rstudio's wrapper breaks loading of .Rprofile and use of R_USER_PROFILE

[unode]

Describe the bug A common mechanism to configure R is to create a .Rprofile file in the current directory, globally in ~/.Rprofile or setting the environment variable R_USER_PROFILE. The current rstudio wrapper makes use of the R_USER_PROFILE environment variable to inject additional paths via R's .libPaths(). However, once R_USER_PROFILE is defined in the environment, R no longer checks for either of the two .Rprofile locations mentioned (as can be read here). The fact that the wrapper uses R_USER_PROFILE also prevents the user from relying on it to customize the session.

To Reproduce Steps to reproduce the behavior:

1. nix-env -iA rstudio
2. create ~/.Rprofile containing cat("Hello from .Rprofile").
3. If the file is sourced, the message should be printed in the R console

Expected behavior The file specified by the user in R_USER_PROFILE should be read or alternatively, .Rprofile files should be read in the above mentioned locations.

Additional context

1. If the user has R_USER_PROFILE set in their environment, the wrapper should detect this and concatenate file specified by the user with the content of the fix_libs.R file (into a temporary file?) and set R_USER_PROFILE to this new location.
2. If the user doesn't have R_USER_PROFILE set, the wrapper should replicate R's behaviour and source .Rprofile as described here.

Notify maintainers @ehmry @changlinli @ciil

Metadata

 - system: `"x86_64-linux"`
 - host os: `Linux 5.4.28, NixOS, 19.09.git.4284573 (Loris)`
 - multi-user?: `yes`
 - sandbox: `yes`
 - version: `nix-env (Nix) 2.3.3`
 - channels(root): `"nixos-20.09pre217261.a2e06fc3423"`
 - nixpkgs: `/var/nixpkgs-channels/nixos`

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[unode]

This is still an issue

[stale[bot]]

I marked this as stale due to inactivity. → More info

[18kimn]

I'd also like to know how to solve this! Thank you!

The relevant file appears to be https://github.com/NixOS/nixpkgs/blob/nixos-22.11/pkgs/development/r-modules/wrapper-rstudio.nix, and the environment variable (I believe?) is R_PROFILE_USER not R_PROFILE_USER

[18kimn]

Ah, anyone else who deals with this issue may be able to solve this by setting R_PROFILE instead of R_PROFILE_USER. Doesn't work for everyone, though

For instance, here's my flake.nix for one of my projects:

  outputs = { self, nixpkgs, utils } :
    utils.lib.eachDefaultSystem (system:
        let pkgs = import nixpkgs {
            inherit system; 
            overlays = [(self: super: {
                    customRstudio = super.rstudioWrapper.override {
                        packages = [super.rPackages.renv];
                    };
                })
            ];};
      in {
        devShell = (pkgs.buildFHSUserEnv {
                    name = "renv-compatible nix";
          targetPkgs = pkgs:
            (with pkgs; [
                            binutils
                            curl.dev
                            gcc
                            libgit2
                            /* Needed for various R dependencies */
                            libssh
                            libpng
                            gdal
                            geos
                            freetype.dev
                            proj.dev
                            libxml2.dev
                            openssl.dev
                            sqlite.dev
                            pandoc
                            zlib.dev
                            unixODBC
                            libmysqlclient.dev
                            udunits
                            pkg-config
                            /* Needed for basic R setup */ 
                            R
                            rPackages.renv
                            customRstudio
                            ]);
                            runScript = "bash";
                            profile = ''
                                export R_PROFILE=${builtins.toString ./.}/.Rprofile
                                '';
                    }).env;
      });
}