/direnv/direnv/issues/231 https://marketplace.visualstudio.com/items?itemName=Rubymaniac.vscode-direnv
https://discourse.nixos.org/t/using-direnv-nix-shell-and-vscode/17225/10

direnv executes arbitrary shell scripts so this extension requires trusted workspaces