test: reproduce Linux libstdc++ assertion crash in isolation_tree - #142
test: reproduce Linux libstdc++ assertion crash in isolation_tree#142Rudhik1904 wants to merge 6 commits into
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📝 WalkthroughWalkthroughThe pull request fixes missing-value handling in isolation forest tree construction. It adds regression coverage for leading missing quality metrics, forwards worker diagnostics, and enables libstdc++ assertions in the Linux dry-run build. ChangesAnomaly score handling
Estimated code review effort: 3 (Moderate) | ~20 minutes Possibly related PRs
Suggested reviewers: Poem
🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
✨ Finishing Touches📝 Generate docstrings
🧪 Generate unit tests (beta)
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Actionable comments posted: 2
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⚠️ Outside diff range comments (1)
src/isolation_forest.cpp (1)
112-117: 🎯 Functional Correctness | 🟠 Major | ⚡ Quick winHonor
is_missing_splitduring path scoring.
isolation_treeroutesNaNvalues to the left child whenis_missing_splitis set, butpath_lengthignores this and uses onlyit->second < node->value. SinceNaNcomparisons are false, scoring traverses the right child instead. Updatepath_lengthto routeNaNvalues left and non-missing values right before applying the numeric comparison.Proposed fix
- if (it->second < node->value) { + if (node->is_missing_split) { + if (std::isnan(it->second)) { + return path_length(node->left.get(), obs, depth + 1); + } + return path_length(node->right.get(), obs, depth + 1); + } + if (it->second < node->value) {🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@src/isolation_forest.cpp` around lines 112 - 117, Update path_length to honor is_missing_split when routing split values: detect NaN inputs and traverse the left child, while non-missing inputs traverse the right child before applying the existing numeric comparison. Keep the current comparison-based routing for ordinary numeric splits.
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@R/utils_anomaly_score.R`:
- Line 214: In .runAnomalyModel, register cleanup immediately after
parallel::makeCluster(cores, outfile = "") by adding an on.exit handler that
calls parallel::stopCluster(cl) with add = TRUE, ensuring the cluster is stopped
on normal returns and errors.
In `@src/isolation_forest.cpp`:
- Around line 108-112: Update the feature-selection and partition logic around
has_valid and is_missing_split so a selected feature with !has_valid is never
used for a non-partitioning split. Select another feature that can produce two
non-empty children, or terminate by returning a leaf when none exists; ensure
recursion never proceeds with an unchanged dataset and an empty right_data.
---
Outside diff comments:
In `@src/isolation_forest.cpp`:
- Around line 112-117: Update path_length to honor is_missing_split when routing
split values: detect NaN inputs and traverse the left child, while non-missing
inputs traverse the right child before applying the existing numeric comparison.
Keep the current comparison-based routing for ordinary numeric splits.
🪄 Autofix
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
ℹ️ Review info
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📒 Files selected for processing (3)
.github/workflows/dry-run-build.ymlR/utils_anomaly_score.Rsrc/isolation_forest.cpp
🚧 Files skipped from review as they are similar to previous changes (1)
- .github/workflows/dry-run-build.yml
| # native C++ assertion/abort messages) to the master process instead of | ||
| # discarding it, to confirm the exact crash text on Linux CI. Revert | ||
| # once confirmed. | ||
| cl = parallel::makeCluster(cores, outfile = "") |
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🩺 Stability & Availability | 🟠 Major | ⚡ Quick win
🧩 Analysis chain
🏁 Script executed:
#!/bin/bash
set -euo pipefail
printf 'Files matching utils_anomaly_score.R:\n'
fd -a 'utils_anomaly_score\.R$' . || true
if [ -f R/utils_anomaly_score.R ]; then
printf '\nRelevant source section:\n'
sed -n '180,255p' R/utils_anomaly_score.R | nl -ba -v180
fi
printf '\nSearch for stopCluster and .runAnomalyModel:\n'
rg -n "stopCluster|makeCluster|\.runAnomalyModel|parLapply|clusterExport" -S .Repository: Vitek-Lab/MSstatsConvert
Length of output: 369
🏁 Script executed:
#!/bin/bash
set -euo pipefail
printf 'Relevant source section R/utils_anomaly_score.R:\n'
awk 'NR>=180 && NR<=255 { printf "%5d\t%s\n", NR, $0 }' R/utils_anomaly_score.R
printf '\nSearch for stopCluster and parallel/cluster calls:\n'
rg -n "stopCluster|makeCluster|\.runAnomalyModel|parLapply\(|clusterExport\(" -S .
printf '\nOn.exit occurrences in target file:\n'
rg -n "on\.exit|tryCatch|try\(" R/utils_anomaly_score.R || trueRepository: Vitek-Lab/MSstatsConvert
Length of output: 3744
🏁 Script executed:
#!/bin/bash
set -euo pipefail
printf 'Continue relevant source section R/utils_anomaly_score.R:\n'
awk 'NR>=255 && NR<=320 { printf "%5d\t%s\n", NR, $0 }' R/utils_anomaly_score.R
printf '\nCheck whether .runAnomalyModel has any later return path or cleanup:\n'
python3 - <<'PY'
from pathlib import Path
p = Path('R/utils_anomaly_score.R')
text = p.read_text().splitlines()
for i, line in enumerate(text, start=1):
if 'clusterExport' in line or 'parLapply' in line or 'makeCluster' in line or 'stopCluster' in line or line.strip().startswith('on.exit'):
print(f"{i}: {line.strip()}")
PYRepository: Vitek-Lab/MSstatsConvert
Length of output: 578
Stop the parallel cluster before returning.
.runAnomalyModel creates the cluster but never calls parallel::stopCluster(cl); add on.exit(parallel::stopCluster(cl), add = TRUE) after makeCluster(). This stops workers on both normal return and error paths.
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@R/utils_anomaly_score.R` at line 214, In .runAnomalyModel, register cleanup
immediately after parallel::makeCluster(cores, outfile = "") by adding an
on.exit handler that calls parallel::stopCluster(cl) with add = TRUE, ensuring
the cluster is stopped on normal returns and errors.
1 participant
Motivation and context
This testing-only PR reproduces a Linux
libstdc++assertion crash inisolation_tree. It forwards worker stderr and enables runtime assertions during the dry-run build. It also preventsNAandNaNvalues from corrupting isolation-tree split bounds. The PR must not be merged.Changes
.github/workflows/dry-run-build.yml.~/.R/Makevarsto undefineNDEBUGand enablelibstdc++runtime assertions..runAnomalyModel.Tests
inst/tinytest/test_utils_anomaly_score.R.NAandNaNquality metrics.Coding guideline violations