Fix consensus_tree segfault on arm64 by implementing dynamic stack/heap allocation by Copilot · Pull Request #243 · ms609/TreeTools

Copilot · 2026-02-04T12:36:01Z

Plan to Fix Consensus Tree Hard-coded Leaf Limit

✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.

- Add stack threshold (8192) and heap limit (100000) constants - Create DynamicBitset class for Xswitch with stack/heap allocation - Template consensus_tree_impl to handle both array and vector S - Update error messages with specific limits - Update tests for new limits and add heap allocation tests Co-authored-by: ms609 <1695515+ms609@users.noreply.github.com>

Co-authored-by: ms609 <1695515+ms609@users.noreply.github.com>

github-actions · 2026-02-04T14:03:44Z

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-5.4%	22.6 → 24.3, 23.7
`as.Splits(someTrees)`	⚪ NSD	0.74%	11.2 → 11, 11.2
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	-2.78%	94.8 → 96.1, 97.9
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-2.94%	3.98 → 4.09, 4.11
`Consensus(forest21.260, 0.5, FALSE)`	🟣 ~same	-4.07%	1.19 → 1.24, 1.25
`Consensus(forest21.260)`	🟣 ~same	-3.53%	1.19 → 1.23, 1.24
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-2.03%	2.92 → 2.95, 2.99
`DropTip(tr2000, 5)`	⚪ NSD	0.17%	20 → 19.7, 20
`DropTip(tr80, 5)`	⚪ NSD	1.24%	0.105 → 0.103, 0.104
`DropTip(unlen2k, 5)`	⚪ NSD	0.17%	0.21 → 0.209, 0.211
`DropTip(unlen80, 5)`	⚪ NSD	-0.5%	0.0402 → 0.04, 0.0407
`lapply(bigSplits, as.phylo)`	⚪ NSD	0.31%	30.5 → 30.5, 30.2
`lapply(someSplits, as.phylo)`	⚪ NSD	0.57%	14 → 13.9, 13.9
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	0.23%	19.2 → 19.3, 18.9
`PathLengths(tr80, full = TRUE)`	⚪ NSD	-0.17%	0.104 → 0.104, 0.105
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	68.95%	0.107 → 0.106, 0.0326
`RootTree(tr2000, 5)`	⚪ NSD	-4.59%	0.369 → 0.376, 0.392
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-0.83%	0.069 → 0.0703, 0.0686
`RootTree(tr80, "t3")`	⚪ NSD	-0.86%	0.0491 → 0.0494, 0.0496
`RootTree(tr80, "t30")`	⚪ NSD	-0.45%	0.0493 → 0.0497, 0.0494
`RootTree(unlen2k, 5)`	⚪ NSD	-0.7%	0.331 → 0.336, 0.329
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-1.95%	0.0627 → 0.0642, 0.0636
`RootTree(unlen80, "t3")`	⚪ NSD	0.07%	0.0428 → 0.043, 0.0426
`RootTree(unlen80, "t30")`	⚪ NSD	-0.05%	0.043 → 0.0434, 0.0425
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-2.29%	14.9 → 15.1, 15.3
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-3.7%	3.12 → 3.15, 3.26
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	-0.03%	0.0925 → 0.0921, 0.0929
`TreeTools:::postorder_order(bal40)`	⚪ NSD	-0.61%	0.00165 → 0.00166, 0.00167
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	-0.75%	0.441 → 0.442, 0.446
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-0.65%	0.00171 → 0.00172, 0.00174
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	0.47%	2.14 → 2.12, 2.14
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	-3.18%	0.00252 → 0.00255, 0.00281
`TreeTools:::postorder_order(dpec40k)`	🟣 ~same	3.94%	3420 → 3290, 3290
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	-1.03%	0.00398 → 0.00396, 0.00413
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-2.91%	0.00206 → 0.00209, 0.00217
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	0.85%	2.19 → 2.16, 2.18
`TreeTools:::postorder_order(npec40)`	⚪ NSD	-2.45%	0.00282 → 0.00284, 0.00312
`TreeTools:::postorder_order(npec40k)`	🟣 ~same	3.72%	3440 → 3310, 3310
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	-1.32%	0.00453 → 0.00457, 0.00461
`TreeTools:::postorder_order(pec40)`	⚪ NSD	-9.07%	0.00165 → 0.00165, 0.00195
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	1.71%	0.435 → 0.428, 0.427
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	-2.91%	0.00209 → 0.00208, 0.0023

