tjh.dev
1R packages
2==========
3
4## Installation
5
6Define an environment for R that contains all the libraries that you'd like to
7use by adding the following snippet to your $HOME/.nixpkgs/config.nix file:
8
9```nix
10{
11 packageOverrides = super: let self = super.pkgs; in
12 {
13
14 rEnv = super.rWrapper.override {
15 packages = with self.rPackages; [
16 devtools
17 ggplot2
18 reshape2
19 yaml
20 optparse
21 ];
22 };
23 };
24}
25```
26
27Then you can use `nix-env -f "<nixpkgs>" -iA rEnv` to install it into your user
28profile. The set of available libraries can be discovered by running the
29command `nix-env -f "<nixpkgs>" -qaP -A rPackages`. The first column from that
30output is the name that has to be passed to rWrapper in the code snipped above.
31
32## Updating the package set
33
34```bash
35Rscript generate-r-packages.R cran > cran-packages.nix.new
36mv cran-packages.nix.new cran-packages.nix
37
38Rscript generate-r-packages.R bioc > bioc-packages.nix.new
39mv bioc-packages.nix.new bioc-packages.nix
40
41Rscript generate-r-packages.R irkernel > irkernel-packages.nix.new
42mv irkernel-packages.nix.new irkernel-packages.nix
43```
44
45`generate-r-packages.R <repo>` reads `<repo>-packages.nix`, therefor the renaming.
46
47
48## Testing if the Nix-expression could be evaluated
49
50```bash
51nix-build test-evaluation.nix --dry-run
52```
53
54If this exits fine, the expression is ok. If not, you have to edit `default.nix`
55