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# R {#r}
## Installation {#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:
```nix
{
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:
```nix
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}
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`:
```nix
{
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:
```nix
{
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 {#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:
```bash
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.
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