NixOS Wiki

R: Difference between revisions

← Older edit
VisualWikitext
imported>Brentscott
Adds a section specifying how to install and R-package from GitHub
Add an "Install an R package from source" section.
 
(5 intermediate revisions by 5 users not shown)
Line 23: Line 23:
RStudio-with-my-packages = rstudioWrapper.override{ packages = with rPackages; [ ggplot2 dplyr xts ]; };
RStudio-with-my-packages = rstudioWrapper.override{ packages = with rPackages; [ ggplot2 dplyr xts ]; };
</syntaxhighlight>
</syntaxhighlight>
== Positron ==
Currently, the easiest way to use positron with nix is with mkShell:<syntaxhighlight lang="nix">
let
  pkgs = import <nixpkgs> { };
in
pkgs.mkShell {
  packages = [
    # Positron
    pkgs.positron-bin
    # R & packages.
    pkgs.R
    pkgs.rPackages.httr
    pkgs.rPackages.ggplot2
    # Python, ipykernel & packages.
    # pkgs.python313
    # pkgs.python313Packages.ipykernel # NOTE: Required for python.
    # pkgs.python313Packages.pandas
    # pkgs.python313Packages.requests
  ];
}
</syntaxhighlight>Other utilities like rWrapper are not compatible.


== Jupyter Notebook ==
== Jupyter Notebook ==
Line 77: Line 101:
== R with Flakes and nix-direnv==
== R with Flakes and nix-direnv==


R and accompanying R-packages can be installed using a [https://nixos.wiki/wiki/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:  
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" >
<syntaxhighlight lang = "nix" >
Line 134: Line 158:
</syntaxhighlight>
</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.  
You will need to obtain the `rev` and `sha256` for the package on github [https://search.nixos.org/packages?show=nix-prefetch-git&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.
 
== Install an R package from source ==
If you need a specific version of a package or find one that is not available in Nixpkgs, you can use `rPackages.buildRPackage` to build from source. The example below builds S4Arrays from BioConductor.<syntaxhighlight lang="nix">
let
  pkgs = import <nixpkgs> { };
  customPackage = pkgs.rPackages.buildRPackage {
    name = "S4Arrays";
    src = pkgs.fetchurl {
      url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/S4Arrays_1.8.1.tar.gz";
      hash = "sha256-8f2oA0xgwI6CucXbMU1yJC4W6tiVMcDAk8D3Ur3zxw8=";
    };
    buildInputs = with pkgs.rPackages; [
      pkgs.R
      Matrix
      abind
      BiocGenerics
      S4Vectors
      IRanges
      crayon
    ];
  };
in
pkgs.mkShell {
  packages = with pkgs.rPackages; [
    pkgs.R
    Matrix
    abind
    BiocGenerics
    S4Vectors
    IRanges
    crayon
    customPackage # the package we built from source.
  ];
}
</syntaxhighlight>
 
== A note on knitr ==
== A note on knitr ==


Line 142: Line 201:
== Other Editors ==
== Other Editors ==


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




Line 149: Line 208:
== 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 ==
== Officer package ==
Line 166: Line 225:
However officer does work if installed using the conventional install.packages() which can be enabled as discussed in
However officer does work if installed using the conventional install.packages() which can be enabled as discussed in
https://churchman.nl/tag/r/
https://churchman.nl/tag/r/
[[Category:Languages]]
Retrieved from "https://wiki.nixos.org/wiki/R"