fix #118 + unsupervised varPro wrappers (gg_beta_uvarpro / gg_sdependent) [dev] by ehrlinger · Pull Request #121 · ehrlinger/ggRandomForests

ehrlinger · 2026-06-12T14:31:47Z

Re-cut as 3.1.3. This content was the originally-planned 3.1.2 (fix #118 + the unsupervised varPro wrappers), but that version number was consumed by the gcc-UBSAN re-fix shipped as 3.1.2. Rebased onto current main and bumped to 3.1.3.

Fix gg_varpro(): intermittent failure on survival fits — varPro importance() returns 0 rows #118: gg_varpro() no longer dies with "differing number of rows: p, 0" on a degenerate varPro::importance() table — clear scoped error instead (not a survival-family block; cf. reverted fix(gg_varpro): clear error on survival fits instead of cryptic cbind #116).
gg_beta_uvarpro() / plot.*: unsupervised analogue of gg_beta_varpro() (wraps varPro::get.beta.entropy()).
gg_sdependent() / plot.*: ranked signal-variable detection (varPro::sdependent()), complements gg_udependent().

Fixes applied during the re-cut

pkgdown CI failure → added the 4 new exported topics to _pkgdown.yml's reference index (they were documented exports missing from the index; pkgdown aborts on that).
Merge with main → resolved DESCRIPTION/NEWS only (code didn't conflict with the 3.1.1/3.1.2 test-skip changes); notes re-homed under a v3.1.3 heading.
Folded in the vignette \VignetteIndexEntry fix ("Vignette's Title" → real title) — supersedes docs(vignette): fix placeholder VignetteIndexEntry #124 (close it).

Notes

New exported functions → if you'd prefer a minor bump (3.2.0) over 3.1.3 by semver, it's a 2-line change; say the word.
Watch the re-run CI: pkgdown should now pass; the full R CMD matrix passed before the rebase.

🤖 Generated with Claude Code

@return

* 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>

codecov · 2026-06-12T14:35:44Z

Codecov Report

❌ Patch coverage is 97.46377% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 87.90%. Comparing base (8ece071) to head (fef4bd5).

Files with missing lines	Patch %	Lines
R/gg_beta_uvarpro.R	95.41%	5 Missing ⚠️
R/gg_sdependent.R	98.73%	1 Missing ⚠️
R/plot.gg_beta_uvarpro.R	97.61%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #121      +/-   ##
==========================================
+ Coverage   87.26%   87.90%   +0.63%     
==========================================
  Files          48       52       +4     
  Lines        4090     4364     +274     
==========================================
+ Hits         3569     3836     +267     
- Misses        521      528       +7

Files with missing lines	Coverage Δ
R/gg_varpro.R	`100.00% <100.00%> (ø)`
R/plot.gg_sdependent.R	`100.00% <100.00%> (ø)`
R/gg_sdependent.R	`98.73% <98.73%> (ø)`
R/plot.gg_beta_uvarpro.R	`97.61% <97.61%> (ø)`
R/gg_beta_uvarpro.R	`95.41% <95.41%> (ø)`

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❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

…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>

gg_varpro() failed with the cryptic "arguments imply differing number of rows: <p>, 0" when varPro::importance() returns a degenerate importance table — 0 rows, or p named variables with no usable `z` column — observed intermittently on survival fits where the release-rule step selects no variables. .build_varpro_imp_dfs() now detects that (length(z) != length(vars), or 0 vars) and stops with a clear, specific message suggesting a larger ntree. Scoped to the degenerate case only: well-formed fits (survival included) have length(z) == length(vars) > 0 and are unaffected. This is NOT a blanket survival-family block (cf. the reverted #116). Tests exercise the guard via the internal with a constructed importance table (CRAN-safe, no varPro grow), including a positive case proving the working path is preserved. Version bump to 3.1.2 (DESCRIPTION + NEWS). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Fold the unsupervised varPro wrappers (originally PR #120 on dev) into the 3.1.2 release line alongside the #118 fix: - gg_beta_uvarpro() / plot/print/summary/autoplot: tidy wrapper for varPro::get.beta.entropy() (unsupervised lasso importance), the analogue of gg_beta_varpro(); colMeans(|beta|) per variable + cutoff/selected, with a precomputed beta_fit cache path. - gg_sdependent() / plot/print/summary/autoplot: tidy wrapper for varPro::sdependent() signal-variable detection (imp_score / degree / signal flag), complementing gg_udependent()'s graph. Frame-building split into .gg_sdependent_build() to keep cyclomatic complexity under the lint cap. Tests are CRAN-safe (constructed matrices, no varPro grow) with skip_on_cran live-integration cases. lint_package() = 0; NEWS entries under v3.1.2. 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>

submit_cran() recorded the submitted commit (SHA 83d8021, the merged #122) and timestamp 2026-06-13. ggRandomForests 3.1.2 submitted to CRAN to clear the gcc-UBSAN additional issue. Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

Copilot

Pull request overview

This PR prepares ggRandomForests 3.1.2 by (1) hardening gg_varpro() against degenerate/empty varPro::importance() output (issue #118) and (2) adding new unsupervised varPro (uvarpro) wrappers for lasso-beta importance and signal-variable detection, with companion plot/print/summary/autoplot support and tests.

