chore: forward-merge main (v3.1.2) into dev → 3.1.2.9000#126
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* docs: v3.1.0 documentation-sweep design spec * docs: v3.1.0 spec — fix bugs surfaced by canonical-source reconciliation (with severity triage) * docs: v3.1.0 doc-sweep implementation plan * docs: deepen varPro-family roxygen (release-rules framing, vimp-vs-varpro) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * docs: add the gg_vimp-vs-gg_varpro distinction to gg_vimp (Task 2 fix) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * docs: deepen rfsrc partial/survival/rfsrc roxygen (ensemble + partial-dependence framing) * docs: address Task 2 review (drop invented first-person in gg_survival; non-positive VIMP wording) * docs: voice/drift cleanup on remaining roxygen topics Remove stale yvar @return item from gg_roc — the function returns sens/spec/pct (from calc_roc), not a yvar column per observation. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * docs(vignette): deepen varpro — release-rules framing, refs Deepens all prose sections of varpro.qmd with release-rules/guided-splitting framing; adds Lee:2021 bib key (AOS 49:4) cited in PBC section; adds varProtools URL in Further Reading. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * docs(vignette): regression — vimp-vs-varpro contrast, rfsrc ref Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * docs(vignette): survival — rfsrc ensemble framing, ref Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * docs(vignette): intro — voice/drift pass * docs(comments): correctness + gap pass on R/ source Fix a misleading AUC trapezoidal-rule comment in calc_roc.R (the old text introduced Δ(FPR) but the code uses Δspec; reworded to state the equivalence plainly). Remove a stale varPro-specific note from the categorical branch of gg_partial.R (plot.variable output has no connection to varPro one-hot encoding). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * docs(NEWS): open v3.1.0 development heading (version unchanged) * docs(vignette): trim em-dashes in varpro per voice standard Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * fix(PR#109 review): gg_vimp positive flag (VIMP vs vimp case), Brier 0.25 precision * chore(release): prepare v3.1.0 for CRAN Bump DESCRIPTION + NEWS to 3.1.0 (CRAN never saw v3.0.0; jump from 2.7.3 is intentional) and finalize the v3.1.0 NEWS heading. Trim em-dashes and right-arrows from roxygen and code comments per the package voice standard (68 replacements across R/), then re-document so man/*.Rd carries no raw non-ASCII into the PDF manual build. Rewrite cran-comments.md for the 2.7.3 -> 3.1.0 submission: fold in the v3.0.0 feature layer, correct the local test env (R 4.6.0/darwin23). R CMD check --as-cran (with manual build, ggraph present): 0/0/0. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * docs(cran-comments): correct v3.0.0 history v3.0.0 was submitted but did not complete the CRAN review cycle; 3.1.0 supersedes it. Prior wording said it was never submitted. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * docs(cran-comments): note v3.0.0 pretests were clean, hold was heuristic Per the release handoff: tell the CRAN reviewer the 2026-05-28 v3.0.0 submission cleared incoming pretests on Windows + Debian (0/0/0) and the auto-hold looked like a version-jump/Depends-to-Imports heuristic, not a defect, in case the same heuristic flags v3.1.0. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * docs(dev/plans): mark v3.0.0-held release mechanics as superseded The plan/design docs described the held workflow (keep Version 3.0.0, merge only after CRAN accepts v3.0.0, cut 3.1.0 at a post-acceptance RC). v3.0.0 lapsed un-reviewed, so we ship 3.1.0 directly. Banners note this; the documentation-content plan is unchanged. Addresses Copilot review. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> --------- Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
…ze (#110) The regression and survival partial-dependence surfaces were interactive plotly widgets; self-contained quarto inlined plotly.js (~3.5 MB) into each vignette HTML, and figures rendered at retina 2x. Installed size was 17.1 MB (doc 16.3 MB), well over CRAN's 5 MB guideline. Replace both surfaces with static ggplot2 heat maps, set fig-format png / fig-dpi 96 in all four vignettes, and drop the now-unused plotly Suggests. Installed size drops to ~5.5 MB (doc 4.7 MB); source tarball 9.0 -> 3.7 MB. R CMD check --as-cran (with manual, ggraph present): pending confirmation. Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