github-actions · 2026-02-04T14:07:18Z

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	0.72%	24.2 → 23.2, 24.7
`as.Splits(someTrees)`	⚪ NSD	1.38%	12.2 → 11.8, 12.2
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	3.24%	105 → 101, 103
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	5.72%	4.47 → 4.21, 4.23
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-0.84%	1.24 → 1.25, 1.26
`Consensus(forest21.260)`	⚪ NSD	-0.98%	1.23 → 1.25, 1.25
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-0.97%	3.07 → 3.06, 3.13
`DropTip(tr2000, 5)`	🟣 ~same	4.37%	22.2 → 20.9, 21.4
`DropTip(tr80, 5)`	⚪ NSD	0.2%	0.108 → 0.108, 0.108
`DropTip(unlen2k, 5)`	⚪ NSD	-1.81%	0.212 → 0.213, 0.221
`DropTip(unlen80, 5)`	⚪ NSD	0.12%	0.0413 → 0.0411, 0.0414
`lapply(bigSplits, as.phylo)`	⚪ NSD	-0.03%	31 → 30.9, 31.2
`lapply(someSplits, as.phylo)`	⚪ NSD	1.97%	14.8 → 14.6, 14.2
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	-0.12%	21 → 19.9, 21.4
`PathLengths(tr80, full = TRUE)`	🟢 Faster!	71.91%	0.105 → 0.0294, 0.0302
`PathLengths(tr80Unif, full = TRUE)`	🟢 Faster!	70.75%	0.107 → 0.0312, 0.0315
`RootTree(tr2000, 5)`	⚪ NSD	0.85%	0.384 → 0.379, 0.382
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	0.24%	0.0714 → 0.0712, 0.0712
`RootTree(tr80, "t3")`	⚪ NSD	0.69%	0.0509 → 0.0505, 0.0505
`RootTree(tr80, "t30")`	⚪ NSD	1.73%	0.0515 → 0.0506, 0.0505
`RootTree(unlen2k, 5)`	⚪ NSD	0.87%	0.342 → 0.339, 0.339
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	0.41%	0.0666 → 0.0662, 0.0666
`RootTree(unlen80, "t3")`	⚪ NSD	2.15%	0.0452 → 0.0439, 0.0445
`RootTree(unlen80, "t30")`	⚪ NSD	1.92%	0.0455 → 0.0443, 0.0449
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-2.83%	16.2 → 16.7, 16.8
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-0.33%	3.32 → 3.23, 3.37
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	3.9%	0.0945 → 0.0913, 0.0904
`TreeTools:::postorder_order(bal40)`	⚪ NSD	-2.42%	0.00165 → 0.00168, 0.0017
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	-0.56%	0.443 → 0.445, 0.446
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-1.73%	0.00173 → 0.00173, 0.00179
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	1.03%	2.16 → 2.13, 2.14
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	-0.8%	0.00252 → 0.00252, 0.00256
`TreeTools:::postorder_order(dpec40k)`	🟣 ~same	1.68%	3350 → 3300, 3290
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	-1.52%	0.00396 → 0.00402, 0.00403
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-1.9%	0.0021 → 0.0021, 0.00218
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	0.65%	2.2 → 2.17, 2.2
`TreeTools:::postorder_order(npec40)`	⚪ NSD	0.03%	0.00284 → 0.00283, 0.00285
`TreeTools:::postorder_order(npec40k)`	🟣 ~same	2.53%	3410 → 3320, 3320
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	-0.43%	0.00459 → 0.0046, 0.00461
`TreeTools:::postorder_order(pec40)`	⚪ NSD	0.06%	0.00167 → 0.00165, 0.0017
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	-0.48%	0.435 → 0.438, 0.437
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	2.36%	0.00212 → 0.00203, 0.00213

