TransferConsensus() by ms609 · Pull Request #189 · ms609/TreeDist

ms609 · 2026-03-19T16:33:54Z

Initial R-side prototype from Takazawa et al. 2026

github-actions · 2026-03-20T12:25:36Z

⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call	Status	Change	Time (ms)
`ClusteringInfoDistance(tr200)`	⚪ NSD	-1.47%	15.1 → 15.4, 15.3
`ClusteringInfoDistance(tr50)`	⚪ NSD	1.13%	11.6 → 11.5, 11.5
`LAPJV(test2000)`	🟠 Slower 🙁	-7.6%	86.3 → 91.3, 93.6
`LAPJV(test40)`	⚪ NSD	0.88%	0.0148 → 0.0147, 0.0146
`LAPJV(test400)`	🟠 Slower 🙁	-7.34%	2.86 → 3.08, 3.07
`MutualClusteringInfo(tr200)`	⚪ NSD	2.75%	23 → 22.4, 22.3
`MutualClusteringInfo(tr50)`	⚪ NSD	3.17%	24.4 → 23.3, 23.8
`PathDist(postTrees)`	⚪ NSD	4.72%	3.5 → 3.34, 3.34
`PhylogeneticInfoDistance(tr200)`	⚪ NSD	-0.13%	229 → 230, 229
`PhylogeneticInfoDistance(tr50)`	🟣 ~same	1.64%	79.4 → 78.4, 77.9
`RobinsonFoulds(tr200)`	⚪ NSD	1.84%	2.89 → 2.83, 2.83
`RobinsonFoulds(tr200)`	⚪ NSD	2.99%	2.68 → 2.6, 2.61
`RobinsonFoulds(tr50)`	⚪ NSD	2.17%	4.43 → 4.32, 4.34

github-actions · 2026-03-20T14:24:40Z

⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call	Status	Change	Time (ms)
`ClusteringInfoDistance(tr200)`	⚪ NSD	1.34%	15.3 → 15.1, 15.2
`ClusteringInfoDistance(tr50)`	⚪ NSD	-1.94%	11.3 → 11.5, 11.6
`LAPJV(test2000)`	🟠 Slower 🙁	-6.2%	82 → 86.4, 88
`LAPJV(test40)`	⚪ NSD	-0.41%	0.0146 → 0.0146, 0.0146
`LAPJV(test400)`	🟠 Slower 🙁	-7.33%	2.86 → 3.06, 3.07
`MutualClusteringInfo(tr200)`	⚪ NSD	-0.49%	21.4 → 21.7, 21.3
`MutualClusteringInfo(tr50)`	⚪ NSD	-0.55%	21.3 → 21.5, 21.2
`PathDist(postTrees)`	⚪ NSD	4.18%	3.48 → 3.33, 3.35
`PhylogeneticInfoDistance(tr200)`	⚪ NSD	-0.04%	228 → 228, 229
`PhylogeneticInfoDistance(tr50)`	🟣 ~same	1.59%	78.8 → 77.5, 77.7
`RobinsonFoulds(tr200)`	⚪ NSD	1.8%	2.84 → 2.78, 2.79
`RobinsonFoulds(tr200)`	⚪ NSD	2.37%	2.64 → 2.57, 2.58
`RobinsonFoulds(tr50)`	⚪ NSD	1.85%	4.37 → 4.3, 4.28

github-actions · 2026-03-20T15:26:41Z

⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call	Status	Change	Time (ms)
`ClusteringInfoDistance(tr200)`	🟢 Faster!	7.3%	16 → 14.9, 14.8
`ClusteringInfoDistance(tr50)`	⚪ NSD	-4.56%	10.4 → 11.1, 10.6
`LAPJV(test2000)`	🟠 Slower 🙁	-4.73%	101 → 104, 107
`LAPJV(test40)`	⚪ NSD	-2.19%	0.0141 → 0.0144, 0.0144
`LAPJV(test400)`	🟠 Slower 🙁	-5.76%	3.03 → 3.2, 3.21
`MutualClusteringInfo(tr200)`	🟢 Faster!	7.04%	22.5 → 21.2, 20.8
`MutualClusteringInfo(tr50)`	⚪ NSD	-5.39%	20.7 → 21.8, 21.7
`PathDist(postTrees)`	⚪ NSD	-0.18%	3.27 → 3.3, 3.27
`PhylogeneticInfoDistance(tr200)`	🟣 ~same	1.89%	231 → 226, 226
`PhylogeneticInfoDistance(tr50)`	⚪ NSD	-0.35%	75.2 → 76.1, 75
`RobinsonFoulds(tr200)`	⚪ NSD	-0.58%	2.68 → 2.71, 2.68
`RobinsonFoulds(tr200)`	⚪ NSD	-1.46%	2.39 → 2.43, 2.41
`RobinsonFoulds(tr50)`	⚪ NSD	-1.61%	4.03 → 4.15, 4.07

