Configuring Positron and nix on Windows WSL

[atsyplenkov]

Hey guys, looking for some help and advice. I cannot connect to a custom R installation on Positron v2025.01.0-39 when connecting to a remote machine via SSH (Ubuntu 24 on WSL2).

I am trying to configure the Nix environment with the help of the rix package. The problem arises when Positron cannot find the R executable, which is stored in a non-standard location. Setting positron.r.customBinaries doesn't seem to help.

I am running a fresh install of Ubuntu 24.04.1 LTS on WSL2, and Positron connects via SSH, configured on WSL with openssh-server. Apart from system dependencies like libcurl4-openssl-dev and curl, everything was configured with Nix. Below is the content of the default.nix file.

# This file was generated by the {rix} R package v0.14.3 on 2025-01-14
# with following call:
# >rix(r_ver = "4.4.2",
#  > r_pkgs = c("dplyr",
#  > "ggplot2"),
#  > system_pkgs = NULL,
#  > git_pkgs = NULL,
#  > ide = "code",
#  > project_path = ".",
#  > overwrite = TRUE)
# It uses the `rstats-on-nix` fork of `nixpkgs` which provides improved
# compatibility with older R versions and R packages for Linux/WSL and
# Apple Silicon computers.
# Report any issues to https://github.com/ropensci/rix
let
 pkgs = import (fetchTarball "https://github.com/rstats-on-nix/nixpkgs/archive/2024-12-14.tar.gz") {};
 
  rpkgs = builtins.attrValues {
    inherit (pkgs.rPackages) 
      dplyr
      ggplot2
      languageserver;
  };
    
  system_packages = builtins.attrValues {
    inherit (pkgs) 
      glibcLocales
      nix
      R;
  };
  
in

pkgs.mkShell {
  LOCALE_ARCHIVE = if pkgs.system == "x86_64-linux" then "${pkgs.glibcLocales}/lib/locale/locale-archive" else "";
  LANG = "en_US.UTF-8";
   LC_ALL = "en_US.UTF-8";
   LC_TIME = "en_US.UTF-8";
   LC_MONETARY = "en_US.UTF-8";
   LC_PAPER = "en_US.UTF-8";
   LC_MEASUREMENT = "en_US.UTF-8";

  buildInputs = [  rpkgs  system_packages   ];
  
}

After running nix-build and nix-shell, I am able to run R in nix-shell in my terminal, but not in the Positron Console, which is expected, as R was installed into /nix/store/lw2scvxw0vfgzva4qmglh03vk27yxaqg-R-4.4.2/bin/R, which is not the default location. While, I can configure positron.r.customBinaries in the remote machine's Positron settings to look at and run R from the Nix store. But how can I run R in the Positron console from nix-shell?

In other words, these settings work, and I can run at least some R:

"positron.r.customBinaries": "/nix/store/lw2scvxw0vfgzva4qmglh03vk27yxaqg-R-4.4.2/bin/R"

However, I want to run R from nix-shell; therefore, I tried to configure a shell script, which can then be passed to the positron.r.customBinaries:

#!/usr/bin/env bash
nix-shell /mnt/c/Users/TsyplenkovA/Desktop/temp_project/default.nix --run "R"

and don't forget to make it executable with chmod +x nixr.sh. So now my Positron settings look like:

{
    "positron.r.customBinaries": [
        "~/nixr.sh",
        "/nix/store/lw2scvxw0vfgzva4qmglh03vk27yxaqg-R-4.4.2/bin/R"
    ],
    "positron.r.trace.server": "messages"
}

The output console shows me, that it ignores my shell script, and just using the nix/store version:

2025-01-15 11:01:25.093 [info] Log level: Debug
2025-01-15 11:01:25.093 [info] Refreshing testthat status
2025-01-15 11:01:25.093 [info] Not working in an R package
2025-01-15 11:01:25.093 [info] Context key 'testthatIsConfigured' is 'false'
2025-01-15 11:01:25.093 [info] Context key 'testthatHasTests' is 'false'
2025-01-15 11:01:25.525 [info] Candidate R binary at C:\Program Files\R\R-4.4.1patched\bin\x64\R.exe
2025-01-15 11:01:25.588 [info] User-specified R binaries:
[
  "~/nixr.sh",
  "/nix/store/lw2scvxw0vfgzva4qmglh03vk27yxaqg-R-4.4.2/bin/R"
]
2025-01-15 11:01:25.588 [info] Skipping registry check on non-Windows platform
2025-01-15 11:01:25.616 [info] Candidate R binary at /nix/store/lw2scvxw0vfgzva4qmglh03vk27yxaqg-R-4.4.2/bin/R
2025-01-15 11:01:25.616 [info] R installation discovered: {
  "valid": true,
  "supported": true,
  "binpath": "/nix/store/lw2scvxw0vfgzva4qmglh03vk27yxaqg-R-4.4.2/bin/R",
  "homepath": "/nix/store/lw2scvxw0vfgzva4qmglh03vk27yxaqg-R-4.4.2/lib/R",
  "semVersion": {
    "options": {},
    "loose": false,
    "includePrerelease": false,
    "raw": "4.4.2",
    "major": 4,
    "minor": 4,
    "patch": 2,
    "prerelease": [],
    "build": [],
    "version": "4.4.2"
  },
  "version": "4.4.2",
  "arch": "x86_64",
  "current": false,
  "orthogonal": true
}
2025-01-15 11:01:31.026 [info] Creating Positron R 4.4.2 language client (port 43108)
2025-01-15 11:01:31.026 [info] ARK (R 4.4.2) language client state changed uninitialized => starting
2025-01-15 11:01:31.046 [info] ARK (R 4.4.2) language client init successful
2025-01-15 11:01:31.046 [info] ARK (R 4.4.2) language client state changed starting => running

So the question is, how can I make Positron work within the Nix environment on remote machines? Is it even possible?