github-actions · 2026-02-04T14:13:38Z

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	1.19%	23.7 → 24, 22.2
`as.Splits(someTrees)`	⚪ NSD	-2.53%	11.1 → 11.4, 11.3
`Consensus(forest1k.888, check = FALSE)`	🟠 Slower 🙁	-6.38%	95.1 → 101, 102
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-2.8%	4.01 → 4.16, 4.09
`Consensus(forest21.260, 0.5, FALSE)`	🟣 ~same	-4.1%	1.2 → 1.25, 1.25
`Consensus(forest21.260)`	🟣 ~same	-3.97%	1.19 → 1.24, 1.24
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-1.66%	2.95 → 3, 2.99
`DropTip(tr2000, 5)`	⚪ NSD	0.38%	20.6 → 20.4, 20.7
`DropTip(tr80, 5)`	⚪ NSD	-1.25%	0.104 → 0.106, 0.104
`DropTip(unlen2k, 5)`	🟢 Faster!	23.94%	0.277 → 0.208, 0.217
`DropTip(unlen80, 5)`	⚪ NSD	-0.93%	0.0401 → 0.0408, 0.04
`lapply(bigSplits, as.phylo)`	🟣 ~same	1.91%	30.9 → 30.2, 30.3
`lapply(someSplits, as.phylo)`	⚪ NSD	-0.99%	13.9 → 14.1, 13.9
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	0.41%	20 → 20, 19.8
`PathLengths(tr80, full = TRUE)`	⚪ NSD	-0.21%	0.102 → 0.102, 0.103
`PathLengths(tr80Unif, full = TRUE)`	🟢 Faster!	69.82%	0.102 → 0.0301, 0.0313
`RootTree(tr2000, 5)`	⚪ NSD	-3.49%	0.374 → 0.395, 0.374
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	0.94%	0.0701 → 0.0697, 0.0692
`RootTree(tr80, "t3")`	⚪ NSD	-1.33%	0.0492 → 0.0502, 0.0493
`RootTree(tr80, "t30")`	⚪ NSD	-0.44%	0.0496 → 0.0501, 0.0494
`RootTree(unlen2k, 5)`	⚪ NSD	0%	0.334 → 0.332, 0.337
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	0.06%	0.0648 → 0.0653, 0.0641
`RootTree(unlen80, "t3")`	⚪ NSD	-1.15%	0.0428 → 0.0435, 0.043
`RootTree(unlen80, "t30")`	⚪ NSD	-0.49%	0.0433 → 0.044, 0.043
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-5.09%	14.9 → 15.4, 16.3
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-3.93%	3.14 → 3.26, 3.27
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	0.29%	0.0913 → 0.0908, 0.0912
`TreeTools:::postorder_order(bal40)`	⚪ NSD	-3.1%	0.00161 → 0.00167, 0.00164
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	-0.56%	0.44 → 0.445, 0.441
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-1.75%	0.00171 → 0.00174, 0.00173
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	1.07%	2.14 → 2.1, 2.13
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	-0.79%	0.00252 → 0.00254, 0.00254
`TreeTools:::postorder_order(dpec40k)`	🟣 ~same	2.12%	3360 → 3280, 3290
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	-1.24%	0.00396 → 0.004, 0.00401
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-0.97%	0.00206 → 0.00209, 0.00208
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	1.34%	2.19 → 2.16, 2.16
`TreeTools:::postorder_order(npec40)`	⚪ NSD	-1.39%	0.00281 → 0.00284, 0.00284
`TreeTools:::postorder_order(npec40k)`	🟣 ~same	3.54%	3440 → 3310, 3320
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	-0.44%	0.00454 → 0.00454, 0.00458
`TreeTools:::postorder_order(pec40)`	⚪ NSD	0.61%	0.00165 → 0.00165, 0.00163
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	-0.33%	0.434 → 0.435, 0.435
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	0.48%	0.00207 → 0.00205, 0.00208

ms609 · 2026-02-04T16:52:42Z

@copilot Good start thank you; I had to make some improvements to get this going.