…113) win-builder R-oldrelease flagged the plot.gg_variable example at 10.33s elapsed (just over CRAN's 10s; under 10s on release/devel). Wrap the loess-heavy regression panel plot and the full survival section (veteran forest + multi-time variable/panel plots) in \donttest so they are excluded from the timed example run; the fast classification + basic regression plots still run. No behaviour change. R CMD check --as-cran: examples [14s] OK, examples --run-donttest [28s] OK, Status: OK (0/0/0). Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
* perf(check): cut CRAN overall check time below 10 min CRAN flagged the 3.1.0 submission's overall check time (13 min > 10 min), driven by the vignette rebuild (331s) and tests (209s). Reduce both per Uwe Ligges' suggested levers (toy data / fewer iterations / precomputed results), with no change to test coverage or vignette content. Vignettes: - regression: Boston forest ntree 200, PD-surface grid 25 -> 10 - survival: impute ntree 100, forest ntree 150, PD-surface grid 25 -> 8 - varpro: the three gg_partial_varpro() calls (11-17s each) and the Boston beta.varpro() fit (~3s) -- the bulk of that vignette -- are precomputed offline by precompute_varpro.R and loaded from varpro_precomputed.rds (167 KB, xz), with an automatic live-computation fallback if absent. Tests: - test_gg_udependent memoised varPro::get.beta.entropy() (~1.5s, a pure function of the fit) per argument signature instead of recomputing it once per test (this file was ~24s of the suite, now ~9s). Verified: R CMD check --as-cran with manual is OK (0/0/0); local vignette rebuild 33s and tests 28s (were 331s/209s on CRAN's r-devel-windows). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * review: address Copilot feedback on the check-time PR - varpro.qmd: load the precompute via tryCatch(readRDS) so a missing OR unreadable .rds falls back to live computation instead of erroring. - precompute_varpro.R: mirror the vignette's requireNamespace/pkgload fallback instead of bare library(ggRandomForests), so the script runs in a fresh clone before the package is installed. - test_gg_udependent.R: make make_ggu() warning suppression opt-in (.quiet = FALSE by default); pass .quiet = TRUE only to the empty-graph (threshold = 999) cases that legitimately warn, so an unexpected warning on any other call still fails the test. Verified: test_gg_udependent 19 tests, 0 fail / 0 warn; varpro vignette renders in 20s with 0 errors (precompute still loaded). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * review(#114): search both paths for varpro_precomputed.rds The precomputed-load chunk read only the cwd-relative 'varpro_precomputed.rds'; depending on how Quarto sets the working directory during R CMD check this could miss the file and silently fall back to (slower) live computation. Search both the vignette-dir and package-root locations before the live fallback. Addresses Copilot review. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
v3.1.0 accepted to CRAN (2026-06-11). Bump main to the post-release .9000 dev version (DESCRIPTION + NEWS, dual update so the news-version test sees the DESCRIPTION version), and record the release submission in CRAN-SUBMISSION (SHA a7d8052). Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
…p + vignette precompute) (#119) * fix(cran): skip_on_cran the varPro tests to avoid upstream UBSAN (v3.1.1) CRAN's gcc-UBSAN additional check flagged 3.1.0 with a 0-length array access in randomForestSRC's compiled rfsrcGrow (entry.c:184), reached when varPro::varpro()/beta.varpro() grow a forest in our tests. ggRandomForests is pure R (NeedsCompilation: no) — the overflow is in a dependency, surfaced by our tests. Gate every varPro forest-growing test fixture/builder with testthat::skip_on_cran() so CRAN's machines (incl. gcc-UBSAN) never run them. No package code changed; the tests still run on CI and locally. Bump to 3.1.1; NEWS + cran-comments explain the fix. Upstream reported. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * docs(cran-comments): note the benign 'days since last update' NOTE Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * fix(cran): precompute all varPro vignette fits to avoid upstream UBSAN The varpro vignette grew ~10 varPro forests live (varpro/uvarpro/isopro/ ivarpro/beta.varpro), each reaching randomForestSRC's rfsrcGrow rule-grow path that trips the gcc-UBSAN "0-length array" report (entry.c:184, a length-0 yvar.wt decremented to an out-of-bounds pointer). Cache every fit in vignettes/varpro_precomputed.rds and load it with a live fallback, so R CMD check performs no live varPro grow. Strip the unused embedded forests ($rf, $isoforest, redundant ivarpro attrs) before saving — validated that every gg_* wrapper call returns output identical to the un-stripped object — keeping the file at 414 KB (tarball 4.13 MB, under CRAN's 5 MB limit). R CMD check --as-cran (with manual): 0 errors, 0 warnings, 1 NOTE (days-since-update, expected). Overall check time 2:43. dev/randomForestSRC-ubsan-report.md records the upstream root cause + suggested patch (maintainers are aware and staging a fix). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * style(vignette): satisfy lintr (brace/semicolon) in fallback chunks Lint CI flagged 16 brace_linter/semicolon_linter issues in the vignette hardening: - varpro.qmd: the load-with-fallback chunks braced the `if` branch but not `else` (`} else .vp$x`); brace both branches to match the existing precomputed chunks. - precompute_varpro.R: rewrite the one-line .strip_* helpers (compound semicolons + inline braces) as multi-line. Behaviour-preserving; lint_package() now returns 0. The shipped varpro_precomputed.rds is unchanged. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * docs: address Copilot review — accurate CI claims, scoped strip comments Copilot flagged that skip_on_cran() also skips under R CMD check in CI (NOT_CRAN unset in the workflows), so the varPro tests run nowhere in CI: - NEWS.md / cran-comments.md no longer claim the tests "run on CI"; they state the tests run locally (devtools::test()) and are skipped under R CMD check, including the CI check jobs. (Restoring CI coverage via NOT_CRAN=true is deferred to 3.1.2, coupled with the issue #118 fix so the intermittent survival gg_varpro test doesn't flake CI.) - precompute_varpro.R: scope the "forests unused" comments — the survival C-path gg_partial_varpro() and gg_isopro(newdata=) DO use $rf/$isoforest, but the vignette never invokes those on a stripped object (pd_pbc cached, gg_isopro training-path only). No behaviour change; lint_package() = 0. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * ci: set NOT_CRAN=true so varPro tests run in CI (Copilot review) Copilot noted skip_on_cran() also skips the varPro tests under R CMD check in CI (NOT_CRAN unset), so they ran nowhere. Set NOT_CRAN=true in all check/coverage workflows to restore that coverage. Safe: CI is not a sanitizer build, so the upstream randomForestSRC UBSAN path is harmless here; only CRAN's own check machines (NOT_CRAN unset) skip them, which is what avoids the gcc-UBSAN additional issue. The CI-run varPro tests cover regression + classification only (no survival), so issue #118 cannot flake CI. Verified locally under NOT_CRAN=true: 0 failures across the varPro suite. NEWS.md / cran-comments.md restore the accurate "runs in CI and locally; skipped only on CRAN" claim. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
…BSAN trigger (#122) * fix(cran): v3.1.2 — skip_on_cran the isopro fixture (clear gcc-UBSAN) v3.1.1 guarded the varPro forest-growing test fixtures with skip_on_cran() but missed make_iso_fit() in tests/testthat/test_gg_isopro.R. It was gated only by skip_if_not_installed("varPro"), and varPro IS installed on CRAN's check machines — so the ~23 isopro tests still ran there. varPro::isopro() grows an *unsupervised* isolation forest (do.call("rfsrc", ...) with the unsupv family → yvar.wt length 0). That is the exact path that trips randomForestSRC's gcc-UBSAN report at entry.c:184 (unconditional RF_yWeight-- on a 0-length weight vector → out-of-bounds pointer, UB). It was the one unsupervised grow v3.1.1 left unguarded, so the additional check re-flagged the issue against 3.1.1. Fix: add testthat::skip_on_cran() to make_iso_fit(), matching the other varPro fixtures. ggRandomForests is pure R (NeedsCompilation: no); package code is unchanged. The isopro tests still run in CI and locally (NOT_CRAN=true). Verified: R CMD check --as-cran (with manual) → 0 errors, 0 warnings, 1 NOTE (days-since-update), 2.6 min. test-all.Rout shows all 23 isopro tests in the "On CRAN" skip list, so the unsupervised grow no longer executes under the check. Bumps DESCRIPTION + NEWS to 3.1.2; cran-comments updated. Upstream fix is randomForestSRC commit 92ec283 (not yet on CRAN). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * fix(cran): narrow the UBSAN skip to only isopro(method="unsupv") Empirically pinned the gcc-UBSAN trigger with -fsanitize=undefined on CRAN's randomForestSRC 3.6.2: of every varPro/rfsrc grow in the suite, ONLY varPro::isopro(method="unsupv") fires entry.c:184. It is the sole grow with a length-0 yvar.wt (unsupervised family). Everything else is supervised or synthetic-supervised and UBSAN-clean: - varpro / ivarpro / beta.varpro: real Y -> non-empty yvar.wt - isopro(method="rnd"): synthetic supervised forest - uvarpro: grows yxyz123 ~ . with an rnorm response (synthetic supervised) So: - make_iso_fit() now skip_on_cran() ONLY when method == "unsupv" (the rnd isopro tests run on CRAN again). - Reverted v3.1.1's blanket skip_on_cran() on the varpro/uvarpro/ivarpro/ beta fixtures (helper-varpro-fixtures.R, test_gg_varpro.R, test_gg_udependent.R) -> ~126 varPro tests run on CRAN again. Verified: - Full suite under CRAN conditions (NOT_CRAN unset) against a GCC-equivalent UBSAN rfsrc (-fsanitize=undefined -fno-sanitize=float-cast-overflow): 0 runtime errors, FAIL 0 / PASS 1093 / SKIP 7. Only 2 tests skip On CRAN (isopro-unsupv + the pre-existing slow ivarpro test). - R CMD check --as-cran (with manual): 0 errors, 0 warnings, 1 NOTE (days-since-update); overall 2.68 min, well under the 10-min budget. Note: a local clang UBSAN build also surfaces partial.c:92 (a (uint)NaN float-cast in test_gg_partial_varpro's categorical survival partial dependence). CRAN does not see it: GCC's -fsanitize=undefined excludes float-cast-overflow (clang's includes it). Confirmed by rebuilding with that check disabled. Separate latent upstream issue, not a CRAN blocker. NEWS + cran-comments updated to describe the narrowed fix. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * test(isopro): namespace-qualify skip_* in make_iso_fit Use testthat::skip_on_cran()/skip_if_not_installed() so the helper does not depend on testthat being attached. Addresses a Copilot review note on #122; qualifies both calls for internal consistency. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * docs(cran-comments): correct NOTE disposition + narrowed-skip wording R CMD check --as-cran returns 1 NOTE (days since last update), not 0; only the single unsupervised isopro test skips on CRAN now (all other varPro tests run). Genericise the day count so the submitted comment is not stale. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
Brings the v3.1.1 + v3.1.2 CRAN gcc-UBSAN fixes onto the dev/v4.0.0 line and reconciles the dev version to 3.1.2.9000 (strictly ahead of CRAN 3.1.2). Conflict resolutions (squash-merge history made the merge base stale, so most conflicts were artifacts, not competing edits): - DESCRIPTION/NEWS: version 3.1.2.9000; kept dev's v4.0.0 (development) section + randomForestRHF Suggests; folded in main's v3.1.1 + v3.1.2 NEWS sections. - R/print_helpers.R, tests/testthat/test_gg_vimp.R: kept DEV — main made no post-3.1.0 changes to these; dev has the RHF provenance block + the evolved (deterministic const-predictor) gg_vimp test. - vignettes/precompute_varpro.R, varpro_precomputed.rds: took MAIN — these are the 3.1.1 hardened precompute (all 14 fits, 414 KB rds); varpro.qmd auto-merged to match. - CRAN-SUBMISSION, cran-comments.md: took MAIN (the 3.1.2 release records). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Pull request overview
Forward-merge of main CRAN hotfixes (v3.1.1 + v3.1.2) onto the dev line, reconciling the development version to 3.1.2.9000 while carrying over the UBSAN-related mitigations for randomForestSRC that are triggered via varPro forest grows.
Changes:
- Reconciles package version metadata to 3.1.2.9000 and updates release documentation (NEWS/CRAN records).
- Updates the varPro vignette + precompute script to prefer precomputed fits (with live-fit fallbacks) to avoid expensive/UBSAN-sensitive grows during
R CMD check. - Refines varPro-related tests/CI behavior so only the known UBSAN-triggering unsupervised
isopro(method = "unsupv")path is skipped on CRAN, while still running those tests in CI viaNOT_CRAN=true.
