RStudio server ignores XDG_CONFIG_HOME

RStudio IDE
#1

Dear developers,

I downloaded and installed RStudio Server v2022.12.0+353 for Ubuntu 22, following directions on RStudio Server - Posit However, I can't seem to get it to recognize the $XDG_CONFIG_HOME environmental variable, and all settings continue to be written to ~/.config/.

I set the variable using the standard export XDG_CONFIG_HOME=/full/path/ mechanism and run the server with sudo /usr/lib/rstudio-server/bin/rserver --server-daemonize=0. Similar questions on the forum seem to indicate that this should be sufficient, but I also tried writing the environmental variable to various .Renviron and .Renviron.site locations, all to no avail. What am I missing?

Happy to throw together a reproducible example, if helpful.

#2

Reproducible example with Docker + Gitpod

  • Define the following Dockerfile:
FROM gitpod/workspace-base:2023-03-06-18-43-51

USER root

# Configuration for tzdata
ENV TZ=US/Eastern
RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone

# Install R
RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc |\
    tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc && \
    add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
RUN apt-get update && apt-get install -y r-base gdebi-core

# Install RStudio
ARG RSTUDIO_VER="rstudio-server-2022.12.0-353-amd64.deb"
RUN wget "https://download2.rstudio.org/server/jammy/amd64/$RSTUDIO_VER" && \
    gdebi -n "$RSTUDIO_VER"

# Clean up
RUN rm -rf "$RSTUDIO_VER" && \
    rm -rf /var/lib/apt/lists/*

# Reset gitpod user credentials (for Rstudio login)
RUN echo "gitpod:gitpod" | chpasswd
USER gitpod

  • Build the container image with docker build -t rstudio:test .

  • Start a container from the above image:
    docker run -it --rm -p 8787:8787 -v "$PWD":/config -e XDG_CONFIG_HOME=/config rstudio:test

  • Inside the container, verify that XDG_CONFIG_HOME has been set:

gitpod ~ $ echo $XDG_CONFIG_HOME
/config

  • Launch the server with sudo /usr/lib/rstudio-server/bin/rserver, which will be served on port 8787. If requested to log in, use gitpod for both username and password.

  • Modify a global option, e.g., change the appearance theme.

  • Examine the location of saved options:

gitpod ~ $ ls -la /config
total 0
drwxr-xr-x 2 gitpod gitpod  6 Mar 15 12:03 .
drwxr-xr-x 1 root   root   65 Mar 15 12:14 ..

gitpod ~ $ ls ~/.config/rstudio/
dictionaries  rstudio-prefs.json

gitpod ~ $ cat ~/.config/rstudio/rstudio-prefs.json 
{
    "initial_working_directory": "~",
    "editor_theme": "Tomorrow Night 80s",
    "posix_terminal_shell": "bash"
}

Even though XDG_CONFIG_HOME is set to /config, the server continues to write settings to ~/.config.

#3

It doesn't really matter what env vars rserver sees in this case; XDG_CONFIG_HOME is read by a separate process, rsession, and it reads the value only when that process starts up (not when it starts R, so you can't use .Renviron, etc).

So what I'd suggest as a first debugging step is to remove all the Renviron changes, start a new session, and run Sys.getenv("XDG_CONFIG_HOME") to confirm that the session is seeing the correct value.

#4

Hi Jonathan,

I've never run the rsession process directly. Are there any flags to pass? For me, it fails with the following error message when I run it inside the container that I built in my previous post:

$ docker run -it --rm -p 8787:8787 -v "$PWD":/config -e XDG_CONFIG_HOME=/config rstudio:test