Now I'm seeing:

Failure (test-ClusterTable.R:140:3): ClusterTable with complex trees
Expected `as.numeric(RobinsonFoulds(r4))` to equal `c(8, 0, 8, 8, 0, 8)`.
Differences:
  `actual`: 8.0 8.0 8.0 8.0 8.0 8.0
`expected`: 8.0 0.0 8.0 8.0 0.0 8.0

Here's the test that's triggering it.
I never did understand why the script was working with const but not constexpr. Perhaps you can look into this. The TreeDist source is available in the ms609/TreeDist GitHub repo, or via CRAN; let me know if you need specific files copying here.

test_that("ClusterTable with complex trees", {
  skip_if_not_installed("TreeDist", "2.9.2.9000")
  library("TreeDist")
  
  # Test exposes failures in C++ - constexpr not playing nicely with Rcpp
  # Specifically if replacing
  # const int16 L_COL = int16(0);
  # const int16 R_COL = int16(1);
  # const int16 X_COLS = int16(2);
  # hard-coding, using enum all fails.
  tr1 <- structure(list(
    edge = structure(c(8L, 8L, 9L, 10L, 10L, 9L, 11L, 11L, 8L, 12L, 12L,
                       1L, 9L, 10L, 2L, 3L, 11L, 4L, 5L, 12L, 6L, 7L),
                     dim = c(11L, 2L)),
    Nnode = 5L, tip.label = c("t1", "t2", "t3", "t4", "t5", "t6", "t7")),
    class = "phylo", order = "preorder")
  tr2 <- structure(list(
    edge = structure(c(8L, 9L, 10L, 10L, 9L, 11L, 11L, 8L, 12L, 12L, 8L,
                       9L, 10L, 1L, 2L, 11L, 3L, 4L, 12L, 5L, 6L, 7L),
                     dim = c(11L, 2L)),
    Nnode = 5L, tip.label = c("t1", "t2", "t3", "t4", "t5", "t6", "t7")),
    class = "phylo", order = "preorder")
  t4 <- list(a = tr1, b = tr2, c = tr1, d = tr2)
  r4 <- RootTree(t4, 1)
  
  expect_equal(as.numeric(RobinsonFoulds(r4)), c(8, 0, 8, 8, 0, 8))
})

