[Tutorial/Workflow/Doc] arf: Alternative R Frontend

[TinasheMTapera]

🧾 Summary

We should use arf as the R interpreter

🎯 Learning Goals / Outcomes

What should a reader understand or be able to do after following this tutorial/workflow?

• Install cargo as the rust package manager
• Install arf as the R interpreter
• Goal 3

📦 Required Tools, Packages, or Data

List any software packages, datasets, or computing platforms used (e.g., R, Python, FASRC, GeoPandas, etc.).

• Tools: https://doc.rust-lang.org/cargo/getting-started/installation.html curl https://sh.rustup.rs -sSf | sh
• Libraries:
• Data source(s):

📄 Outline / Structure

Provide a brief outline of the sections or steps in the document:

1. Introduction
2. Setup
3. Key Steps
4. Conclusion / Next Steps

🔗 Related Materials

Link to related GitHub repos, issues, lab protocols, or previous examples:

• example-link-1
• example-link-2

🚦Status & Next Steps

What is the current status?

• Proposal
• In Progress
• Ready for Review
• Completed

Any notes on who will write or review the content?

[TinasheMTapera]

Installing cargo requires rust. The reason we have to do this is because the system glib C is too old to build arf from binary. So we built cargo from binary (which is great coz it allows us to install all other rust tools like uv) but this takes a while, at least 30 mins on login:

(base) [ttapera@holylogin06 ~]$ curl https://sh.rustup.rs -sSf | sh
info: downloading installer
warn: It looks like you have an existing rustup settings file at:
warn: /n/home03/ttapera/.rustup/settings.toml
warn: Rustup will install the default toolchain as specified in the settings file,
warn: instead of the one inferred from the default host triple.

Welcome to Rust!

This will download and install the official compiler for the Rust
programming language, and its package manager, Cargo.

Rustup metadata and toolchains will be installed into the Rustup
home directory, located at:

  /n/home03/ttapera/.rustup

This can be modified with the RUSTUP_HOME environment variable.

The Cargo home directory is located at:

  /n/home03/ttapera/.cargo

This can be modified with the CARGO_HOME environment variable.

The cargo, rustc, rustup and other commands will be added to
Cargo's bin directory, located at:

  /n/home03/ttapera/.cargo/bin

This path will then be added to your PATH environment variable by
modifying the profile files located at:

  /n/home03/ttapera/.profile
  /n/home03/ttapera/.bash_profile
  /n/home03/ttapera/.bashrc
  /n/home03/ttapera/.zshenv
  /n/home03/ttapera/.tcshrc

You can uninstall at any time with rustup self uninstall and
these changes will be reverted.

Current installation options:


   default host triple: x86_64-unknown-linux-gnu
     default toolchain: stable (default)
               profile: default
  modify PATH variable: yes

1) Proceed with standard installation (default - just press enter)
2) Customize installation
3) Cancel installation
>

info: profile set to default
info: default host triple is x86_64-unknown-linux-gnu
info: syncing channel updates for stable-x86_64-unknown-linux-gnu
info: latest update on 2026-04-16 for version 1.95.0 (59807616e 2026-04-14)
info: downloading 6 components
        cargo installed                       10.48 MiB
       clippy installed                        4.48 MiB
    rust-docs unpacking   [####           ]   21.18 MiB (58.79 KiB/s, ETA: 5m)
     rust-std pending installation            28.20 MiB
    rust-docs installed                       21.18 MiB
     rust-std installed                       28.20 MiB
        rustc installed                       76.63 MiB
      rustfmt installed                        2.06 MiB                                                                                       info: default toolchain set to stable-x86_64-unknown-linux-gnu

  stable-x86_64-unknown-linux-gnu installed - rustc 1.95.0 (59807616e 2026-04-14)


Rust is installed now. Great!

To get started you may need to restart your current shell.
This would reload your PATH environment variable to include
Cargo's bin directory ($HOME/.cargo/bin).

To configure your current shell, you need to source
the corresponding env file under $HOME/.cargo.

This is usually done by running one of the following (note the leading DOT):
. "$HOME/.cargo/env"            # For sh/bash/zsh/ash/dash/pdksh
source "$HOME/.cargo/env.fish"  # For fish
source "~/.cargo/env.nu"  # For nushell
source "$HOME/.cargo/env.tcsh"  # For tcsh
. "$HOME/.cargo/env.ps1"        # For pwsh
source "$HOME/.cargo/env.xsh"   # For xonsh

Then finally install arf, also takes a while but works:

cargo install --git https://github.com/eitsupi/arf.git

  Installing /n/home03/ttapera/.cargo/bin/arf
   Installed package `arf-console v0.3.0 (https://github.com/eitsupi/arf.git#4f71ca91)` (executable `arf`)
(base) [ttapera@holylogin06 ~]$ 
(base) [ttapera@holylogin06 ~]$ which arf
~/.cargo/bin/arf