R - Revision history

JeppeX: /* A note on knitr */: add example

2026-01-24T00:27:28Z

A note on knitr: : add example

← Older revision		Revision as of 00:27, 24 January 2026
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	To knit a .Rmd file to a pdf (or .Rnw), you need to have included in your envronment <code> pkgs.texlive.combined.scheme-full</code>as well as <code> pandoc </code> or it will fail to knit. None of the other texlive packages contain the proper "frame" package. Note there are likely other workarounds but this requires the least effort.		To knit a .Rmd file to a pdf (or .Rnw), you need to have included in your envronment <code> pkgs.texlive.combined.scheme-full</code>as well as <code> pandoc </code> or it will fail to knit. None of the other texlive packages contain the proper "frame" package. Note there are likely other workarounds but this requires the least effort.

			If <code>R</code> is included (using wrapper) but <code>pandoc</code> is not wanted in the user environment, one can expose it just for the R with
			<syntaxhighlight lang="nix">
			(rWrapper.override{
			packages = with rPackages; [
			markdown
			# other plugins go also here
			];
			}).overrideAttrs (old: {
			buildInputs = (old.buildInputs or []) ++ [
			pkgs.pandoc
			];
			});
			</syntaxhighlight>
	== Other Editors ==		== Other Editors ==

Detroyejr: Add an "Install an R package from source" section.

2025-08-28T13:58:24Z

Add an "Install an R package from source" section.

← Older revision		Revision as of 13:58, 28 August 2025
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	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.		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 ==

Pigs: /* Install an R-package from GitHub */Use current channel for search.nixos.org link

2025-05-07T17:15:24Z

Install an R-package from GitHub: Use current channel for search.nixos.org link

← Older revision		Revision as of 17:15, 7 May 2025
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	</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.

	== A note on knitr ==		== A note on knitr ==

Detroyejr: Add a section for positron.

2025-03-29T18:53:20Z

Add a section for positron.

@@ Line 23: / Line 23: @@
 RStudio-with-my-packages = rstudioWrapper.override{ packages = with rPackages; [ ggplot2 dplyr xts ]; };
 </syntaxhighlight>
 == Jupyter Notebook ==

Mic92: fix links

2024-04-01T13:42:37Z

fix links

← Older revision		Revision as of 13:42, 1 April 2024
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	== 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 142:		Line 142:
	== Other Editors ==		== Other Editors ==

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

imported>IgorM: Added category

2023-09-27T09:29:56Z

Added category

← Older revision		Revision as of 09:29, 27 September 2023
Line 166:		Line 166:
	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]]

imported>Michael-J-Ward: Fix link to the R user guide in nixpkgs manual

2023-03-31T10:02:01Z

Fix link to the R user guide in nixpkgs manual

← Older revision		Revision as of 10:02, 31 March 2023
Line 149:		Line 149:
	== 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 ==

imported>Brentscott: Adds a section specifying how to install and R-package from GitHub

2022-11-22T17:50:37Z

Adds a section specifying how to install and R-package from GitHub

← Older revision		Revision as of 17:50, 22 November 2022
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	[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 ==

imported>Brentscott: Adds a section specifying how to setup R + packages using Flakes and nix-direnv

2022-11-22T17:29:32Z

Adds a section specifying how to setup R + packages using Flakes and nix-direnv

← Older revision		Revision as of 17:29, 22 November 2022
Line 74:		Line 74:

	</syntaxhighlight>		</syntaxhighlight>

			== 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:

			<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.


	== A note on knitr ==		== A note on knitr ==

imported>MikiVanousek: The lorri repo has been moved

2022-09-08T13:27:50Z

The lorri repo has been moved

← Older revision		Revision as of 13:27, 8 September 2022
Line 59:		Line 59:

	== 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">