r_bg() error in Docker container

[dejan94it]

Hi!
I have a script which works perfectly fine on my pc (windows) but stuck inside a docker container with rocker/r-ver:4.3.3 image.
In particular, following ChatGPT suggestions, for the container I tried with arch, env and cmdargs arguments SEPARATELY but The error is always the same

cat("R binary path:", Sys.which("R"), "\n")
cat("R binary directory:", dirname(Sys.which("R")), "\n")

 callr::r_bg(
  func = start_telegram_bot,
  args = list(path = ".",
              bot_token = Sys.getenv("BOT_TOKEN"),
              admin_chat_id = Sys.getenv("ADMIN_CHAT_ID")),
  # arch = Sys.which("R"), THIS
  # env = c(PATH = dirname(Sys.which("R"))),  OR THIS
  # cmdargs = c(
  # Sys.which("R"),  #  OR THIS
  #  "--slave", "--no-save", "--no-restore"
  # ),
  stdout = "logs/output.log",
  stderr = "logs/error.log",
  supervise = TRUE # per terminare il processo se la sessione R principale viene chiusa
); bot_bg_process$is_alive()

R binary path: /usr/local/bin/R
R binary directory: /usr/local/bin

Error in `process_initialize(self, private, command, args, stdin, stdout, …` at process.R:212:18:
! Native call to `processx_exec` failed
Caused by error in `chain_call(c_processx_exec, command, c(command, args), pty, pty_options, …` at initialize.R:138:3:
! cannot start processx process '/usr/local/bin/R' (system error 2, No such file or directory) @unix/processx.c:611 (processx_exec)

Any other suggestions?
thanks!

[gaborcsardi]

You'll have to show how exactly you are running Docker, the full code, and also the full output.

[dejan94it]

FROM rocker/r-ver:4.3.3

RUN apt-get update -qq && \ 
  apt-get install -y --no-install-recommends \
    libcurl4-openssl-dev \
    libfontconfig1-dev \
    libfreetype6-dev \
    libfribidi-dev \
    libharfbuzz-dev \
    libicu-dev \
    libjpeg-dev \
    libpng-dev \
    libsasl2-dev \
    libssl-dev \
    libtiff-dev \
    libxml2-dev \
    libxt6 \
    make \
    pandoc \
    zlib1g-dev && \
  apt-get clean && \ 
  rm -rf /var/lib/apt/lists/*

COPY renv.lock renv.lock

RUN Rscript -e "install.packages('renv')"

RUN Rscript -e "renv::restore()"

COPY . . 

CMD ["Rscript", "bot_main.R"]

docker run --env-file .env my_image

bot_main.R

library(DBI)
library(RSQLite)
library(telegram.bot)
cat("R binary path:", Sys.which("R"), "\n")
cat("R binary directory:", dirname(Sys.which("R")), "\n")

db_con <- dbConnect(SQLite(), dbname = Sys.getenv("DB_PATH"))

start_telegram_bot <- function(path = ".",
                               bot_token,
                               admin_chat_id = NULL){
  library(telegram.bot)
  library(tidyverse)
  library(DBI)
  library(RSQLite)
  library(glue)
  
  db_con <- dbConnect(SQLite(), dbname = Sys.getenv("DB_PATH"))
  bot <- Bot(token = bot_token)
  updater <- Updater(token = bot_token)

  
  source("./messageHandlers.R", local = T)
  source("./commandHandlers.R", local = T)
  source("./callbackQueryHandlers.R", local = T)
  source("./filters.R", local = T)
  

  bot$send_message(chat_id = Sys.getenv("ADMIN_CHAT_ID"), text = "Bot Avviato")
  updater$start_polling(clean = T)
}


bot_bg_process <- callr::r_bg(
  func = start_telegram_bot,
  args = list(path = ".",
              bot_token = Sys.getenv("BOT_TOKEN"),
              admin_chat_id = Sys.getenv("ADMIN_CHAT_ID")),
  # arch = Sys.which("R"),
  # env = c(PATH = dirname(Sys.which("R"))), # Set the directory of the R binary
  # cmdargs = c(
  #  Sys.which("R"),  
  # "--slave", "--no-save", "--no-restore"
  # ),
  stdout = "logs/output.log",
  stderr = "logs/error.log",
  supervise = TRUE 
); bot_bg_process$is_alive()

I cannot provide the entire code and folders, but you should be able to reproduce the error removing functions which require env variables.

[dejan94it]

update:
this is the full error backtrace:

Error in `process_initialize(self, private, command, args, stdin, stdout, …` at process.R:212:18:
! Native call to `processx_exec` failed
Caused by error in `chain_call(c_processx_exec, command, c(command, args), pty, pty_options, …` at initialize.R:138:3:
! cannot start processx process '/usr/local/bin/R' (system error 2, No such file or directory) @unix/processx.c:611 (processx_exec)
---
Backtrace:
 1. callr::r_bg(func = start_telegram_bot, args = list(path = ".", …
 2. r_process$new(options = options) at eval-bg.R:42:3
 3. local initialize(...) at new.R:156:5
 4. callr:::rp_init(self, private, super, options) at r-process.R:29:18
 5. callr:::with_envvar(options$env, do.call(super$initialize, c(list(options$bin, … at r-process.R:69:3
 6. base::force(code) at utils.R:66:3
 7. base::do.call(super$initialize, c(list(options$bin, options$real_cmdargs, … at r-process.R:69:3
 8. (function (command = NULL, args = character(), stdin = NULL, …
 9. processx:::process_initialize(self, private, command, args, stdin, stdout, … at process.R:212:18
10. processx:::chain_call(c_processx_exec, command, c(command, args), pty, pty_options, … at initialize.R:138:3
11. | base::withCallingHandlers(do.call(".Call", list(.NAME, ...)), error = function(e) { … at standalone-errors.R:379:5
12. | base::do.call(".Call", list(.NAME, ...)) at standalone-errors.R:379:5
13. | base::.handleSimpleError(function (e) …
14. | local h(simpleError(msg, call))
15. | processx:::throw_error(err, parent = e) at standalone-errors.R:390:9

[dejan94it]

after a thousand tries, even directly with processx, the problem were

  stdout = "logs/output.log",
  stderr = "logs/error.log",

even if thy works fine outside the container.
Anyway I commented those lines and I don't give a hell anymore about logs