rPackages: mark packages as broken when generating package sets

The current behaviour for generate-r-packages.R is to delete
packages that have been remove upstream. This patch changes the
behaviour to mark packages as broken rather than removing them.
This has the advantage of never breaking expressions, which
previously occured when a package with overrides in default.nix
was deleted. As a result, the update procedure is simplified,
allowing automated updates to the package tree to run, and
additionally if a package is re-established upstream the previous
overrides still exist.

2021-09-24 21:25:53 +10:00

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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:

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

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.

3.0 KiB Raw Blame History

R

Installation

RStudio

Updating the package set

3.0 KiB

Raw Blame History