pyrox.dev
1# R {#r}
2
3## Installation
4
5Define an environment for R that contains all the libraries that you'd like to
6use by adding the following snippet to your $HOME/.config/nixpkgs/config.nix file:
7
8```nix
9{
10 packageOverrides = super: let self = super.pkgs; in
11 {
12
13 rEnv = super.rWrapper.override {
14 packages = with self.rPackages; [
15 devtools
16 ggplot2
17 reshape2
18 yaml
19 optparse
20 ];
21 };
22 };
23}
24```
25
26Then you can use `nix-env -f "<nixpkgs>" -iA rEnv` to install it into your user
27profile. The set of available libraries can be discovered by running the
28command `nix-env -f "<nixpkgs>" -qaP -A rPackages`. The first column from that
29output is the name that has to be passed to rWrapper in the code snipped above.
30
31However, if you'd like to add a file to your project source to make the
32environment available for other contributors, you can create a `default.nix`
33file like so:
34```nix
35with import <nixpkgs> {};
36{
37 myProject = stdenv.mkDerivation {
38 name = "myProject";
39 version = "1";
40 src = if lib.inNixShell then null else nix;
41
42 buildInputs = with rPackages; [
43 R
44 ggplot2
45 knitr
46 ];
47 };
48}
49```
50and then run `nix-shell .` to be dropped into a shell with those packages
51available.
52
53## RStudio
54
55RStudio uses a standard set of packages and ignores any custom R
56environments or installed packages you may have. To create a custom
57environment, see `rstudioWrapper`, which functions similarly to
58`rWrapper`:
59
60```nix
61{
62 packageOverrides = super: let self = super.pkgs; in
63 {
64
65 rstudioEnv = super.rstudioWrapper.override {
66 packages = with self.rPackages; [
67 dplyr
68 ggplot2
69 reshape2
70 ];
71 };
72 };
73}
74```
75
76Then like above, `nix-env -f "<nixpkgs>" -iA rstudioEnv` will install
77this into your user profile.
78
79Alternatively, you can create a self-contained `shell.nix` without the need to
80modify any configuration files:
81
82```nix
83{ pkgs ? import <nixpkgs> {}
84}:
85
86pkgs.rstudioWrapper.override {
87 packages = with pkgs.rPackages; [ dplyr ggplot2 reshape2 ];
88}
89
90```
91
92Executing `nix-shell` will then drop you into an environment equivalent to the
93one above. If you need additional packages just add them to the list and
94re-enter the shell.
95
96## Updating the package set
97
98```bash
99nix-shell generate-shell.nix
100
101Rscript generate-r-packages.R cran > cran-packages.nix.new
102mv cran-packages.nix.new cran-packages.nix
103
104Rscript generate-r-packages.R bioc > bioc-packages.nix.new
105mv bioc-packages.nix.new bioc-packages.nix
106
107Rscript generate-r-packages.R bioc-annotation > bioc-annotation-packages.nix.new
108mv bioc-annotation-packages.nix.new bioc-annotation-packages.nix
109
110Rscript generate-r-packages.R bioc-experiment > bioc-experiment-packages.nix.new
111mv bioc-experiment-packages.nix.new bioc-experiment-packages.nix
112```
113
114`generate-r-packages.R <repo>` reads `<repo>-packages.nix`, therefor the renaming.
115
116
117## Testing if the Nix-expression could be evaluated
118
119```bash
120nix-build test-evaluation.nix --dry-run
121```
122
123If this exits fine, the expression is ok. If not, you have to edit `default.nix`