Update iris_interaction.R#2
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missing a quote in the documentation example
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Thanks... issues with \dontrun{} examples. |
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May 19, 2026
) * docs: add v2.8.0 Phase 0 plan + Rbuildignore dev/ Plans live in dev/plans/ (tracked, excluded from CRAN tarball via ^dev$, mirrors the ^memory$ precedent). docs/ stays reserved for pkgdown render output. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * chore: open v2.7.3.9000 dev cycle for v2.8.0 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: match v2.8.0 NEWS heading underline to title length Underline is now 36 = chars, equal to the title "ggRandomForests v2.8.0 (development)" (36), following the file convention where every release heading underlines to its own title length (e.g. v2.7.3 = 22/22). The plan's Step 3 spec block and its length note are corrected to 36 to keep plan and deliverable from drifting. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: patch Phase 0 plan — full dep closure + roxygen2 pin Execution surfaced two gaps in Task 1: (1) the dependency list only enumerated new/changed deps + tooling, not the full declared Imports/Suggests closure a fresh R env needs for an as-cran 0/0/0 gate (e.g. patchwork); (2) roxygen2 >= 8.0.0 migrates RoxygenNote -> Config/roxygen2/version on document(), churning unrelated metadata. Plan now requires the full closure and pins roxygen2 to the committed RoxygenNote value; Task 6 stops if the migration appears. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test: add namespace-hygiene regression guard (failing, drives Phase 0) Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test: fix namespace-hygiene guard regex + path robustness Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: sync Phase 0 plan Task 4 block with approved fix The plan's Task 4 spec carried the broken `^R\b` regex (backspace, not word boundary), the fragile `../../DESCRIPTION` path, and an incomplete skip set. Code review caught these in the deliverable; sync the plan block to the approved test so the canonical plan and the four component plans do not reintroduce the bug. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * build: move randomForestSRC/randomForest to Imports; add varPro, igraph, callr Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * build: declare varPro in Suggests for Phase 0 (promote to Imports in Phase 1) Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: correct NEWS + plan for varPro Suggests-in-Phase-0 decision varPro is declared in Suggests for Phase 0 (no varPro:: code yet; Imports would NOTE under R CMD check and break the 0/0/0 gate). NEWS bullet, plan Goal/Task 5 block/commit msg/self-review, and a new authoritative cross-plan decision note are synced; Phase 1 promotes varPro Suggests->Imports with the first varPro:: call. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: qualify rfsrc/randomForest in examples after Imports migration Replace bare rfsrc()/randomForest()/partial()/get.partial.plot.data() calls in @examples blocks with fully-qualified forms (randomForestSRC:: and randomForest::) so examples resolve without package attachment after Task 5 moved these packages from Depends: to Imports:. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * chore: gitignore root Rplots.pdf; note run_examples is Task 7 completeness gate run_examples side-effects a top-level Rplots.pdf; ignore it so later check/example tasks keep a clean tree. Plan Task 7 now states the rfsrc/randomForest grep is a seed list and devtools::run_examples() is the authoritative completeness gate (execution surfaced bare partial()/get.partial.plot.data() the grep missed). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test: attach dependency surface in testthat setup post-Imports migration v2.8.0 Phase 0: create tests/testthat/setup.R to attach survival, randomForestSRC, and randomForest to the testthat session. Tests used bare Surv()/rfsrc()/randomForest() calls which resolved only because Depends: attached those packages; after the Depends→Imports migration the setup file provides the equivalent test-session attachment without weakening the package's own namespace-qualified code. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test: skip namespace-hygiene clean-session test unless truly installed Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: sync plan Task 4 skip predicate + Task 8 Step 4 expectation Task 8 surfaced that skip_if_not_installed("ggRandomForests") does not skip under devtools::test() (load_all makes requireNamespace succeed) -> spurious FAIL. Plan Task 4 block now uses skip_if_not(installed.packages() membership); Task 8 Step 4 expectation corrected (test2 SKIPs outside R CMD check; clean- session proof deferred to Task 10). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * build: resolve final as-cran gate items for v2.8.0 Phase 0 Fix test_namespace_hygiene.R test 1 DESCRIPTION path under R CMD check: use system.file() first (resolves inside installed package), falling back to the relative path for devtools::test() / pkgload context. This makes the guard robust in both environments and eliminates the 1 error that blocked the as-CRAN gate. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test: document namespace-hygiene DESCRIPTION dual-path rationale Code review (APPROVED w/ minor) asked for a comment explaining why test 1 tries system.file() then falls back to test_path(): the test_path-only form does not resolve under R CMD check. Plan Task 4 block synced to the final guard form so the Phase 1-3 component plans inherit the R-CMD-check-robust version. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: list callr in NEWS Suggests; record Phase 1 follow-ups Final holistic review: NEWS bullet omitted callr (added to Suggests in Task 5 for the namespace-hygiene guard) — corrected to "igraph, callr, and varPro". Plan now records Phase 1 follow-ups (varPro Suggests->Imports, full test-body qualification incl. test_gg_vimp.R:82, setup.R reduction). None are Phase 0 blockers; as-cran gate is 0/0/0. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test: qualify bare rfsrc() call in test_gg_vimp at line 82 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * build: upgrade roxygen2 to 8.x and regenerate documentation Upgrades roxygen2 from 7.3.3 to 8.0.0. Migrates DESCRIPTION field from RoxygenNote: 7.3.3 to Config/roxygen2/version: 8.0.0 per roxygen2 8.x standard. NAMESPACE and man/*.Rd output is semantically identical. R CMD check --as-cran remains 0/0/0; tests remain FAIL 0 | PASS 678. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: add lint and pkgdown CI badges to README Adds lint and pkgdown workflow status badges to README.md, grouped with the existing R-CMD-check CI badge between R-CMD-check and Codecov lines. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: reconcile plan after roxygen2 8.x upgrade + late test fix - roxygen2 toolchain note (authoritative): branch upgraded to 8.0.0 at user request; Config/roxygen2/version committed; component plans use roxygen2 >= 8.0.0, do NOT re-pin 7.3.3. Task 1 Step 3 / Task 6 pin guidance annotated as superseded. - Phase 1 follow-up #2 updated: test_gg_vimp.R:82 already qualified in 618bf9b; Phase 1 audits remaining test bodies only. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: record minor-version-boundary rationale for roxygen2 upgrade The doc-toolchain bump belongs in the 2.8.0 cycle: a minor-version boundary is the correct release point for disruptive non-functional toolchain changes; deferring lets them creep into a later patch. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix: add print.gg/summary.gg to _pkgdown.yml reference index Fixes a pre-existing pkgdown CI failure on main (red since 2026-05-12, the v2.7.3 PR #75 added print.gg/summary.gg Rd topics without indexing them). check_missing_topics() errored. They are user-facing S3 methods, so indexed under "S3 Methods" alongside autoplot.gg. pkgdown::check_pkgdown(".") -> no problems found. Makes the pkgdown badge added in this PR green. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test: gate clean-session guard on R CMD check env, pass libpath to callr Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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missing a quote in the documentation example