nixpkgs/doc/languages-frameworks/r.section.md
Frederik Rietdijk 95dfbe2d63 doc: organize chapters into parts, and reduce toc depth
Reorganize the chapters into parts and reduce the TOC depth to make the
TOC useful again. The top-level TOC is very brief, but that is fine
because every part will have its own TOC.

Section titles of languages/frameworks are also simplified to just
the name of the language/framework.
2019-10-20 13:35:04 +02:00

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Markdown

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:
```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
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`:
```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
```bash
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
```bash
nix-build test-evaluation.nix --dry-run
```
If this exits fine, the expression is ok. If not, you have to edit `default.nix`