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<syntaxhighlight lang = "nix" >
<syntaxhighlight lang = "nix" >
{ pkgs ? import <nixpkgs> {} }:                                                 
{ pkgs ? import <nixpkgs> {} }:                                                 
let                                                                            
let                                                            
  packageOverrides = pkgs: {                                                   
    JupyterKernel = pkgs.juniper;                                             
  };                                                                           
                                                                               
   jupyter = import (pkgs.fetchFromGitHub {                                       
   jupyter = import (pkgs.fetchFromGitHub {                                       
     owner = "tweag";                                                             
     owner = "tweag";                                                             
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== R with Lorri ==
== R with Lorri ==
An example of a '''shell.nix''' for usage with [https://github.com/target/lorri lorri] is shown below:
An example of a '''shell.nix''' for usage with [https://github.com/nix-community/lorri lorri] is shown below:


<syntaxhighlight lang = "nix">
<syntaxhighlight lang = "nix">
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</syntaxhighlight>
</syntaxhighlight>


== R with Flakes and nix-direnv==
R and accompanying R-packages can be installed using a [[Flakes | Flake]] and then managed/activated with [https://github.com/nix-community/nix-direnv nix-direnv] to create a reproducible development environment. After the initial setup of nix-direnv (instructions provided on the GitHub README), there is a [https://github.com/nix-community/nix-direnv/blob/master/templates/flake/flake.nix flake template] provided by the nix-direnv maintainers to get started. Run <code>nix flake new -t github:nix-community/nix-direnv .</code> to initialize the flake template in your current directory. This will create a `flake.nix` file that can be edited to setup the R-environment:
<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.${system};
    in {
      devShells.default = pkgs.mkShell {
        nativeBuildInputs = [ pkgs.bashInteractive ];
        buildInputs = with pkgs; [ R rPackages.pagedown chromium pandoc ];
      };
    });
}
</syntaxhighlight>
Saving the file and then running <code>direnv allow</code> in the terminal of the project directory will execute the `flake.lock` and build the shell. This will install the current version of R and the R-package {pagedown} that is in <nixpkgs>. Note additional system dependencies may need installed for certain packages to work such as pandoc for document conversion with {rmarkdown}. Here, chromium is installed in the `buildInputs` so the <code>chrome_print</code> function can be used from {pagedown}. 
[https://github.com/wbolster/emacs-direnv Emacs has support for direnv] which can be setup to use R with ESS. Direnv functionality can also be set in Doom Emacs under :tools in the `init.el` file in `.doom.d` folder.
==Install an R-package from GitHub==
The R-packages available in <nixpkgs> are generated from a recent snapshot of CRAN. You may find certain packages a version behind or want to install a package not on CRAN/Bioconducter. R-packages can be installed from GitHub using `buildRPackage` and `fetchFromGitHub`. An example of installing {rmarkdown} from GitHub using a Flake:
<syntaxhighlight lang = "nix" >
{
  description = "A basic flake with a shell";
  inputs.nixpkgs.url = "github:NixOS/nixpkgs/nixpkgs-unstable";
  inputs.flake-utils.url = "github:numtide/flake-utils";
  outputs = { self, nixpkgs, flake-utils }:
    flake-utils.lib.eachDefaultSystem (system: let
      pkgs = nixpkgs.legacyPackages.${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 ==


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== Other Editors ==
== Other Editors ==


'''with vim''' -  [https://nixos.wiki/wiki/Nvim-r nvim-r]
'''with vim''' -  [[Nvim-r | nvim-r]]




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== External Documentation ==
== External Documentation ==


* [https://nixos.org/nixpkgs/manual/#r-packages R user guide in nixpkgs manual]
* [https://nixos.org/manual/nixpkgs/stable/#r R user guide in nixpkgs manual]
 
== Officer package ==
 
When the R package "officer" has been installed from the Nix package manager, "save_as_docx" does not work:
 
Error in write_xml.xml_document(private$doc, file = private$filename) :
Error closing file
Calls: save_as_docx ... print.rdocx -> <Anonymous> -> write_xml -> write_xml.xml_document
In addition: Warning messages:
1: In write_xml.xml_document(private$doc, file = private$filename) :
Permission denie [1501]
2: In write_xml.xml_document(private$doc, file = private$filename) :
Permission denie [1501]
 
However officer does work if installed using the conventional install.packages() which can be enabled as discussed in
https://churchman.nl/tag/r/
 
[[Category:Languages]]
Retrieved from "https://wiki.nixos.org/wiki/R"