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:

with import <nixpkgs> {};
{
  myProject = stdenv.mkDerivation {
    name = "myProject";
    version = "1";
    src = if 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

There is a script and associated environment for regenerating the package sets and synchronising the rPackages tree to the current CRAN and matching BIOC release. These scripts are found in the pkgs/development/r-modules directory and executed as follows:

nix-shell generate-shell.nix

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

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

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

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

generate-r-packages.R <repo> reads <repo>-packages.json, therefore the renaming.

The contents of a generated *-packages.json file will be used to create a package derivation for each R package listed in the file.

Some packages require overrides to specify external dependencies or other patches and special requirements. These overrides are specified in the pkgs/development/r-modules/default.nix file. As the *-packages.json contents are automatically generated it should not be edited and broken builds should be addressed using overrides.

3.7 KiB Raw Permalink Blame History

R

Installation

RStudio

Updating the package set

3.7 KiB

Raw Permalink Blame History