github-actions · 2026-03-20T16:26:38Z

⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call	Status	Change	Time (ms)
`ClusteringInfoDistance(tr200)`	⚪ NSD	0.33%	15.3 → 15.3, 15.3
`ClusteringInfoDistance(tr50)`	⚪ NSD	1.22%	11.7 → 11.6, 11.4
`LAPJV(test2000)`	⚪ NSD	-0.01%	84 → 83.1, 84.4
`LAPJV(test40)`	⚪ NSD	-3.02%	0.0146 → 0.0151, 0.015
`LAPJV(test400)`	⚪ NSD	0.11%	2.89 → 2.87, 2.9
`MutualClusteringInfo(tr200)`	⚪ NSD	-1.17%	22.1 → 22.4, 22.3
`MutualClusteringInfo(tr50)`	⚪ NSD	-0.57%	23 → 23.1, 23.3
`PathDist(postTrees)`	⚪ NSD	2.09%	3.53 → 3.45, 3.46
`PhylogeneticInfoDistance(tr200)`	🟣 ~same	0.18%	229 → 228, 228
`PhylogeneticInfoDistance(tr50)`	⚪ NSD	0.53%	80.2 → 80.4, 79
`RobinsonFoulds(tr200)`	⚪ NSD	1.91%	2.88 → 2.82, 2.82
`RobinsonFoulds(tr200)`	⚪ NSD	3.43%	2.68 → 2.59, 2.6
`RobinsonFoulds(tr50)`	⚪ NSD	3.53%	4.49 → 4.34, 4.32

Exported functions (thin wrappers) use Rcpp::stop() for input validation — the exception is caught immediately by BEGIN_RCPP/END_RCPP in the generated RcppExports wrapper. Implementation functions retain Rf_error() for defensive guards that should never be reached if wrappers validate correctly (LCOV_EXCL, This pattern avoids C++ exception unwinding through complex stack frames, which can cause std::terminate() on ARM. Revert "Rf_error →Rcpp:stop()" This reverts commit b20e03e. Test R-level guards instead of C++ error paths (ARM safety)

These guards are unreachable when exported wrappers validate correctly. ASSERT() is active in debug builds and compiles to nothing in release.

Rcpp::stop() causes std::terminate() on ARM regardless of call depth. All input validation now happens in R wrappers before entering C++. C++ functions use ASSERT() for debug-only invariant checks. Tests updated to exercise R-level guards instead of calling C++ with deliberately invalid input.

Commit 87e6cd8 removed Rcpp::stop() from C++ and replaced with ASSERT() (compiled out in release). Tests still expected errors from C++ calls. This commit: - mismatch_size(), confusion(): Add R validation wrappers (nTip, nrow checks) shadowing RcppExports versions - consensus_info(): Add R wrapper checking p range and CT_MAX_LEAVES (16383) limit - HierarchicalMutualInfo(): Check tip count mismatch for phylo inputs - test-hmi.cpp.R: Test EHMI() R guards instead of EHMI_xptr() - test-tree_distance.R: Replace direct cpp_* error tests with .ValidateSplitArgs test (R-level validation path) Fixes all 19 test failures from GHA.

* Surface headers for Linking To

github-actions · 2026-03-23T08:21:22Z

⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call	Status	Change	Time (ms)
`ClusteringInfoDistance(tr200)`	🟢 Faster!	8.25%	16.1 → 14.8, 14.8
`ClusteringInfoDistance(tr50)`	⚪ NSD	-0.88%	10.6 → 10.6, 10.7
`LAPJV(test2000)`	🟠 Slower 🙁	-15.84%	103 → 117, 123
`LAPJV(test40)`	🟠 Slower 🙁	-19.73%	0.0141 → 0.0169, 0.0169
`LAPJV(test400)`	🟠 Slower 🙁	-6.08%	3.03 → 3.21, 3.22
`MutualClusteringInfo(tr200)`	🟢 Faster!	6.26%	22.6 → 20.9, 21.9
`MutualClusteringInfo(tr50)`	⚪ NSD	-3.17%	21.9 → 21.9, 23.5
`PathDist(postTrees)`	⚪ NSD	-1.14%	3.28 → 3.27, 3.34
`PhylogeneticInfoDistance(tr200)`	🟣 ~same	2.71%	232 → 225, 225
`PhylogeneticInfoDistance(tr50)`	🟣 ~same	2.27%	75.5 → 74, 73.7
`RobinsonFoulds(tr200)`	⚪ NSD	0.46%	2.67 → 2.64, 2.69
`RobinsonFoulds(tr200)`	⚪ NSD	2.35%	2.4 → 2.33, 2.36
`RobinsonFoulds(tr50)`	⚪ NSD	1.77%	4.03 → 3.95, 3.96

