nixpkgs/pkgs/development/r-modules
Daiderd Jordan 5a02143c20
Merge pull request #33010 from LnL7/cacert-hook
cacert: add hook that sets SSL_CERT_FILE
2018-01-07 09:55:15 +01:00
..
patches rPackages: remove old cuda-related patches 2017-02-28 17:31:07 +03:00
bioc-annotation-packages.nix R: update package set 2017-08-31 21:59:06 +02:00
bioc-experiment-packages.nix R: update package set 2017-08-31 21:59:06 +02:00
bioc-packages.nix R: update package set 2017-08-31 21:59:06 +02:00
cran-packages.nix R: update package set 2017-12-01 13:48:26 +01:00
default.nix Merge pull request #33010 from LnL7/cacert-hook 2018-01-07 09:55:15 +01:00
generate-r-packages.R r-modules: drop broken irkernel package set 2017-03-07 14:56:46 +01:00
generate-shell.nix R: update list of broken packages (and some cosmetic) 2017-04-24 15:39:54 +02:00
generic-builder.nix stdenv setup: Always use both propagated files 2017-11-21 10:44:44 -05:00
README.md nixpkgs manual: add rstudio shell.nix example 2017-11-04 12:26:08 +01:00
test-evaluation.nix R: improve support for CRAN and Bioconductor package sets 2015-06-17 23:19:56 +02:00
wrapper-rstudio.nix rstudio: Fix recompilation issue with custom package set 2017-05-01 09:46:40 -04:00
wrapper.nix rstudio: Fix recompilation issue with custom package set 2017-05-01 09:46:40 -04:00

R packages

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

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