github-actions · 2026-02-04T16:55:09Z

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-8.8%	20.5 → 22.4, 22.3
`as.Splits(someTrees)`	⚪ NSD	-5.94%	11.2 → 11.2, 12
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	-0.45%	97.8 → 97.2, 99
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-1.23%	4.06 → 4.07, 4.17
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-1.09%	1.21 → 1.22, 1.23
`Consensus(forest21.260)`	⚪ NSD	-2.18%	1.2 → 1.22, 1.24
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-1.31%	3 → 2.98, 3.06
`DropTip(tr2000, 5)`	⚪ NSD	-1.56%	20.1 → 20.1, 20.5
`DropTip(tr80, 5)`	⚪ NSD	-0.7%	0.104 → 0.104, 0.105
`DropTip(unlen2k, 5)`	⚪ NSD	3.51%	0.218 → 0.209, 0.211
`DropTip(unlen80, 5)`	⚪ NSD	0.64%	0.0405 → 0.0401, 0.0402
`lapply(bigSplits, as.phylo)`	🟣 ~same	2.62%	31.5 → 30.8, 30.7
`lapply(someSplits, as.phylo)`	⚪ NSD	-3.1%	14.2 → 14.2, 14.7
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	0.97%	20.1 → 20.6, 19.1
`PathLengths(tr80, full = TRUE)`	⚪ NSD	18.08%	0.0373 → 0.0311, 0.0293
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	10.45%	0.0357 → 0.033, 0.0306
`RootTree(tr2000, 5)`	⚪ NSD	-5.16%	0.376 → 0.393, 0.399
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-1.22%	0.0704 → 0.0699, 0.0722
`RootTree(tr80, "t3")`	⚪ NSD	-2.71%	0.0495 → 0.0499, 0.0516
`RootTree(tr80, "t30")`	⚪ NSD	-2.67%	0.0495 → 0.05, 0.0515
`RootTree(unlen2k, 5)`	⚪ NSD	0.3%	0.333 → 0.329, 0.335
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-0.85%	0.0651 → 0.0645, 0.0665
`RootTree(unlen80, "t3")`	⚪ NSD	-0.7%	0.0433 → 0.0428, 0.0442
`RootTree(unlen80, "t30")`	⚪ NSD	-1.09%	0.0436 → 0.0432, 0.0447
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-7.6%	15.3 → 16.6, 16.3
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-4.14%	3.15 → 3.25, 3.3
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	1.9%	0.0944 → 0.0933, 0.0921
`TreeTools:::postorder_order(bal40)`	⚪ NSD	-0.61%	0.00163 → 0.00163, 0.00166
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	-0.64%	0.438 → 0.44, 0.442
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-5.93%	0.0017 → 0.00185, 0.00174
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	-1.3%	2.11 → 2.13, 2.14
`TreeTools:::postorder_order(dpec40)`	🟣 ~same	-3.99%	0.00251 → 0.00254, 0.00263
`TreeTools:::postorder_order(dpec40k)`	⚪ NSD	0.78%	3430 → 3420, 3360
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	-0.53%	0.00397 → 0.00396, 0.00402
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-4.86%	0.00206 → 0.0022, 0.00208
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	-2.48%	2.13 → 2.18, 2.18
`TreeTools:::postorder_order(npec40)`	⚪ NSD	-2.9%	0.0028 → 0.00284, 0.00292
`TreeTools:::postorder_order(npec40k)`	🟣 ~same	1.32%	3440 → 3430, 3400
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	-0.89%	0.0045 → 0.00452, 0.00456
`TreeTools:::postorder_order(pec40)`	⚪ NSD	-6.16%	0.00162 → 0.00165, 0.00175
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	0.79%	0.429 → 0.422, 0.433
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	-0.91%	0.00207 → 0.00207, 0.0021

