nixpkgs/doc/languages-frameworks/r.section.md
Jan Tojnar 6ecc641d08
doc: prepare for commonmark
We are still using Pandoc’s Markdown parser, which differs from CommonMark spec slightly.

Notably:
- Line breaks in lists behave differently.
- Admonitions do not support the simpler syntax https://github.com/jgm/commonmark-hs/issues/75
- The auto_identifiers uses a different algorithm – I made the previous ones explicit.
- Languages (classes) of code blocks cannot contain whitespace so we have to use “pycon” alias instead of Python “console” as GitHub’s linguist

While at it, I also fixed the following issues:
- ShellSesssion was used
- Removed some pointless docbook tags.
2021-06-07 06:34:59 +02:00

124 lines
3.2 KiB
Markdown

# 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}
```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
Rscript generate-r-packages.R bioc-annotation > bioc-annotation-packages.nix.new
mv bioc-annotation-packages.nix.new bioc-annotation-packages.nix
Rscript generate-r-packages.R bioc-experiment > bioc-experiment-packages.nix.new
mv bioc-experiment-packages.nix.new bioc-experiment-packages.nix
```
`generate-r-packages.R <repo>` reads `<repo>-packages.nix`, therefor the renaming.
## Testing if the Nix-expression could be evaluated {#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`