Reviewed changes
Copilot reviewed 15 out of 16 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| vignettes/varpro.qmd | Loads precomputed varPro fits when available, falling back to live computation per object. |
| vignettes/precompute_varpro.R | Expands the set of precomputed objects and strips heavy slots to reduce shipped artifact size. |
| tests/testthat/test_gg_varpro.R | Clarifies CRAN/UBSAN behavior in regression varPro fixture comments. |
| tests/testthat/test_gg_udependent.R | Clarifies why uvarpro() grow is UBSAN-clean on CRAN (synthetic-supervised). |
| tests/testthat/test_gg_isopro.R | Skips only the CRAN-unsuitable unsupervised isopro(method=\"unsupv\") grow. |
| tests/testthat/helper-varpro-fixtures.R | Documents why supervised varPro grows are intended to run on CRAN. |
| NEWS.md | Bumps dev version header and adds v3.1.1/v3.1.2 release notes. |
| dev/randomForestSRC-ubsan-report.md | Adds a detailed upstream UBSAN report and suggested C-side guard. |
| DESCRIPTION | Updates Version/Date to 3.1.2.9000 / 2026-06-13. |
| CRAN-SUBMISSION | Updates submission record to v3.1.2. |
| cran-comments.md | Updates CRAN commentary to describe the v3.1.2 UBSAN mitigation approach. |
| .github/workflows/test-coverage.yaml | Sets NOT_CRAN=true so skip_on_cran() tests run in CI. |
| .github/workflows/R-CMD-check.yaml | Sets NOT_CRAN=true so skip_on_cran() tests run in CI. |
| .github/workflows/check-standard.yaml | Sets NOT_CRAN=true so skip_on_cran() tests run in CI. |
| .github/workflows/check-release.yaml | Sets NOT_CRAN=true so skip_on_cran() tests run in CI. |
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| # --- Regression: Boston housing ------------------------------------------ | ||
| if (!requireNamespace("MASS", quietly = TRUE)) { | ||
| stop("Package 'MASS' is required for the Boston housing data; install it to ", | ||
| "run this script.") | ||
| } | ||
| data("Boston", package = "MASS") | ||
| boston_x <- Boston[, setdiff(names(Boston), "medv")] |
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| # --- Regression: Boston housing ------------------------------------------ | ||
| if (!requireNamespace("MASS", quietly = TRUE)) { | ||
| stop("Package 'MASS' is required for the Boston housing data; install it to ", | ||
| "run this script.") | ||
| } | ||
| data("Boston", package = "MASS") | ||
| boston_x <- Boston[, setdiff(names(Boston), "medv")] |
Addresses Copilot review on #126: MASS is only in Suggests, so guard the `data("Boston", package = "MASS")` call with an explicit requireNamespace("MASS") check + clear stop, instead of failing with a non-obvious error in a minimal dev environment. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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ehrlinger
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Jun 13, 2026
3.1.2 just shipped to CRAN; the #118 fix + new unsupervised varPro wrappers are normal development, not a back-to-back CRAN update. Drop the 3.1.3 version bump back to the dev version (3.1.2.9000) and file the notes under the v4.0.0 (development) line. To be retargeted onto dev and rebased after the forward-merge (#126) lands. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The forward-merge kept dev's version of this test, which relied on a zero-variance 'const' predictor having non-positive VIMP. Permutation VIMP of a weak/constant variable can land slightly >0 (rfsrc may also drop a constant column), so `any(!positive)` was FALSE on R-release -> CI failure. Inject one non-positive importance (`rf$importance[1] <- -1`) so the test reliably exercises the bug condition on every platform; the invariant assertion (positive == VIMP>0) is unchanged. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
ehrlinger
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Jun 13, 2026
Now that the forward-merge (#126) landed on dev, bring dev into this branch so the diff is just the new work (#118 fix + gg_beta_uvarpro / gg_sdependent). Resolutions: - test_gg_vimp.R, precompute_varpro.R, R/print_helpers.R: took dev (the deterministic gg_vimp fix, the MASS guard, the RHF provenance block; this branch made no competing changes to those). - NEWS.md: combined both v4.0.0 (development) sections (RHF + the new wrappers). - NAMESPACE + man/: regenerated via roxygen so both the RHF and the new unsupervised-varPro exports are present. Stays a draft: development work at 3.1.2.9000, not a release. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Forward-merges the v3.1.1 + v3.1.2 CRAN gcc-UBSAN fixes from
mainonto thedev/ v4.0.0 (RHF) line, and reconciles the dev version to 3.1.2.9000 (strictly ahead of CRAN 3.1.2, per the post-release version-reconciliation rule).Why there were conflicts
The prior forward-merge (#117) was squash-merged, so the merge base is stale (pre-3.1.0). Most of the 8 conflicts were artifacts of that history, not competing edits — verified by checking which side actually changed each file post-3.1.0.
Conflict resolutions
DESCRIPTION,NEWS.md3.1.2.9000; kept dev'sv4.0.0 (development)section +randomForestRHFSuggests; folded in main's v3.1.1 + v3.1.2 NEWS sectionsR/print_helpers.R,tests/testthat/test_gg_vimp.Rgg_vimptestvignettes/precompute_varpro.R,varpro_precomputed.rdsvarpro.qmdauto-merged to matchCRAN-SUBMISSION,cran-comments.mdLocal checks
DESCRIPTIONandNEWS.mdboth3.1.2.9000(news-version test passes); R files parse.Please squash-merge (matches #117) once the 3-OS required checks are green.
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