Add Cloud Agent development environment for caret

.cursor/environment.json

@@ -0,0 +1,5 @@
+{
+  "name": "caret (R package)",
+  "user": "ubuntu",
+  "install": "bash .cursor/install.sh"
+}

.cursor/install.sh

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+#!/usr/bin/env bash
+#
+# Cloud Agent install script for the caret R package (source lives in pkg/caret).
+#
+# Idempotent: safe to run repeatedly. It (1) ensures the R toolchain and system
+# libraries exist, (2) configures a fast binary CRAN mirror plus legacy-compat
+# compiler flags, (3) installs caret's runtime + test dependencies, and
+# (4) builds and installs the in-repo caret package.
+set -euo pipefail
+
+REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+cd "$REPO_ROOT"
+
+# ---------------------------------------------------------------------------
+# 1. System toolchain (R + build deps). Only runs when R is not already present
+#    (e.g. a cold VM). On snapshot-backed builds R is baked in, so this is a
+#    fast no-op.
+# ---------------------------------------------------------------------------
+if ! command -v Rscript >/dev/null 2>&1; then
+  echo "==> Installing R and system build dependencies"
+  export DEBIAN_FRONTEND=noninteractive
+  sudo apt-get update -qq
+  sudo apt-get install -y --no-install-recommends \
+    dirmngr gnupg ca-certificates curl
+
+  sudo install -d -m 0755 /etc/apt/keyrings
+  curl -fsSL https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc \
+    | sudo tee /etc/apt/keyrings/cran.asc >/dev/null
+  echo "deb [signed-by=/etc/apt/keyrings/cran.asc] https://cloud.r-project.org/bin/linux/ubuntu noble-cran40/" \
+    | sudo tee /etc/apt/sources.list.d/cran.list >/dev/null
+
+  sudo apt-get update -qq
+  sudo apt-get install -y --no-install-recommends \
+    r-base-dev gfortran build-essential pandoc \
+    libcurl4-openssl-dev libssl-dev libxml2-dev libgit2-dev \
+    libfontconfig1-dev libharfbuzz-dev libfribidi-dev \
+    libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
+fi
+
+echo "==> R version: $(R --version | head -1)"
+
+# ---------------------------------------------------------------------------
+# 2. R configuration: fast binary mirror + legacy-compat build flags.
+# ---------------------------------------------------------------------------
+# Posit Public Package Manager serves precompiled binaries for Ubuntu 24.04
+# (noble), making dependency installs seconds instead of many minutes.
+cat > "$HOME/.Rprofile" <<'EOF'
+local({
+  options(
+    repos = c(P3M = "https://packagemanager.posit.co/cran/__linux__/noble/latest"),
+    HTTPUserAgent = sprintf(
+      "R/%s R (%s)",
+      getRversion(),
+      paste(getRversion(), R.version["platform"], R.version["arch"], R.version["os"])
+    ),
+    Ncpus = max(1L, parallel::detectCores())
+  )
+})
+EOF
+
+# caret's src/caret.c derives from the legacy `class` package and relies on the
+# `Sint` type and `DOUBLE_XMAX` constant, both removed from modern R headers.
+# Restore their historical definitions (Sint == int, DOUBLE_XMAX == DBL_MAX)
+# via compiler flags so the package builds without patching its source.
+mkdir -p "$HOME/.R"
+cat > "$HOME/.R/Makevars" <<'EOF'
+CPPFLAGS += -DSint=int -DDOUBLE_XMAX=DBL_MAX
+EOF
+
+# Ensure the standard site library is user-writable so install.packages() and
+# R CMD INSTALL work without root.
+SITE_LIB="$(Rscript -e 'cat(.Library.site[1])')"
+if [ -n "$SITE_LIB" ] && [ ! -w "$SITE_LIB" ]; then
+  sudo mkdir -p "$SITE_LIB"
+  sudo chown -R "$(id -un):$(id -gn)" "$SITE_LIB"
+fi
+
+# ---------------------------------------------------------------------------
+# 3. R package dependencies (runtime Imports/Depends + packages exercised by
+#    the test suite). Only missing packages are installed, so reruns are fast.
+# ---------------------------------------------------------------------------
+echo "==> Installing R package dependencies"
+Rscript - <<'EOF'
+pkgs <- c(
+  # caret Depends / Imports
+  "lattice", "ggplot2", "foreach", "plyr", "ModelMetrics", "nlme",
+  "reshape2", "recipes", "withr",
+  # test harness + models exercised directly by the testthat suite
+  "testthat", "arm", "C50", "earth", "gam", "glmnet", "fastICA",
+  "rpart", "kernlab", "ipred", "mda", "MASS", "dplyr", "e1071", "pROC",
+  # additional dependencies declared by the project's CI (.travis.yml)
+  "MLmetrics", "mgcv", "klaR", "mlbench", "nnet", "party", "pls",
+  "proxy", "randomForest", "RANN", "ellipse", "data.table", "subselect",
+  "spls", "pamr", "superpc", "Cubist", "knitr"
+)
+missing <- setdiff(pkgs, rownames(installed.packages()))
+if (length(missing)) {
+  cat("Installing:", paste(missing, collapse = ", "), "\n")
+  install.packages(missing)
+} else {
+  cat("All R dependencies already present.\n")
+}
+still_missing <- setdiff(pkgs, rownames(installed.packages()))
+if (length(still_missing)) {
+  stop("Failed to install: ", paste(still_missing, collapse = ", "))
+}
+EOF
+
+# ---------------------------------------------------------------------------
+# 4. Build & install the in-repo caret package.
+# ---------------------------------------------------------------------------
+echo "==> Building and installing caret from pkg/caret"
+R CMD INSTALL --no-multiarch --with-keep.source pkg/caret
+
+echo "==> Verifying caret loads"
+Rscript -e 'suppressPackageStartupMessages(library(caret)); cat("caret", as.character(packageVersion("caret")), "loaded OK\n")'
+
+echo "==> install.sh complete"