How to install python rpy2 so it sees installed r packages?

Help
1

I would like to use rpy2 to access R from Python. I just tried to install the R, Python, and Rpy2 packages, but they don’t work. It looks like rpy2 installs its own R and it’s not looking for r packages where they are installed already and I get an error

library ‘/home/user/R/x86_64-pc-linux-gnu-library/4.3’ contains no packages

my shell.nix is

with import <nixpkgs> { };

let
  py = python312Packages;
  r-with-my-packages = rWrapper.override{
      packages = with rPackages; [ tidyverse ggplot2 data_table metafor ]; };
in pkgs.mkShell {
  propagatedBuildInputs = [
    r-with-my-packages
    py.python
    py.numpy
    py.scipy
    py.scikit-learn
    py.matplotlib
    py.rpy2
    py.pytest
		];
}

Any idea how to make it work?

2

Recommendation: search GitHub for examples.

3

I did that already looking for rpy2 and shell.nix, and I didn’t find anything besides just having rpy2 with other python pacakges

4

This seems to be what you’re looking for:

1 Like
5

Thanks for your reply. I weren’t able to make it work with the extraRpackages. I put

extraRPackages = [ metafor data_table ]

in my nix shell, but it didn’t work. I suppose that’s not how it’s supposed to be used. However just removing rpackages from the rWarpper.override, and putting them in the list with the rest of the python packages worked. So my now working shell is this

with import <nixpkgs> { };

let
  py = python312Packages;
in pkgs.mkShell {
  packages = [
    #r-with-my-packages
    R
    rPackages.metafor
    rPackages.data_table
    py.python
    py.numpy
    py.scipy
    py.scikit-learn
    py.matplotlib
    py.rpy2
    py.pytest
  ];
6

try (py.rpy2.override {extraRPackages = with rPackages; [ metafor data_table ];})

PS when you say “didn’t work”, please be specific. It’s basic troubleshooting etiquette, and also gets others to understand if you applied the fix incorrectly vs if the suggested fix itself was incorrect. If there’s an error, give the full error without truncation.

1 Like
7

Thanks. By not working I just meant that nothing changed, the error is the same, i.e., the r packages are not visible from python, with an error

rpy2.robjects.packages.PackageNotInstalledError: The R package "metafor" is not installed.

and warning

R[write to console]:  library ‘/home/brick/R/x86_64-pc-linux-gnu-library/4.3’ contains no packages

I should have been more specific.

Your solution with rpy2.overide works, as well as just puting the r packages in the same list with other packages, without rWrapper.overide. The difference is that with rpy.override, the packages are not accessible from R itself, which might or might not be desirable for different situations.