r2modman is often associated with Windows game modding, but current releases also provide native Linux builds. That means Linux users generally do not need to run the Windows version of the manager through Wine.
The important part is choosing the package that fits the distribution. Debian and Ubuntu based systems can use the Debian package, Fedora-style systems have RPM builds, Arch users have their own options, and AppImage provides a portable route. Steam Deck and other immutable systems need slightly different treatment.
A second point that causes confusion is Proton. r2modman itself can run natively on Linux while the Windows version of the game still runs through Proton. Because those are separate layers, troubleshooting the manager and troubleshooting the modded game are not always the same problem.
If a game launches normally but none of the installed mods appear, check how it was started. Launching directly from Steam may not use the profile arguments r2modman normally supplies. The manager's Help screen can provide the launch arguments for the active profile.
Another common mistake is copying launch commands from an old tutorial. These can become outdated as the manager and loaders change. It is safer to use the arguments generated by the copy of r2modman actually installed on the machine.
For a more detailed breakdown of packages, Proton behaviour, Steam Deck differences and common launch problems, see this guide to r2modman on Linux.
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