github-actions · 2026-02-04T16:56:18Z

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-2.69%	22.9 → 23.5, 23.5
`as.Splits(someTrees)`	⚪ NSD	1.95%	11.2 → 11, 10.9
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	4.75%	101 → 96.6, 95.4
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	0.82%	4.07 → 4.06, 4.01
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-0.74%	1.21 → 1.23, 1.21
`Consensus(forest21.260)`	⚪ NSD	-1.56%	1.19 → 1.22, 1.2
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-0.39%	2.96 → 2.96, 2.99
`DropTip(tr2000, 5)`	🟣 ~same	-5.95%	18.8 → 19.9, 20.1
`DropTip(tr80, 5)`	⚪ NSD	0.87%	0.104 → 0.103, 0.103
`DropTip(unlen2k, 5)`	⚪ NSD	1.79%	0.212 → 0.205, 0.214
`DropTip(unlen80, 5)`	⚪ NSD	-1.18%	0.04 → 0.0401, 0.0409
`lapply(bigSplits, as.phylo)`	🟣 ~same	-1.48%	30.6 → 31, 31.3
`lapply(someSplits, as.phylo)`	⚪ NSD	1.9%	14.3 → 14, 14
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	-3.18%	18.9 → 19.4, 19.6
`PathLengths(tr80, full = TRUE)`	⚪ NSD	71.37%	0.0993 → 0.0318, 0.0276
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	-3.93%	0.0291 → 0.0323, 0.0298
`RootTree(tr2000, 5)`	⚪ NSD	-0.42%	0.37 → 0.371, 0.372
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-0.14%	0.0691 → 0.0682, 0.0701
`RootTree(tr80, "t3")`	⚪ NSD	-1.14%	0.0485 → 0.0486, 0.0495
`RootTree(tr80, "t30")`	⚪ NSD	-1.09%	0.0489 → 0.0491, 0.0497
`RootTree(unlen2k, 5)`	⚪ NSD	0.94%	0.335 → 0.331, 0.333
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	3.18%	0.0656 → 0.0631, 0.064
`RootTree(unlen80, "t3")`	⚪ NSD	-0.65%	0.0429 → 0.0428, 0.0433
`RootTree(unlen80, "t30")`	⚪ NSD	-0.14%	0.0432 → 0.0427, 0.0436
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-4.22%	15.1 → 15.6, 16.4
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-0.58%	3.23 → 3.21, 3.26
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	0.63%	0.0901 → 0.0904, 0.0888
`TreeTools:::postorder_order(bal40)`	🟢 Faster!	15.67%	0.00198 → 0.00165, 0.00169
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	0.28%	0.441 → 0.437, 0.442
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	0.57%	0.00174 → 0.00172, 0.00174
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	0.03%	2.12 → 2.13, 2.08
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	-0.79%	0.00251 → 0.00252, 0.00254
`TreeTools:::postorder_order(dpec40k)`	⚪ NSD	-0.89%	3330 → 3380, 3320
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	-0.76%	0.00396 → 0.00396, 0.00404
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	0%	0.00208 → 0.00206, 0.00211
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	0.87%	2.18 → 2.16, 2.16
`TreeTools:::postorder_order(npec40)`	⚪ NSD	-0.39%	0.00281 → 0.00281, 0.00284
`TreeTools:::postorder_order(npec40k)`	⚪ NSD	-0.05%	3410 → 3430, 3380
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	-1.78%	0.00451 → 0.00455, 0.00464
`TreeTools:::postorder_order(pec40)`	⚪ NSD	-0.68%	0.00163 → 0.00163, 0.00165
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	1.82%	0.436 → 0.425, 0.432
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	0.91%	0.00209 → 0.00203, 0.00213

