Make 01_setup_native.sh actually fail on partial install failure

install.packages() failing for one package doesn't make Rscript exit
non-zero -- it just warns and continues -- so set -euo pipefail never
caught it, and the script printed "Setup complete" unconditionally
regardless of whether packages actually installed. Observed on Monsoon:
RcppEigen got OOM-killed under a low default srun --pty bash allocation
(no explicit --mem), which cascaded to ranger/reticulate/CodeCarbonR
itself all failing to install, and the script still reported success.

Now verifies installed.packages()/pandoc_available()/CodeCarbonR's own
namespace explicitly after each install step and stop()s (which does
exit non-zero) with a clear message if anything's still missing.

Author: beabock

hpc/monsoon/01_setup_native.sh

@@ -44,24 +44,46 @@ echo
 echo "=== R packages -> $RLIBS_DIR ==="
 mkdir -p "$RLIBS_DIR"
 export R_LIBS_USER="$RLIBS_DIR"
+# install.packages() failing for one package doesn't make Rscript exit
+# non-zero -- it just warns and moves on -- so `set -euo pipefail` alone
+# won't catch a partial failure here. Verify explicitly and stop() (which
+# does exit non-zero) if anything's still missing after the install
+# attempt. A package needing real memory to compile (RcppEigen
+# especially -- observed OOM-killed under a low default `srun --pty bash`
+# allocation with no explicit --mem) is exactly the kind of failure this
+# guards against silently sailing past.
 Rscript -e '
   options(repos = c(CRAN = "https://cloud.r-project.org"))
   needed <- c("rmarkdown", "knitr", "reticulate", "ranger", "dplyr",
               "tidyr", "readr", "testthat", "roxygen2", "remotes")
   have <- rownames(installed.packages())
   missing <- setdiff(needed, have)
   if (length(missing) > 0) install.packages(missing)
+  still_missing <- setdiff(needed, rownames(installed.packages()))
+  if (length(still_missing) > 0) {
+    stop(
+      "Failed to install: ", paste(still_missing, collapse = ", "),
+      ". Common cause: not enough memory to compile a package (RcppEigen ",
+      "especially) -- rerun with more memory, e.g. `srun --mem=8G ",
+      "--cpus-per-task=4 --pty bash` instead of a bare `srun --pty bash`.",
+      call. = FALSE
+    )
+  }
   # Pandoc via a plain download, not conda -- rmarkdown needs it, and this
   # sidesteps the same conda issue this whole script exists to avoid.
   if (!rmarkdown::pandoc_available()) rmarkdown::install_pandoc()
-  cat("pandoc:", if (rmarkdown::pandoc_available()) "OK" else "MISSING", "\n")
+  if (!rmarkdown::pandoc_available()) stop("pandoc install failed.", call. = FALSE)
+  cat("pandoc: OK\n")
 '
 
 echo
 echo "=== Installing CodeCarbonR itself from this clone ==="
 Rscript -e '
   options(repos = c(CRAN = "https://cloud.r-project.org"))
   install.packages(".", repos = NULL, type = "source")
+  if (!requireNamespace("CodeCarbonR", quietly = TRUE)) {
+    stop("CodeCarbonR install failed -- see the install.packages() output above.", call. = FALSE)
+  }
 '
 
 echo