github-actions · 2026-04-01T09:09:45Z

⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call	Status	Change	Time (ms)
`ClusteringInfoDistance(tr200)`	⚪ NSD	1.26%	15.2 → 15.1, 15
`ClusteringInfoDistance(tr50)`	⚪ NSD	0.23%	11.4 → 11.4, 11.5
`LAPJV(test2000)`	🟠 Slower 🙁	-10.89%	80.6 → 87.5, 91.1
`LAPJV(test40)`	🟠 Slower 🙁	-16.37%	0.0146 → 0.017, 0.017
`LAPJV(test400)`	🟠 Slower 🙁	-8.54%	2.87 → 3.12, 3.12
`MutualClusteringInfo(tr200)`	⚪ NSD	1.31%	21.2 → 20.9, 21
`MutualClusteringInfo(tr50)`	⚪ NSD	1.74%	20.9 → 20.8, 20.3
`PathDist(postTrees)`	🟠 Slower 🙁	-45.07%	3.63 → 5.27, 5.27
`PhylogeneticInfoDistance(tr200)`	🟣 ~same	1.3%	228 → 225, 225
`PhylogeneticInfoDistance(tr50)`	🟣 ~same	1.81%	79 → 77.1, 78
`RobinsonFoulds(tr200)`	⚪ NSD	-2.27%	2.81 → 2.87, 2.87
`RobinsonFoulds(tr200)`	⚪ NSD	-2.34%	2.62 → 2.68, 2.68
`RobinsonFoulds(tr50)`	⚪ NSD	-1.79%	4.3 → 4.35, 4.39

github-actions · 2026-04-01T10:18:48Z

⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call	Status	Change	Time (ms)
`ClusteringInfoDistance(tr200)`	⚪ NSD	0.59%	15.3 → 15.2, 15.3
`ClusteringInfoDistance(tr50)`	⚪ NSD	-2.31%	11.5 → 11.5, 11.9
`LAPJV(test2000)`	🟠 Slower 🙁	-8.29%	84.7 → 94.6, 88.9
`LAPJV(test40)`	🟠 Slower 🙁	-18.11%	0.0146 → 0.0173, 0.0172
`LAPJV(test400)`	🟠 Slower 🙁	-8.62%	2.87 → 3.13, 3.11
`MutualClusteringInfo(tr200)`	⚪ NSD	0.36%	22.1 → 22.1, 22
`MutualClusteringInfo(tr50)`	⚪ NSD	1.51%	24.1 → 23.3, 24
`PathDist(postTrees)`	🟠 Slower 🙁	-52.95%	3.45 → 5.28, 5.28
`PhylogeneticInfoDistance(tr200)`	🟣 ~same	1.33%	230 → 227, 227
`PhylogeneticInfoDistance(tr50)`	🟣 ~same	1.95%	79.8 → 78.3, 78.2
`RobinsonFoulds(tr200)`	⚪ NSD	-2.17%	2.86 → 2.92, 2.93
`RobinsonFoulds(tr200)`	⚪ NSD	-2.83%	2.64 → 2.71, 2.72
`RobinsonFoulds(tr50)`	⚪ NSD	-1.79%	4.39 → 4.48, 4.47

github-actions · 2026-04-01T11:03:07Z

⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call	Status	Change	Time (ms)
`ClusteringInfoDistance(tr200)`	⚪ NSD	0.35%	15.7 → 15.8, 15.5
`ClusteringInfoDistance(tr50)`	⚪ NSD	-2.4%	11.9 → 12.4, 12.2
`LAPJV(test2000)`	🟠 Slower 🙁	-8.82%	87.4 → 95, 95.1
`LAPJV(test40)`	🟠 Slower 🙁	-17.63%	0.0147 → 0.0172, 0.0175
`LAPJV(test400)`	🟠 Slower 🙁	-8.21%	2.92 → 3.15, 3.16
`MutualClusteringInfo(tr200)`	⚪ NSD	-0.01%	23.1 → 23, 23.1
`MutualClusteringInfo(tr50)`	⚪ NSD	0.14%	25 → 25, 25
`PathDist(postTrees)`	🟠 Slower 🙁	-50.27%	3.55 → 5.37, 5.32
`PhylogeneticInfoDistance(tr200)`	🟣 ~same	2.24%	234 → 231, 228
`PhylogeneticInfoDistance(tr50)`	🟣 ~same	1.03%	79.6 → 78.8, 78.8
`RobinsonFoulds(tr200)`	⚪ NSD	-2.41%	2.9 → 2.96, 2.99
`RobinsonFoulds(tr200)`	⚪ NSD	-2.44%	2.67 → 2.73, 2.74
`RobinsonFoulds(tr50)`	⚪ NSD	-1.21%	4.49 → 4.6, 4.47