Changes:

Add a scoped guard in .build_varpro_imp_dfs() to stop with a clear error when importance() returns an unusable table (0 rows or missing/empty z), addressing #118.
Introduce gg_beta_uvarpro() and gg_sdependent() wrappers (plus plot/print/summary/autoplot methods) and add CRAN-safe tests.
Bump package version/docs to 3.1.2 (DESCRIPTION, NEWS, NAMESPACE, Rd updates).

Reviewed changes

Copilot reviewed 11 out of 17 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/testthat/test_gg_varpro_empty_importance.R	Adds regression tests for the #118 degenerate-importance guard without requiring a live varPro grow.
tests/testthat/test_gg_sdependent.R	Adds matrix-driven and integration tests for `gg_sdependent()` and companions.
tests/testthat/test_gg_beta_uvarpro.R	Adds deterministic and integration tests for `gg_beta_uvarpro()` and companions.
R/plot.gg_sdependent.R	New plot method for `gg_sdependent` (lollipop chart).
R/plot.gg_beta_uvarpro.R	New plot method for `gg_beta_uvarpro` (bar chart + cutoff line).
R/gg_varpro.R	Adds guard to prevent cryptic failures when `importance()` output is degenerate.
R/gg_sdependent.R	New `gg_sdependent()` wrapper + print/summary/autoplot + empty handling.
R/gg_beta_uvarpro.R	New `gg_beta_uvarpro()` wrapper + validation + print/summary/autoplot + empty handling.
NEWS.md	Adds 3.1.2 release notes covering #118 fix and new wrappers.
NAMESPACE	Registers/exports new S3 methods and functions; imports `geom_segment`.
man/summary.gg.Rd	Updates summary method documentation to include new summary methods.
man/print.gg.Rd	Updates print method documentation to include new print methods.
man/plot.gg_sdependent.Rd	New Rd for `plot.gg_sdependent`.
man/plot.gg_beta_uvarpro.Rd	New Rd for `plot.gg_beta_uvarpro`.
man/gg_sdependent.Rd	New Rd for `gg_sdependent`.
man/gg_beta_uvarpro.Rd	New Rd for `gg_beta_uvarpro`.
DESCRIPTION	Bumps version to 3.1.2.

Files not reviewed (6)

man/gg_beta_uvarpro.Rd: Generated file
man/gg_sdependent.Rd: Generated file
man/plot.gg_beta_uvarpro.Rd: Generated file
man/plot.gg_sdependent.Rd: Generated file
man/print.gg.Rd: Generated file
man/summary.gg.Rd: Generated file

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The originally-planned 3.1.2 content (fix #118 + the gg_beta_uvarpro/ gg_sdependent unsupervised varPro wrappers) lost its version number to the gcc-UBSAN re-fix that shipped as 3.1.2. Re-cut here as 3.1.3. - Merge main (v3.1.2): DESCRIPTION/NEWS reconciled to 3.1.3; #121's notes re-homed under a v3.1.3 heading above main's v3.1.2 (UBSAN) section. - Fix the failing pkgdown build: add the 4 new exported topics (gg_beta_uvarpro, gg_sdependent, + plot.* ) to _pkgdown.yml's reference index (they were documented exports missing from the index). - Fold in the vignette \VignetteIndexEntry fix (was the template placeholder 'Vignette's Title') so 3.1.3 ships it; supersedes PR #124. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Copilot

Pull request overview

Copilot reviewed 38 out of 120 changed files in this pull request and generated 5 comments.

Files not reviewed (6)

man/gg_beta_uvarpro.Rd: Generated file
man/gg_sdependent.Rd: Generated file
man/plot.gg_beta_uvarpro.Rd: Generated file
man/plot.gg_sdependent.Rd: Generated file
man/print.gg.Rd: Generated file
man/summary.gg.Rd: Generated file

Copilot

Pull request overview

Copilot reviewed 38 out of 120 changed files in this pull request and generated 7 comments.

