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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:
```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 by default will not use the libraries installed like above.
You must override its R version with your custom R environment, and
set `useRPackages` to `true`, like below:
```nix
{
packageOverrides = super: let self = super.pkgs; in
{
rEnv = super.rWrapper.override {
packages = with self.rPackages; [
devtools
ggplot2
reshape2
yaml
optparse
];
};
rstudioEnv = super.rstudio.override {
R = rEnv;
useRPackages = true;
};
};
}
```
Then like above, `nix-env -f "<nixpkgs>" -iA rstudioEnv` will install
this into your user profile.
## Updating the package set
```bash
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
Rscript generate-r-packages.R irkernel > irkernel-packages.nix.new
mv irkernel-packages.nix.new irkernel-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`
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