To repdroduce the issue from scratch

wsl --install -d Ubuntu-24.04 --web-download

Setup username and password

# Update and install dependencies
sudo apt-get update && sudo apt-get upgrade -y
sudo apt-get install curl libcurl4-openssl-dev -y

# Install nix (https://docs.ropensci.org/rix/articles/b1-setting-up-and-using-rix-on-linux-and-windows.html#using-the-determinate-systems-installer)
curl --proto '=https' --tlsv1.2 -sSf -L https://install.determinate.systems/nix | sh -s -- install
# reopen shell
nix-env -iA cachix -f https://cachix.org/api/v1/install
# get root access to wsl user
echo "trusted-users = root atsyp" | sudo tee -a /etc/nix/nix.conf && sudo pkill nix-daemon
cachix use rstats-on-nix

Configure Positron ssh connection

# Install open-ssh server
sudo apt install openssh-server -y
# Configure settings
sudo nano /etc/ssh/sshd_config

Then, add to the end of the file the following lines:

# Configure server to connect from Windows
Port 2222
ListenAddress 0.0.0.0 # <LISTEN ADDRESS>

Start and enable openssh server

sudo systemctl start ssh.service
sudo systemctl enable ssh.service

Edit on Windows your WSL config located at %USERPROFILE%\.ssh\config by adding:

Host Ubuntu
    HostName 172.27.59.242
    Port 2222
    User atsyp

Connect in Positron via remote-ssh extension and wait while positron insalls its server. So, since there is no R installed on the WSL, Positron will not run any interpreters. I was installing R using nix following this

# Create temp project
mkdir nix_project && cd nix_project
# Install R
nix-shell --expr "$(curl -sl https://raw.githubusercontent.com/ropensci/rix/master/inst/extdata/default.nix)"
# Find R executable
nix-shell --expr "$(which R)"
#> /nix/store/lw2scvxw0vfgzva4qmglh03vk27yxaqg-R-4.4.2/bin/R

Then, create a nixr.sh script in home location (~/) and make it executable.

[b-rodrigues]

Hi Anatolii

I don’t use Positron nor Windows, so I don’t know if I’ll be able to help. However, I do have a few thoughts:

• you could install Positron using Nix in WSL2, and from there start the shell using nix-shell, and then Positron. This should (I said should, because I have no idea) start Positron from the activated shell (but it’s going to be the Linux version, not your already installed Windows one). To install Positron, add positron-bin to the system_pkgs and I also recommend to use the very latest date I’ve added yesterday, so use rix(date = "2025-01-14"...., system_pkgs = "positron-bin", ...).

• you could try to make the nix-shell global: I have never tried it, so I don’t know how or if it works, but there’s this discussion here that you might find interesting. From what I understand, activating the shell by editing the .profile should make it always activate as soon as a terminal is spawned.

• you could try to use Nix in combination with Docker and the Visual Studio Code Dev Containers extension. From what I could gather, this allows VS Code / Positron to connect to a running Docker container, and this container could have all the packages you need. Using Nix, you could set up a Docker image that contains all you need. Here is an example Dockerfile that sets up an environment using Nix:

FROM ubuntu:latest

RUN apt update -y

RUN apt install curl -y

# We don't have R nor {rix} in this image, so we can bootstrap it by downloading
# the default.nix file that comes with {rix}. You can also download it beforehand
# and then copy it to the Docker image
RUN curl -O https://raw.githubusercontent.com/ropensci/rix/main/inst/extdata/default.nix

# The next 4 lines install Nix inside Docker. See the Determinate Systems installer's documentation
RUN curl --proto '=https' --tlsv1.2 -sSf -L https://install.determinate.systems/nix | sh -s -- install linux \
  --extra-conf "sandbox = false" \
  --init none \
  --no-confirm

# Adds Nix to the path, as described by the Determinate Systems installer's documentation
ENV PATH="${PATH}:/nix/var/nix/profiles/default/bin"
ENV user=root

# Set up rstats-on-nix cache
# This will download binaries of packages instead of building
# them from source
RUN nix-shell --run "Rscript -e 'rix::setup_cachix()'"

# Generate default.nix that defines environment
RUN nix-shell --run "R -e \"library(rix); rix(date = '2025-01-14', r_pkgs = c('dplyr', 'ggplot2', 'languageserver'), project_path = '.', overwrite = TRUE)\""

# We now build the environment
RUN nix-build

# Finally, we run `nix-shell`. This will get executed when running
# containers from this image. You can of course put anything in here
CMD nix-shell

my guess is that you could then "ssh into" a running container from this image with the right dependencies.

[atsyplenkov]

Thanks, Bruno, for such a detailed answer. I commend you for providing such extensive options.

• The first one will definitely work, i.e., installing Positron inside WSL and running its GUI using WSLg. However, I personally don't prefer this option as it is a bit slower—if you work enough with WSLg, you will start to notice small millisecond freezes, which are, TBH, starting to drive you nuts. Also, language input methods switching is a bit of a pain (need to configure ibus and etc).

• I like the idea of containerization and globalization, and you gave me a thought that I probably need to install an OpenSSH server inside nix-shell. I am not sure how easy it would be to configure and forward the ports, but I'll give it a try.

• I'll also want to try running NixOS on WSL or in a container.

We'll keep this thread updated for future references!

[atsyplenkov]

BTW, Visual Studio Code Dev Containers extension does work only in VS Code as it needs a proprietary server to run inside containers. So, for Positron/VS Codium and other Code OSS-based IDEs, the open-remote-ssh is like the only option.

UPD: It turns out that Cursor supports Dev Containers extension on some machines. Or at least it's possible to connect to a running container configured in VS Code