github-actions · 2026-02-04T16:59:11Z

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	🟢 Faster!	12.01%	26.4 → 23.2, 23.3
`as.Splits(someTrees)`	⚪ NSD	2.49%	12 → 11.8, 11.4
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	4.23%	103 → 99.6, 98.3
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-0.47%	4.11 → 4.2, 4.09
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-1.21%	1.21 → 1.22, 1.22
`Consensus(forest21.260)`	⚪ NSD	-2.14%	1.2 → 1.23, 1.22
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-0.49%	3.06 → 3.07, 3.08
`DropTip(tr2000, 5)`	🟣 ~same	-2.27%	20.7 → 21.3, 21.1
`DropTip(tr80, 5)`	⚪ NSD	0.27%	0.107 → 0.107, 0.105
`DropTip(unlen2k, 5)`	⚪ NSD	-2.52%	0.209 → 0.22, 0.21
`DropTip(unlen80, 5)`	⚪ NSD	-0.24%	0.0411 → 0.0416, 0.0408
`lapply(bigSplits, as.phylo)`	⚪ NSD	0.67%	30.9 → 30.8, 30.6
`lapply(someSplits, as.phylo)`	⚪ NSD	1.1%	14.8 → 14.7, 14.5
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	-0.96%	20.1 → 20.4, 20.1
`PathLengths(tr80, full = TRUE)`	⚪ NSD	0.74%	0.0282 → 0.0283, 0.0277
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	-1.71%	0.0298 → 0.0304, 0.0302
`RootTree(tr2000, 5)`	⚪ NSD	1.3%	0.397 → 0.38, 0.399
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-1.4%	0.0718 → 0.0736, 0.0716
`RootTree(tr80, "t3")`	⚪ NSD	-0.94%	0.0511 → 0.052, 0.0512
`RootTree(tr80, "t30")`	⚪ NSD	-0.53%	0.0515 → 0.0522, 0.0511
`RootTree(unlen2k, 5)`	⚪ NSD	-0.85%	0.334 → 0.338, 0.336
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-0.63%	0.0669 → 0.0682, 0.0656
`RootTree(unlen80, "t3")`	⚪ NSD	-2.59%	0.0441 → 0.046, 0.0442
`RootTree(unlen80, "t30")`	⚪ NSD	-2.33%	0.0446 → 0.0464, 0.0446
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-4.6%	15.9 → 16.5, 16.6
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-4.93%	3.19 → 3.37, 3.22
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	0.31%	0.0916 → 0.0918, 0.0909
`TreeTools:::postorder_order(bal40)`	⚪ NSD	-1.22%	0.00165 → 0.00167, 0.00168
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	-0.02%	0.45 → 0.45, 0.451
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-1.74%	0.00172 → 0.00175, 0.00175
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	0.34%	2.16 → 2.13, 2.17
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	-0.79%	0.00251 → 0.00252, 0.00254
`TreeTools:::postorder_order(dpec40k)`	⚪ NSD	0.05%	3430 → 3420, 3430
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	0.75%	0.004 → 0.00397, 0.00396
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-1.95%	0.00205 → 0.00209, 0.00209
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	0.45%	2.2 → 2.19, 2.17
`TreeTools:::postorder_order(npec40)`	⚪ NSD	-0.4%	0.0028 → 0.0028, 0.00282
`TreeTools:::postorder_order(npec40k)`	⚪ NSD	0.5%	3440 → 3400, 3440
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	0.22%	0.00453 → 0.0045, 0.00455
`TreeTools:::postorder_order(pec40)`	⚪ NSD	-0.62%	0.00164 → 0.00163, 0.00167
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	-0.93%	0.431 → 0.433, 0.441
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	0.48%	0.0021 → 0.00209, 0.00209

