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nixpkgs/doc/languages-frameworks/r.section.md
Tikhon Jelvis 70cd2cb336 r-modules: update cran and bioc packages 
The last snapshot was 4 months ago (2020-08-19). I also found that I needed newer definitions when I was trying to fix the R arrow package.

This update required a couple of manual changes:

  1. Removing a few deleted packages from default.nix
  2. Renaming the "assert" package to "r_assert" in generate-r-packages.R because "assert" is a keyword in Nix
2021-01-02 15:03:06 -08:00

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R

Installation

Define an environment for R that contains all the libraries that you'd like to use by adding the following snippet to your $HOME/.config/nixpkgs/config.nix file:

{
    packageOverrides = super: let self = super.pkgs; in
    {

        rEnv = super.rWrapper.override {
            packages = with self.rPackages; [
                devtools
                ggplot2
                reshape2
                yaml
                optparse
                ];
        };
    };
}

Then you can use nix-env -f "<nixpkgs>" -iA rEnv to install it into your user profile. The set of available libraries can be discovered by running the command nix-env -f "<nixpkgs>" -qaP -A rPackages. The first column from that output is the name that has to be passed to rWrapper in the code snipped above.

However, if you'd like to add a file to your project source to make the environment available for other contributors, you can create a default.nix file like so:

let
  pkgs = import <nixpkgs> {};
  stdenv = pkgs.stdenv;
in with pkgs; {
  myProject = stdenv.mkDerivation {
    name = "myProject";
    version = "1";
    src = if pkgs.lib.inNixShell then null else nix;

    buildInputs = with rPackages; [
      R
      ggplot2
      knitr
    ];
  };
}

and then run nix-shell . to be dropped into a shell with those packages available.

RStudio

RStudio uses a standard set of packages and ignores any custom R environments or installed packages you may have. To create a custom environment, see rstudioWrapper, which functions similarly to rWrapper:

{
    packageOverrides = super: let self = super.pkgs; in
    {

        rstudioEnv = super.rstudioWrapper.override {
            packages = with self.rPackages; [
                dplyr
                ggplot2
                reshape2
                ];
        };
    };
}

Then like above, nix-env -f "<nixpkgs>" -iA rstudioEnv will install this into your user profile.

Alternatively, you can create a self-contained shell.nix without the need to modify any configuration files:

{ pkgs ? import <nixpkgs> {}
}:

pkgs.rstudioWrapper.override {
  packages = with pkgs.rPackages; [ dplyr ggplot2 reshape2 ];
}

Executing nix-shell will then drop you into an environment equivalent to the one above. If you need additional packages just add them to the list and re-enter the shell.

Updating the package set

nix-shell generate-shell.nix

Rscript generate-r-packages.R cran  > cran-packages.nix.new
mv cran-packages.nix.new cran-packages.nix

Rscript generate-r-packages.R bioc  > bioc-packages.nix.new
mv bioc-packages.nix.new bioc-packages.nix

Rscript generate-r-packages.R bioc-annotation > bioc-annotation-packages.nix.new
mv bioc-annotation-packages.nix.new bioc-annotation-packages.nix

Rscript generate-r-packages.R bioc-experiment > bioc-experiment-packages.nix.new
mv bioc-experiment-packages.nix.new bioc-experiment-packages.nix

generate-r-packages.R <repo> reads <repo>-packages.nix, therefor the renaming.

Testing if the Nix-expression could be evaluated

nix-build test-evaluation.nix --dry-run

If this exits fine, the expression is ok. If not, you have to edit default.nix