command_args <- commandArgs(trailingOnly = FALSE)
script_path <- sub("^--file=", "", grep("^--file=", command_args, value = TRUE)[1])
script_dir <- dirname(normalizePath(script_path, winslash = "/"))
project_root <- normalizePath(file.path(script_dir, "..", ".."), winslash = "/")
library_path <- file.path(project_root, ".r-library", "4.6")
dir.create(library_path, recursive = TRUE, showWarnings = FALSE)
.libPaths(c(library_path, .libPaths()))

required_packages <- c(
  "survey", "srvyr",
  "mirt",
  "lavaan", "semTools", "psych",
  "data.table", "jsonlite", "arrow", "haven", "readr",
  "dplyr", "tidyr", "purrr", "stringr",
  "digest", "renv", "targets", "withr"
)

installed <- rownames(installed.packages(lib.loc = .libPaths()))
missing <- setdiff(required_packages, installed)

if (length(missing) > 0L) {
  install.packages(
    missing,
    lib = library_path,
    repos = c(CRAN = "https://cloud.r-project.org"),
    dependencies = c("Depends", "Imports", "LinkingTo"),
    type = "binary",
    Ncpus = max(1L, parallel::detectCores(logical = TRUE) - 2L)
  )
}

installed_after <- rownames(installed.packages(lib.loc = .libPaths()))
still_missing <- setdiff(required_packages, installed_after)
if (length(still_missing) > 0L) {
  stop("Missing R packages after installation: ", paste(still_missing, collapse = ", "))
}

versions <- vapply(
  required_packages,
  function(package) as.character(packageVersion(package, lib.loc = library_path)),
  character(1)
)
writeLines(
  jsonlite::toJSON(as.list(versions), pretty = TRUE, auto_unbox = TRUE),
  file.path(script_dir, "r-package-versions.json"),
  useBytes = TRUE
)
cat("Installed and verified", length(required_packages), "required R packages.\n")