🔧 Add selective image rebuild flags and enhance R dependency scanning
- Added --rebuild-builder, -student, hub flags to start-jupyterhub.sh for granular Docker rebuilds - Updated check_if_image_needs_rebuild to accept per-image force flag and propagate no-cache option - Added libuv1-dev dependency in Dockerfile.builder (likely for quarto or R runtime) - Rewrote install_quarto_deps.R to: a) Manually parse library()/require() and remotes::install_git/github calls b) Distinguish between quarto-required packages (must reside in persistent target_lib) c), CRAN and git/github dependencies d) Install with robust error handling, skipping unavailable packages - Removed dependency on attachment package for scanning
This commit is contained in:
Eric Coissac
+109
-26
@@ -1,17 +1,15 @@
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#!/usr/bin/env Rscript
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# Script to dynamically detect and install R dependencies from Quarto files
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# Uses the {attachment} package to scan .qmd files for library()/require() calls
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# Script to dynamically detect and install R dependencies from Quarto files.
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# Scans library()/require() calls and remotes::install_git/github() calls.
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args <- commandArgs(trailingOnly = TRUE)
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quarto_dir <- if (length(args) > 0) args[1] else "."
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# Target library for installing packages (the mounted volume)
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target_lib <- "/usr/local/lib/R/site-library"
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cat("Scanning Quarto files in:", quarto_dir, "\n")
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cat("Target library:", target_lib, "\n")
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# Find all .qmd files
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qmd_files <- list.files(
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path = quarto_dir,
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pattern = "\\.qmd$",
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@@ -26,34 +24,119 @@ if (length(qmd_files) == 0) {
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cat("Found", length(qmd_files), "Quarto files\n")
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# Extract dependencies using attachment
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deps <- attachment::att_from_rmds(qmd_files, inline = TRUE)
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if (length(deps) == 0) {
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cat("No R package dependencies detected.\n")
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quit(status = 0)
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# Extract package names from library()/require() calls
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extract_cran_packages <- function(files) {
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pattern <- "(?:library|require)\\s*\\(\\s*['\"]?([A-Za-z0-9._]+)['\"]?"
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pkgs <- character(0)
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for (f in files) {
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lines <- tryCatch(readLines(f, warn = FALSE), error = function(e) character(0))
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m <- regmatches(lines, gregexpr(pattern, lines, perl = TRUE))
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hits <- unlist(m)
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if (length(hits) > 0) {
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extracted <- sub(
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"(?:library|require)\\s*\\(\\s*['\"]?([A-Za-z0-9._]+)['\"]?.*",
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"\\1", hits, perl = TRUE
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)
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pkgs <- c(pkgs, extracted)
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}
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}
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unique(pkgs)
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}
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cat("\nDetected R packages:\n")
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cat(paste(" -", deps, collapse = "\n"), "\n\n")
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# Extract git/github URLs from remotes::install_git/github() calls
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extract_git_packages <- function(files) {
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# Matches remotes::install_git('url') or remotes::install_github('user/repo')
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pattern <- "remotes::install_(git|github)\\s*\\(\\s*['\"]([^'\"]+)['\"]"
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result <- list()
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for (f in files) {
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lines <- tryCatch(readLines(f, warn = FALSE), error = function(e) character(0))
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text <- paste(lines, collapse = "\n")
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m <- gregexpr(pattern, text, perl = TRUE)
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hits <- regmatches(text, m)[[1]]
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for (hit in hits) {
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type <- sub("remotes::install_(git|github).*", "\\1", hit, perl = TRUE)
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url <- sub("remotes::install_(?:git|github)\\s*\\(\\s*['\"]([^'\"]+)['\"].*",
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"\\1", hit, perl = TRUE)
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result[[length(result) + 1]] <- list(type = type, url = url)
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}
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}
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result
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}
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cran_deps <- extract_cran_packages(qmd_files)
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git_deps <- extract_git_packages(qmd_files)
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# Quarto's implicit runtime dependencies — must be in target_lib (the persistent
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# volume), not just somewhere in libPaths, because Quarto spawns its own R session.
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quarto_required <- c("rmarkdown", "knitr")
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if (length(git_deps) > 0) quarto_required <- c(quarto_required, "remotes")
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cat("\nDetected CRAN packages:\n")
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cat(paste(" -", unique(c(quarto_required, cran_deps)), collapse = "\n"), "\n")
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if (length(git_deps) > 0) {
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cat("\nDetected git/github packages:\n")
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for (d in git_deps) cat(" -", d$type, ":", d$url, "\n")
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}
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cat("\n")
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# --- Install CRAN packages ---
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# Filter out base R packages that are always available
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base_pkgs <- rownames(installed.packages(priority = "base"))
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deps <- setdiff(deps, base_pkgs)
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# Check which packages are not installed
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installed <- rownames(installed.packages())
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to_install <- setdiff(deps, installed)
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# quarto_required: check only in target_lib so they are guaranteed to be there
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installed_in_target <- rownames(installed.packages(lib.loc = target_lib))
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quarto_missing <- setdiff(quarto_required, c(base_pkgs, installed_in_target))
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# other deps: check anywhere in libPaths (they just need to be loadable)
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cran_deps <- setdiff(cran_deps, c(base_pkgs, quarto_required))
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installed <- rownames(installed.packages())
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to_install <- unique(c(quarto_missing, setdiff(cran_deps, installed)))
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if (length(to_install) == 0) {
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cat("All required packages are already installed.\n")
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cat("All CRAN packages already installed.\n")
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} else {
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cat("Installing missing packages:", paste(to_install, collapse = ", "), "\n\n")
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install.packages(
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to_install,
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lib = target_lib,
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repos = "https://cloud.r-project.org/",
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dependencies = TRUE
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)
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cat("\nPackage installation complete.\n")
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cat("Installing CRAN packages:", paste(to_install, collapse = ", "), "\n\n")
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failed <- character(0)
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for (pkg in to_install) {
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result <- tryCatch({
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withCallingHandlers(
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install.packages(pkg, lib = target_lib, repos = "https://cloud.r-project.org/",
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dependencies = TRUE, quiet = FALSE),
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warning = function(w) {
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if (grepl("not available", conditionMessage(w))) invokeRestart("muffleWarning")
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}
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)
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if (!requireNamespace(pkg, quietly = TRUE)) "unavailable" else "ok"
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}, error = function(e) "error")
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if (result %in% c("unavailable", "error")) {
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cat(" [SKIP]", pkg, "- not available on CRAN\n")
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failed <- c(failed, pkg)
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} else {
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cat(" [OK]", pkg, "\n")
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}
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}
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if (length(failed) > 0)
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cat("\nNot installed (not on CRAN):", paste(failed, collapse = ", "), "\n")
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}
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# --- Install git/github packages ---
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if (length(git_deps) > 0) {
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cat("\nInstalling git/github packages...\n")
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for (d in git_deps) {
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tryCatch({
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if (d$type == "git") {
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remotes::install_git(d$url, lib = target_lib, upgrade = "never")
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} else {
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remotes::install_github(d$url, lib = target_lib, upgrade = "never")
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}
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cat(" [OK]", d$url, "\n")
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}, error = function(e) {
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cat(" [FAIL]", d$url, "-", conditionMessage(e), "\n")
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})
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}
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}
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cat("\nDependency installation complete.\n")
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