R: Difference between revisions

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RStudio-with-my-packages = rstudioWrapper.override{ packages = with rPackages; [ ggplot2 dplyr xts ]; };

</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 ==

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== 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:

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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.

==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:

{

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?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 ==

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== Other Editors ==

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

'''with vim''' - [[Nvim-r | nvim-r]]

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== 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 ==

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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]]

@@ Line 23: / Line 23: @@
 RStudio-with-my-packages = rstudioWrapper.override{ packages = with rPackages; [ ggplot2 dplyr xts ]; };
 </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 ==
@@ Line 77: / Line 101: @@
 == 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" >
@@ Line 101: / Line 125: @@
 [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?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 ==
@@ Line 108: / Line 201: @@
 == Other Editors ==
-'''with vim''' -  [https://nixos.wiki/wiki/Nvim-r nvim-r]
+'''with vim''' -  [[Nvim-r | nvim-r]]
@@ Line 115: / Line 208: @@
 == 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 ==
@@ Line 132: / Line 225: @@
 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]]