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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; }; }; } |
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|---|---|---|
| .. | ||
| patches | ||
| bioc-annotation-packages.nix | ||
| bioc-experiment-packages.nix | ||
| bioc-packages.nix | ||
| cran-packages.nix | ||
| default.nix | ||
| generate-r-packages.R | ||
| generate-shell.nix | ||
| generic-builder.nix | ||
| irkernel-packages.nix | ||
| README.md | ||
| test-evaluation.nix | ||
| wrapper.nix | ||
R packages
Installation
Define an environment for R that contains all the libraries that you'd like to use by adding the following snippet to your $HOME/.nixpkgs/config.nix file:
{
packageOverrides = super: let self = super.pkgs; in
{
rEnv = super.rWrapper.override {
packages = with self.rPackages; [
devtools
ggplot2
reshape2
yaml
optparse
];
};
};
}
Then you can use nix-env -f "<nixpkgs>" -iA rEnv to install it into your user
profile. The set of available libraries can be discovered by running the
command nix-env -f "<nixpkgs>" -qaP -A rPackages. The first column from that
output is the name that has to be passed to rWrapper in the code snipped above.
However, if you'd like to add a file to your project source to make the
environment available for other contributors, you can create a default.nix
file like so:
let
pkgs = import <nixpkgs> {};
stdenv = pkgs.stdenv;
in with pkgs; {
myProject = stdenv.mkDerivation {
name = "myProject";
version = "1";
src = if pkgs.lib.inNixShell then null else nix;
buildInputs = with rPackages; [
R
ggplot2
knitr
];
};
}
and then run nix-shell . to be dropped into a shell with those packages
available.
RStudio
RStudio by default will not use the libraries installed like above.
You must override its R version with your custom R environment, and
set useRPackages to true, like below:
{
packageOverrides = super: let self = super.pkgs; in
{
rEnv = super.rWrapper.override {
packages = with self.rPackages; [
devtools
ggplot2
reshape2
yaml
optparse
];
};
rstudioEnv = super.rstudio.override {
R = rEnv;
useRPackages = true;
};
};
}
Then like above, nix-env -f "<nixpkgs>" -iA rstudioEnv will install
this into your user profile.
Updating the package set
Rscript generate-r-packages.R cran > cran-packages.nix.new
mv cran-packages.nix.new cran-packages.nix
Rscript generate-r-packages.R bioc > bioc-packages.nix.new
mv bioc-packages.nix.new bioc-packages.nix
Rscript generate-r-packages.R irkernel > irkernel-packages.nix.new
mv irkernel-packages.nix.new irkernel-packages.nix
generate-r-packages.R <repo> reads <repo>-packages.nix, therefor the renaming.
Testing if the Nix-expression could be evaluated
nix-build test-evaluation.nix --dry-run
If this exits fine, the expression is ok. If not, you have to edit default.nix