# Inside the container
gitpod ~ $ /usr/lib/rstudio-server/bin/rsession 
TTY detected. Printing informational message about logging configuration. Logging configuration loaded from '/etc/rstudio/logging.conf'. Logging to '/home/gitpod/.local/share/rstudio/log/rsession-.log'.
rsession-[34]: ERROR system error 2 (No such file or directory) [path: ]; OCCURRED AT rstudio::core::Error rstudio::r::session::discoverR(rstudio::r::session::RLocations*) src/cpp/r/session/RDiscovery.cpp:62; LOGGED FROM: int main(int, char* const*) src/cpp/session/SessionMain.cpp:2459

2023-03-16T19:44:38.133648Z [rsession-] ERROR system error 2 (No such file or directory) [path: ]; OCCURRED AT rstudio::core::Error rstudio::r::session::discoverR(rstudio::r::session::RLocations*) src/cpp/r/session/RDiscovery.cpp:62; LOGGED FROM: int main(int, char* const*) src/cpp/session/SessionMain.cpp:2459
#5

Sorry, rsession is started by rserver and represents an R session in the browser. If you start your server and navigate to it in a browser, you are interacting with rsession. It's from your browser RStudio IDE session that you should run Sys.getenv("XDG_CONFIG_HOME"). Let me know what you see!

#6

Ah. Thanks, Jonathan.

The rsession definitely does NOT see the environmental variable:

> Sys.getenv("XDG_CONFIG_HOME")
[1] ""

What's interesting is that the official rstudio container image doesn't have this problem. If I run it with

docker run -it --rm -p 8787:8787 -v "$PWD":/config -e XDG_CONFIG_HOME=/config rocker/rstudio

then the R session sees the environmental variable and the global options correctly appear in /config.

I am trying to understand how rocker/rstudio handles environmental variables, but there is an additional layer of complexity with the S6 server. I see that it copies the variables to ${R_HOME}/etc/Renviron.site on startup:

$ docker run --rm rocker/rstudio cat /etc/cont-init.d/01_set_env 

#!/usr/bin/with-contenv bash
# shellcheck shell=bash

## Set our dynamic variables in Renviron.site to be reflected by RStudio Server or Shiny Server
exclude_vars="HOME PASSWORD RSTUDIO_VERSION BATCH_USER_CREATION"
for file in /var/run/s6/container_environment/*; do
    sed -i "/^${file##*/}=/d" "${R_HOME}/etc/Renviron.site"
    regex="(^| )${file##*/}($| )"
    [[ ! $exclude_vars =~ $regex ]] && echo "${file##*/}=$(cat "${file}")" >>"${R_HOME}/etc/Renviron.site" || echo "skipping ${file}"
done

## only file-owner (root) should read container_environment files:
chmod 600 /var/run/s6/container_environment/*

If I do this manually in my container, the rsession sees those variables and writes dictionaries to /config, but the remaining options still get written to ~/.config/:

# On the host system
$ docker run -it --rm -p 8787:8787 -v "$PWD":/config -e XDG_CONFIG_HOME=/config rstudio:test

# Inside the container
gitpod ~ $ echo "XDG_CONFIG_HOME=$XDG_CONFIG_HOME" | sudo tee -a /etc/R/Renviron.site
gitpod ~ $ sudo /usr/lib/rstudio-server/bin/rserver

# Inside the rsession
> Sys.getenv("XDG_CONFIG_HOME")
[1] "/config"

# Changing appearance theme in Global Options...

# Back inside the container
gitpod ~ $ ls /config
R  rstudio

gitpod ~ $ ls /config/rstudio
dictionaries

gitpod ~ $ ls ~/.config/rstudio/
rstudio-prefs.json

gitpod ~ $ cat ~/.config/rstudio/rstudio-prefs.json 
{
    "initial_working_directory": "~",
    "editor_theme": "Solarized Dark",
    "posix_terminal_shell": "bash"
}

Do dictionaries and rstudio-prefs.json use different env variables, maybe?

#7

They don't. As in the excellent Netflix series "Dark", It's not a question of "where" but "when". There's a lot of startup code that rsession runs before R itself is started. So setting XDG_CONFIG_HOME in Renviron is really too late; only code that runs after R boot will see the desired path.