IHaskell example has problem (MASS package missing)

[djsamperi]

Describe the bug The last graph in the demo tutorial-ihaskell-inline-r.ipynb fails (crashes the kernel). Running it directly using 'stack --nix exec R' shows that the MASS package is missing.

To Reproduce Just execute the ipynb file.

Expected behavior Executing the last cell should produce a graph.

Environment

• Ubuntu Linux 22.04
• HaskellR v1.0.0

Additional context The example works if run in the version of R that is not part of Nix, so Nix configuration seems to have a problem.

[idontgetoutmuch]

The above reminded me that when I use R with packages in nix, not only do I have to have a special R with the required nix package but I also have to set up various environment variables.

Something like

  R-with-my-packages = pkgs.rWrapper.override{
    packages = with pkgs.rPackages; [
      ggplot2
      ggridges
      outbreaks
      tidyverse
      (buildRPackage {
        name = "smcsamplers";
        src = pkgs.fetchFromGitHub {
          owner = "pierrejacob";
          repo = "smcsamplers";
          rev = "097192f7d5df520d9b026d442dfec493a3051374";
          sha256 = "00facn1ylcbai4sbcidpp991899csz2ppmmkv0khvqxfncddr0f2";
        };
        propagatedBuildInputs = [ coda MASS mvtnorm loo shape rstan tidyverse doParallel igraph ggraph doRNG reshape2 ];
    })
    ]; };

and

pkgs.stdenv.mkDerivation {
  name = "xxx";

  buildInputs = [
    pkgs.libintlOrEmpty
    R-with-my-packages
    pkgs.pandoc
    pkgs.cabal-install
    pkgs.inkscape
    pkgs.texlive.combined.scheme-full
    (pkgs.myHaskellPackages.ghcWithPackages haskellDeps)
  ];
  shellHook = ''
    R_LIBS_USER=$(Rscript -e ".libPaths()" | cut -c 6- | sed 's/[ \t]*$//' | sed 's/"//g' | sed -z 's/\n/:/g;s/:'''$/\n/' | sed 's/ //g')
    export R_LIBS_USER
    '';
}

but do not use my mess of sed - it worked for me on that occasion because something was 6 characters long.

If you don’t set this up then inline-r looks in the wrong place for R packages.

[ConnorBaker]

Thanks for the bug report!

I just made a VM on Ubuntu 20.04 and also got a missing package (in my case, ggplot). I'll see what I can do!

EDIT: I also tried stack --nix exec jupyter notebook from within nix-shell and the issue still occurs. I'll try @idontgetoutmuch's suggestion of modifying R_LIBS_USER next.

[djsamperi]

I found a fix (actually, I found this fix years ago). In shell.nix, add the following to buildInputs...

rPackages.MASS rPackages.ggplot2

[ConnorBaker]

@djsamperi can you verify that the example notebook runs without rPackages.MASS?

On Ubuntu 20.04, I was able to use

stack --nix exec -- jupyter nbconvert --to notebook --inplace --execute ./IHaskell/examples/tutorial-ihaskell-inline-r.ipynb

and the notebook ran successfully/regenerated the graphs (without need MASS).

I'll add rPackages.ggplot2 to the shell.nix file the example works.

[djsamperi]

You are probably correct, rPackages.MASS is not needed, as my notes on this do not include this. The MASS R package should be automatically installed.