Fix cran (#99)

* Add devcontainer configuration for R project

- Use `mcr.microsoft.com/devcontainers/r:latest` as base image.
- Exclude `rJava` from dependency installation to keep container Java-free.
- Install Posit Air CLI and VS Code extension.
- Install Quarto extension.

* Add devcontainer configuration for R project

- Use `mcr.microsoft.com/devcontainers/r:latest` as base image.
- Exclude `rJava` from dependency installation to keep container Java-free.
- Install Posit Air CLI and VS Code extension.
- Install Quarto extension.
- Update scripts to address PR review feedback (robust dependency handling, verification).

* Add devcontainer configuration for R project

- Use `mcr.microsoft.com/devcontainers/r:latest` as base image.
- Exclude `rJava` from dependency installation to keep container Java-free.
- Install Posit Air CLI and VS Code extension.
- Install Quarto extension.
- Update scripts to address PR review feedback (pinned version, security, robustness).

* fixes for cran following winbuilder tests

* Update R/java_install.R

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Author: 3 people

.Rbuildignore

@@ -34,5 +34,6 @@
 ^\.jupyter$
 ^[.]?air[.]toml$
 ^\.vscode$
-^\.devcontainer$
+^\.sync$
 ^\.claude$
+^\.devcontainer$

.devcontainer/devcontainer.json

@@ -0,0 +1,20 @@
+{
+  "name": "rJavaEnv Dev Container",
+  "image": "mcr.microsoft.com/devcontainers/r:latest",
+  "features": {
+    "ghcr.io/devcontainers/features/common-utils:2": {}
+  },
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "quarto.quarto",
+        "Posit.air-vscode",
+        "REditorSupport.r"
+      ]
+    }
+  },
+  "postCreateCommand": "bash .devcontainer/setup.sh",
+  "remoteEnv": {
+    "PATH": "${containerEnv:PATH}:/home/vscode/.local/bin"
+  }
+}

.devcontainer/setup.R

@@ -0,0 +1,17 @@
+#!/usr/bin/env Rscript
+
+# Ensure remotes is installed
+if (!requireNamespace("remotes", quietly = TRUE)) {
+  install.packages("remotes")
+}
+
+# Get dependencies from DESCRIPTION in the current directory
+deps <- remotes::dev_package_deps(dependencies = TRUE)
+
+# Filter out rJava to ensure no Java is installed
+# deps is a data.frame with class "package_deps"
+deps <- deps[deps$package != "rJava", ]
+
+# Install/Update the selected packages
+# The update() method for package_deps respects version requirements
+remotes::update(deps, upgrade = "always")

.devcontainer/setup.sh

@@ -0,0 +1,48 @@
+#!/bin/bash
+set -e
+
+# Configuration
+AIR_VERSION="0.8.0"
+INSTALL_DIR="$HOME/.local/bin"
+mkdir -p "$INSTALL_DIR"
+
+# Detect Architecture
+ARCH=$(uname -m)
+if [ "$ARCH" = "x86_64" ]; then
+    AIR_ARCH="x86_64"
+elif [ "$ARCH" = "aarch64" ] || [ "$ARCH" = "arm64" ]; then
+    AIR_ARCH="aarch64"
+else
+    echo "Unsupported architecture: $ARCH"
+    exit 1
+fi
+
+PLATFORM="unknown-linux-gnu"
+FILENAME="air-${AIR_ARCH}-${PLATFORM}.tar.gz"
+URL="https://github.com/posit-dev/air/releases/download/${AIR_VERSION}/${FILENAME}"
+
+echo "Installing Posit Air CLI version ${AIR_VERSION} for ${AIR_ARCH}..."
+
+# Download and install
+# We use a temporary directory to ensure clean cleanup
+TMP_DIR=$(mktemp -d)
+curl -LsSf "$URL" -o "${TMP_DIR}/${FILENAME}"
+tar -xzf "${TMP_DIR}/${FILENAME}" -C "$TMP_DIR"
+mv "${TMP_DIR}/air" "$INSTALL_DIR/air"
+rm -rf "$TMP_DIR"
+
+# Ensure air is on PATH for the remainder of this setup script.
+export PATH="$INSTALL_DIR:$PATH"
+
+# Verify Air CLI installation
+if ! command -v air &> /dev/null; then
+    echo "Error: Air CLI failed to install or is not in PATH."
+    exit 1
+fi
+echo "Air CLI installed successfully: $(air --version)"
+
+# Install R dependencies
+echo "Installing R dependencies (excluding rJava)..."
+Rscript .devcontainer/setup.R
+
+echo "Setup complete!"

R/global_params.R

@@ -15,23 +15,23 @@ global_quiet_param <- function(quiet) {
 #' Documentation template for rJava path-locking behavior.
 #'
 #' @section rJava Path-Locking:
-#' **Important for rJava Users**: This function sets environment variables
-#' (JAVA_HOME, PATH) that affect both command-line Java tools and rJava initialization.
-#' However, due to rJava's path-locking behavior when \code{\link[rJava]{.jinit}} is called
+#' **Important for \emph{rJava} Users**: This function sets environment variables
+#' (JAVA_HOME, PATH) that affect both command-line Java tools and \emph{rJava} initialization.
+#' However, due to \emph{rJava}'s path-locking behavior when \code{\link[rJava]{.jinit}} is called
 #' (see \url{https://github.com/s-u/rJava/issues/25}, \url{https://github.com/s-u/rJava/issues/249}, and \url{https://github.com/s-u/rJava/issues/334}),
 #' this function must be called **BEFORE** \code{\link[rJava]{.jinit}} is invoked. Once \code{\link[rJava]{.jinit}}
 #' initializes, the Java version is locked for that R session and cannot be changed without restarting R.
 #'
 #' \code{\link[rJava]{.jinit}} is invoked (and Java locked) when you:
 #' \itemize{
 #'   \item Explicitly call \code{library(rJava)}
-#'   \item Load any package that imports rJava (which auto-loads it as a dependency)
+#'   \item Load any package that imports \emph{rJava} (which auto-loads it as a dependency)
 #'   \item Even just use IDE autocomplete with \code{rJava::} (this triggers initialization!)
-#'   \item Call any rJava-dependent function
+#'   \item Call any \emph{rJava}-dependent function
 #' }
 #'
-#' Once any of these happen, the Java version used by rJava for that session is locked in.
-#' For command-line Java tools that don't use rJava, this function can be called at any
+#' Once any of these happen, the Java version used by \emph{rJava} for that session is locked in.
+#' For command-line Java tools that don't use \emph{rJava}, this function can be called at any
 #' time to switch Java versions for subsequent system calls.
 #'
 #' @keywords internal

R/internal_utilities.R

@@ -417,6 +417,7 @@ java_check_current_rjava_version <- function() {
 #' @param temp_dir The directory where files were extracted.
 #' @return The path to the first non-hidden directory found.
 #' @keywords internal
+#' @noRd
 ._find_extracted_dir <- function(temp_dir) {
   # Ignore hidden files like .DS_Store or AppleDouble files (._)
   all_files <- list.files(temp_dir, full.names = TRUE)

R/java_install.R

@@ -73,7 +73,8 @@ java_install <- function(
   arch <- parts[vapply(parts, function(x) x %in% architectures, logical(1))][1]
   platform <- parts[vapply(parts, function(x) x %in% platforms, logical(1))][1]
 
-  # Create a symlink in the project directory (new structure with distribution/backend)
+
+  # Create a symlink in the project directory
   project_version_path <- file.path(
     project_path,
     "rjavaenv",