Anonymous user
R: Difference between revisions
Adds a section specifying how to install and R-package from GitHub
imported>Brentscott (Adds a section specifying how to setup R + packages using Flakes and nix-direnv) |
imported>Brentscott (Adds a section specifying how to install and R-package from GitHub) |
||
| Line 101: | Line 101: | ||
[https://github.com/wbolster/emacs-direnv Emacs has support for direnv] which can be setup to use R with ESS. Direnv functionality can also be set in Doom Emacs under :tools in the `init.el` file in `.doom.d` folder. | [https://github.com/wbolster/emacs-direnv Emacs has support for direnv] which can be setup to use R with ESS. Direnv functionality can also be set in Doom Emacs under :tools in the `init.el` file in `.doom.d` folder. | ||
==Install an R-package from GitHub== | |||
The R-packages available in <nixpkgs> are generated from a recent snapshot of CRAN. You may find certain packages a version behind or want to install a package not on CRAN/Bioconducter. R-packages can be installed from GitHub using `buildRPackage` and `fetchFromGitHub`. An example of installing {rmarkdown} from GitHub using a Flake: | |||
<syntaxhighlight lang = "nix" > | |||
{ | |||
description = "A basic flake with a shell"; | |||
inputs.nixpkgs.url = "github:NixOS/nixpkgs/nixpkgs-unstable"; | |||
inputs.flake-utils.url = "github:numtide/flake-utils"; | |||
outputs = { self, nixpkgs, flake-utils }: | |||
flake-utils.lib.eachDefaultSystem (system: let | |||
pkgs = nixpkgs.legacyPackages.${system}; | |||
rmark = pkgs.rPackages.buildRPackage { | |||
name = "rmarkdown"; | |||
src = pkgs.fetchFromGitHub{ | |||
owner = "rstudio"; | |||
repo = "rmarkdown"; | |||
rev = "b87ca50c8c4d5a5876333b598aed4eb84de925a3"; | |||
sha256 = "12mhmmibizbxgmsns80c8h97rr7rclv9hz98zpgsl26hw3s4l0vm"; | |||
}; | |||
propagatedBuildInputs = with pkgs.rPackages; [bslib evaluate jsonlite knitr stringr tinytex yaml xfun]; | |||
}; | |||
in { | |||
devShells.default = pkgs.mkShell { | |||
nativeBuildInputs = [ pkgs.bashInteractive ]; | |||
buildInputs = with pkgs; [ R rmark pandoc ]; | |||
}; | |||
}); | |||
} | |||
</syntaxhighlight> | |||
You will need to obtain the `rev` and `sha256` for the package on github [https://search.nixos.org/packages?channel=22.05&show=nix-prefetch-git&from=0&size=50&sort=relevance&type=packages&query=nix-prefetch-git which can be found by using the `nix-prefetch-git` command line tool.] For the above example, running <code>nix-prefetch-git https://github.com/rstudio/rmarkdown</code> from a terminal will generate the information. You may need to manually specify other R-package/system dependencies for the specific package in the `propagatedBuildInputs`. This information can be found in the `DESCRIPTION` file of the R-package source directory. | |||
== A note on knitr == | == A note on knitr == | ||