Files not reviewed (6)

man/gg_beta_uvarpro.Rd: Generated file
man/gg_sdependent.Rd: Generated file
man/plot.gg_beta_uvarpro.Rd: Generated file
man/plot.gg_sdependent.Rd: Generated file
man/print.gg.Rd: Generated file
man/summary.gg.Rd: Generated file

Addresses Copilot review on #121: - gg_beta_uvarpro(): validate that `cutoff` is a single non-NA numeric (or NULL) so a vector can't be silently recycled into the `selected` comparison. - gg_sdependent(): validate `threshold` (single numeric) and `directed` (single TRUE/FALSE) up front instead of failing cryptically downstream. - .validate_beta_uvarpro(): take a `caller` arg so a bad `beta_fit` passed to gg_sdependent() reports 'gg_sdependent:' rather than 'gg_beta_uvarpro:'. - Untrack and gitignore .superpowers/ (local brainstorm state, leaks abs paths) and vignettes/*_files/ + rendered *.html (regenerated build artifacts, already .Rbuildignore'd). Kept on disk; removed from the repo. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

ehrlinger · 2026-06-13T20:39:46Z

Addressed the review items in 7084f624:

cutoff validation (gg_beta_uvarpro): now errors unless cutoff is a single non-NA numeric (or NULL) — no more silent vector recycling into selected.
gg_sdependent input validation: threshold (single numeric) and directed (single TRUE/FALSE) validated up front.
.validate_beta_uvarpro(caller=): a bad beta_fit passed to gg_sdependent() now reports gg_sdependent:, not gg_beta_uvarpro:.
Repo hygiene: untracked + gitignored .superpowers/ (local brainstorm state) and vignettes/*_files/ + rendered *.html (regenerated build artifacts, already .Rbuildignore'd). Kept on disk; removed from the repo (39k lines of generated assets dropped).

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>

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>

The input-validation added for the Copilot review pushed gg_beta_uvarpro.uvarpro (25) and gg_sdependent.uvarpro (28) over the package's cyclomatic-complexity limit (20). Extract the checks into helpers: - gg_sdependent: reuse the existing .validate_udep_inputs(object, threshold, directed) (the centralized check gg_udependent uses — what Copilot suggested). - gg_beta_uvarpro: .assert_scalar_numeric_or_null() for cutoff. - shared .is_empty_beta_matrix() for the empty-matrix fast-path in both. cyclocomp now ≤20 (lint_package() = 0 lints); test_gg_beta_uvarpro (43) + test_gg_sdependent (27) pass. Validation behaviour unchanged except threshold is now required positive (matching gg_udependent's contract). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

ehrlinger and others added 5 commits June 10, 2026 10:04

ehrlinger changed the title ~~fix(#118): clear error when varPro importance() returns empty (v3.1.2)~~ Release 3.1.2: #118 gg_varpro fix + unsupervised varPro wrappers Jun 12, 2026

ehrlinger mentioned this pull request Jun 12, 2026

feat(varpro): unsupervised lasso importance — gg_beta_uvarpro() + gg_sdependent() #120

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ehrlinger and others added 3 commits June 12, 2026 10:49

ehrlinger force-pushed the fix/118-gg-varpro-empty-importance branch from 51e9c0b to 4d23f4f Compare June 12, 2026 16:37

ehrlinger changed the base branch from fix/cran-ubsan-varpro-skip to main June 12, 2026 16:37

ehrlinger and others added 2 commits June 13, 2026 09:41

chore(cran): record 3.1.2 submission (#123)

fdec398

submit_cran() recorded the submitted commit (SHA 83d8021, the merged #122) and timestamp 2026-06-13. ggRandomForests 3.1.2 submitted to CRAN to clear the gcc-UBSAN additional issue. Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

ehrlinger requested a review from Copilot June 13, 2026 19:09

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Comment thread R/gg_sdependent.R Outdated

ehrlinger changed the title ~~Release 3.1.2: #118 gg_varpro fix + unsupervised varPro wrappers~~ Release 3.1.3: #118 gg_varpro fix + unsupervised varPro wrappers Jun 13, 2026

ehrlinger requested a review from Copilot June 13, 2026 19:40

Copilot started reviewing on behalf of ehrlinger June 13, 2026 19:41 View session

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ehrlinger requested a review from Copilot June 13, 2026 20:03

Copilot started reviewing on behalf of ehrlinger June 13, 2026 20:04 View session

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ehrlinger changed the title ~~Release 3.1.3: #118 gg_varpro fix + unsupervised varPro wrappers~~ fix #118 + unsupervised varPro wrappers (gg_beta_uvarpro / gg_sdependent) [dev] Jun 13, 2026

ehrlinger changed the base branch from main to dev June 13, 2026 20:46

ehrlinger marked this pull request as draft June 13, 2026 20:46

ehrlinger mentioned this pull request Jun 13, 2026

docs(vignette): fix placeholder VignetteIndexEntry #124

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ehrlinger and others added 2 commits June 13, 2026 18:56

ehrlinger marked this pull request as ready for review June 13, 2026 23:46

ehrlinger merged commit 21805e4 into dev Jun 14, 2026
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ehrlinger deleted the fix/118-gg-varpro-empty-importance branch June 14, 2026 14:32

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fix #118 + unsupervised varPro wrappers (gg_beta_uvarpro / gg_sdependent) [dev]#121

fix #118 + unsupervised varPro wrappers (gg_beta_uvarpro / gg_sdependent) [dev]#121
ehrlinger merged 15 commits into
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