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Resolve CRAN submission NOTEs - #85

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Summary

  • Document the unavoidable -Wa,-mbig-obj "non-portable flags" NOTE in cran-comments.md, and make the flag's explanatory comment durable by writing it via configure.win (the actual generator of src/Makevars.win) instead of editing the generated file directly, since manual edits there are silently overwritten on every build.
  • Add skip_on_cran() to the three Stan-fitting test_that() blocks in tests/testthat/test-run_model.R (following the existing precedent in test-rename_chains.R) to resolve the "checking tests ... NOTE" caused by real model sampling running during CRAN's check (previously ~49 CPU-minutes / ~2 elapsed minutes). The lightweight smoke test in test-hestia-smoke.R is intentionally left running on CRAN as an end-to-end sanity check.

Test plan

  • just test run locally: 0 failures, 131 passed, 15 warnings (expected Stan sampler diagnostics from short test chains), 0 skipped (devtools::test() sets NOT_CRAN=true, so the new skip_on_cran() guards only take effect on CRAN's own check run).
  • Re-run R CMD check --as-cran to confirm the two targeted NOTEs no longer appear (or are now documented/justified).

🤖 Generated with Claude Code

@csmith701
csmith701 requested a review from pearsonca September 23, 2026 15:20
Document the -Wa,-mbig-obj Windows compilation NOTE in cran-comments.md
and make the explanation durable by writing it into src/Makevars.win via
configure.win (the actual generator), since manual edits to Makevars.win
are overwritten on every build. Also add skip_on_cran() to the
Stan-fitting tests in test-run_model.R so CRAN's check run doesn't pay
for full model sampling.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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✅ All modified and coverable lines are covered by tests.

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