Luke Granger-Brown
57725ef3ec
git-subtree-dir: third_party/nixpkgs git-subtree-split: 76612b17c0ce71689921ca12d9ffdc9c23ce40b2
130 lines
3.7 KiB
Markdown
130 lines
3.7 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}
|
|
|
|
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.
|