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https://nixos.org/nixpkgs/manual/#r-packages contains a method for setting up an R environment with a specific set of libraries, and it creates an R wrapper which points R to those libraries. The package RStudio relies on the standard R package, which then cannot access any of the libraries specified in a custom R environment. While one may easily use pkgs.rstudio.override to change rstudio's R dependency to the custom R environment, this accomplishes nothing because while RStudio runs the correct R wrapper it clears out the environment variable R_LIBS_SITE - and so it is still unable to use any of those packages. In order to work around this problem, these changes allow the user to optionally modify rstudio's wrapper to set environment variable R_PROFILE_USER to an R script which sets R's .libPaths(..) to point to the same libraries; that script is generated from R_LIBS_SITE in the R wrapper. By default, this change has no effect. If R is overridden to something else, and if useRPackages is changed from its default of false, then the change described above is made; for instance: { packageOverrides = pkgs: let self = pkgs.pkgs; in rec { rEnv = pkgs.rWrapper.override { packages = with self.rPackages; [ dplyr ggplot2 e1071 rpart reshape ]; }; rstudioEnv = pkgs.rstudio.override { R = rEnv; useRPackages = true; }; }; }
111 lines
2.7 KiB
Markdown
111 lines
2.7 KiB
Markdown
R packages
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==========
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## Installation
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Define an environment for R that contains all the libraries that you'd like to
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use by adding the following snippet to your $HOME/.nixpkgs/config.nix file:
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```nix
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{
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packageOverrides = super: let self = super.pkgs; in
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{
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rEnv = super.rWrapper.override {
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packages = with self.rPackages; [
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devtools
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ggplot2
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reshape2
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yaml
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optparse
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];
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};
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};
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}
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```
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Then you can use `nix-env -f "<nixpkgs>" -iA rEnv` to install it into your user
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profile. The set of available libraries can be discovered by running the
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command `nix-env -f "<nixpkgs>" -qaP -A rPackages`. The first column from that
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output is the name that has to be passed to rWrapper in the code snipped above.
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However, if you'd like to add a file to your project source to make the
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environment available for other contributors, you can create a `default.nix`
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file like so:
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```nix
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let
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pkgs = import <nixpkgs> {};
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stdenv = pkgs.stdenv;
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in with pkgs; {
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myProject = stdenv.mkDerivation {
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name = "myProject";
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version = "1";
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src = if pkgs.lib.inNixShell then null else nix;
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buildInputs = with rPackages; [
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R
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ggplot2
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knitr
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];
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};
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}
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```
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and then run `nix-shell .` to be dropped into a shell with those packages
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available.
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## RStudio
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RStudio by default will not use the libraries installed like above.
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You must override its R version with your custom R environment, and
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set `useRPackages` to `true`, like below:
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```nix
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{
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packageOverrides = super: let self = super.pkgs; in
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{
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rEnv = super.rWrapper.override {
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packages = with self.rPackages; [
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devtools
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ggplot2
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reshape2
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yaml
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optparse
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];
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};
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rstudioEnv = super.rstudio.override {
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R = rEnv;
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useRPackages = true;
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};
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};
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}
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```
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Then like above, `nix-env -f "<nixpkgs>" -iA rstudioEnv` will install
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this into your user profile.
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## Updating the package set
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```bash
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Rscript generate-r-packages.R cran > cran-packages.nix.new
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mv cran-packages.nix.new cran-packages.nix
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Rscript generate-r-packages.R bioc > bioc-packages.nix.new
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mv bioc-packages.nix.new bioc-packages.nix
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Rscript generate-r-packages.R irkernel > irkernel-packages.nix.new
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mv irkernel-packages.nix.new irkernel-packages.nix
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```
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`generate-r-packages.R <repo>` reads `<repo>-packages.nix`, therefor the renaming.
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## Testing if the Nix-expression could be evaluated
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```bash
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nix-build test-evaluation.nix --dry-run
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```
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If this exits fine, the expression is ok. If not, you have to edit `default.nix`
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