github-actions · 2026-04-01T12:28:53Z

⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call	Status	Change	Time (ms)
`ClusteringInfoDistance(tr200)`	⚪ NSD	-1.19%	15.6 → 15.7, 16
`ClusteringInfoDistance(tr50)`	⚪ NSD	-4.02%	11.6 → 11.8, 12.4
`LAPJV(test2000)`	🟠 Slower 🙁	-10.75%	89.8 → 98.2, 103
`LAPJV(test40)`	🟠 Slower 🙁	-21.14%	0.0153 → 0.0186, 0.0185
`LAPJV(test400)`	🟠 Slower 🙁	-12.62%	2.94 → 3.27, 3.35
`MutualClusteringInfo(tr200)`	⚪ NSD	2.78%	22.8 → 21.5, 23.5
`MutualClusteringInfo(tr50)`	⚪ NSD	13.44%	24.8 → 20.9, 24.7
`PathDist(postTrees)`	🟠 Slower 🙁	-42.46%	3.67 → 5.21, 5.25
`PhylogeneticInfoDistance(tr200)`	⚪ NSD	0.39%	237 → 236, 237
`PhylogeneticInfoDistance(tr50)`	🟣 ~same	-2.09%	82.5 → 83.3, 84.3
`RobinsonFoulds(tr200)`	⚪ NSD	0.49%	2.98 → 2.94, 2.98
`RobinsonFoulds(tr200)`	⚪ NSD	0.29%	2.76 → 2.7, 2.81
`RobinsonFoulds(tr50)`	⚪ NSD	1.72%	4.59 → 4.47, 4.58

Slight performance win

github-actions · 2026-04-01T13:00:19Z

Performance benchmark results

Call	Status	Change	Time (ms)
`ClusteringInfoDistance(tr200)`	⚪ NSD	-0.04%	15.3 → 15.4, 15.1
`ClusteringInfoDistance(tr50)`	⚪ NSD	-1.97%	11.4 → 11.6, 11.5
`LAPJV(test2000)`	⚪ NSD	1.23%	93 → 89.8, 93.9
`LAPJV(test40)`	⚪ NSD	-0.17%	0.0176 → 0.0177, 0.0176
`LAPJV(test400)`	⚪ NSD	0.42%	3.21 → 3.18, 3.22
`MutualClusteringInfo(tr200)`	⚪ NSD	2.67%	22 → 21.2, 21.8
`MutualClusteringInfo(tr50)`	⚪ NSD	0.25%	22.2 → 21.1, 24.2
`PathDist(postTrees)`	⚪ NSD	1.78%	3.4 → 3.39, 3.32
`PhylogeneticInfoDistance(tr200)`	⚪ NSD	-0.38%	234 → 236, 234
`PhylogeneticInfoDistance(tr50)`	🟣 ~same	-1.25%	80.8 → 81.2, 81.9
`RobinsonFoulds(tr200)`	⚪ NSD	-0.12%	2.86 → 2.84, 2.87
`RobinsonFoulds(tr200)`	⚪ NSD	-1.33%	2.61 → 2.65, 2.65
`RobinsonFoulds(tr50)`	⚪ NSD	-1.1%	4.36 → 4.41, 4.39

ms609 added 6 commits March 19, 2026 16:32

TransferConsensus()

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TransferConsensus opt

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TransferDist()

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Multithreadable

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Spelling

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redoc

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test cov

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Guard errors for ARM

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#nocov

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ms609 marked this pull request as ready for review March 20, 2026 15:20

Rf_error →Rcpp:stop()

b20e03e

ms609 added 7 commits March 20, 2026 16:46

Replace defensive Rf_error() with ASSERT() in impl code

5cd45c2

These guards are unreachable when exported wrappers validate correctly. ASSERT() is active in debug builds and compiles to nothing in release.

NEWS.md: AI-generated branch summary for transfer-consensus

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Merge branch 'main' into transfer-consensus

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Return 0

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Surface headers for Linking To (#190)

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* Surface headers for Linking To

Merge branch 'main' into transfer-consensus

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imporve example

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Test cov

1ad6abc

ms609 added 2 commits April 1, 2026 12:26

Version: 2.13.0.9002

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Rm dead code; Restore performance

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__restrict__

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Slight performance win

ms609 merged commit 8803015 into main Apr 1, 2026
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ms609 deleted the transfer-consensus branch April 1, 2026 12:41

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TransferConsensus()#189

TransferConsensus()#189
ms609 merged 24 commits intomainfrom
transfer-consensus

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