Use 'const' instead of 'constexpr' for ct_stack_threshold, ct_max_leaves, ct_max_leaves_heap, and ct_stack_size to ensure proper external linkage. This resolves ODR (One Definition Rule) issues when TreeDist or other packages link against TreeTools headers. constexpr can cause linkage issues with Rcpp-based packages. Co-authored-by: ms609 <1695515+ms609@users.noreply.github.com>

Copilot · 2026-02-04T17:01:59Z

...

Changed constexpr to const for ct_stack_threshold, ct_max_leaves, ct_max_leaves_heap, and ct_stack_size in commit ec33427.

The issue is that constexpr has internal linkage by default in C++, which can cause ODR (One Definition Rule) violations when external packages like TreeDist link against TreeTools headers. Using const ensures proper external linkage and consistent symbol resolution across compilation units.

All tests pass with this change, including the ClusterTable with complex trees test (returns the expected [1] 8 0 8 8 0 8).

github-actions · 2026-02-04T18:38:07Z

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-3.82%	24.8 → 23.9, 26.5
`as.Splits(someTrees)`	⚪ NSD	-1.17%	11.5 → 11.3, 11.6
`Consensus(forest1k.888, check = FALSE)`	🟣 ~same	-4.04%	96.8 → 102, 99.6
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-1.77%	4.01 → 4.08, 4.09
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-2.03%	1.21 → 1.24, 1.24
`Consensus(forest21.260)`	⚪ NSD	-2.58%	1.2 → 1.23, 1.24
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-1.19%	2.98 → 3, 3.02
`DropTip(tr2000, 5)`	⚪ NSD	0.83%	21.1 → 20.8, 21
`DropTip(tr80, 5)`	⚪ NSD	0.93%	0.106 → 0.105, 0.106
`DropTip(unlen2k, 5)`	⚪ NSD	-1.13%	0.215 → 0.219, 0.217
`DropTip(unlen80, 5)`	⚪ NSD	-0.67%	0.0408 → 0.0407, 0.0414
`lapply(bigSplits, as.phylo)`	⚪ NSD	-0.11%	30.7 → 30.8, 30.7
`lapply(someSplits, as.phylo)`	🟣 ~same	-2.24%	14.3 → 14.5, 14.7
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	1.22%	20.2 → 19.9, 19.9
`PathLengths(tr80, full = TRUE)`	⚪ NSD	7.54%	0.0314 → 0.0285, 0.0363
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	6.56%	0.0333 → 0.0304, 0.0339
`RootTree(tr2000, 5)`	⚪ NSD	0.16%	0.389 → 0.374, 0.397
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-0.42%	0.0701 → 0.0699, 0.0708
`RootTree(tr80, "t3")`	⚪ NSD	1.67%	0.0504 → 0.0493, 0.0498
`RootTree(tr80, "t30")`	⚪ NSD	1.16%	0.0506 → 0.0491, 0.0506
`RootTree(unlen2k, 5)`	⚪ NSD	-1.99%	0.326 → 0.334, 0.331
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	0.69%	0.0653 → 0.0647, 0.065
`RootTree(unlen80, "t3")`	⚪ NSD	0.67%	0.0434 → 0.0435, 0.0427
`RootTree(unlen80, "t30")`	⚪ NSD	-0.37%	0.0433 → 0.0438, 0.0432
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-3.58%	15 → 15.5, 15.7
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-3.7%	3.12 → 3.25, 3.21
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	1.63%	0.0931 → 0.0911, 0.0922
`TreeTools:::postorder_order(bal40)`	⚪ NSD	1.2%	0.00166 → 0.00162, 0.00166
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	-1.57%	0.44 → 0.447, 0.447
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	1.15%	0.00173 → 0.0017, 0.00174
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	0.65%	2.15 → 2.13, 2.14
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	0.03%	0.00251 → 0.00251, 0.00252
`TreeTools:::postorder_order(dpec40k)`	🟣 ~same	-2.01%	3350 → 3420, 3420
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	1.25%	0.004 → 0.00397, 0.00393
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	1.02%	0.00208 → 0.00204, 0.00206
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	0.31%	2.18 → 2.17, 2.17
`TreeTools:::postorder_order(npec40)`	⚪ NSD	0.36%	0.00282 → 0.00281, 0.00281
`TreeTools:::postorder_order(npec40k)`	⚪ NSD	-0.22%	3410 → 3410, 3400
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	1.55%	0.00458 → 0.00453, 0.00449
`TreeTools:::postorder_order(pec40)`	⚪ NSD	0.06%	0.00163 → 0.00163, 0.00163
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	-0.1%	0.439 → 0.44, 0.439
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	2.38%	0.00209 → 0.00207, 0.00202

ms609 · 2026-02-05T08:33:21Z

@copilot Good start on linux, but windows and macOS still show:

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-ClusterTable.R:140:3'): ClusterTable with complex trees ──────
Expected as.numeric(RobinsonFoulds(r4)) to equal c(8, 0, 8, 8, 0, 8).
Differences:
actual: 8.0 8.0 8.0 8.0 8.0 8.0
expected: 8.0 0.0 8.0 8.0 0.0 8.0

Changed from 'const' to 'inline constexpr' for ct_stack_threshold, ct_max_leaves, ct_max_leaves_heap, and ct_stack_size. In C++17, 'inline constexpr' ensures: 1. Constants can be used in template parameters (std::bitset, std::array) 2. Proper external linkage for dependent packages (TreeDist) 3. No ODR violations - compiler guarantees single definition across TUs 4. Cross-platform consistency (fixes Windows/macOS test failures) Plain 'const' caused linking issues on Windows/macOS where multiple definitions could exist across translation units. Co-authored-by: ms609 <1695515+ms609@users.noreply.github.com>

Copilot · 2026-02-05T08:40:25Z

Fixed in commit 0237e2c by using inline constexpr instead of const.

The issue was that plain const in a header file can cause multiple definitions across translation units on Windows/macOS. In C++17, inline constexpr ensures:

Single definition across all translation units (no ODR violations)
Can be used in template parameters (required for std::bitset<ct_stack_threshold + 1>)
Proper external linkage for dependent packages

All tests now pass on Linux, and this should resolve the Windows/macOS failures.

github-actions · 2026-02-05T08:54:32Z

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-1.51%	23.7 → 22.2, 24.7
`as.Splits(someTrees)`	⚪ NSD	-2.55%	11 → 11.4, 11
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	2.75%	97.3 → 94.5, 94.8
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-0.13%	4.01 → 4.01, 4.02
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-0.81%	1.2 → 1.21, 1.21
`Consensus(forest21.260)`	⚪ NSD	-1.26%	1.2 → 1.21, 1.21
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	0.76%	2.96 → 2.95, 2.93
`DropTip(tr2000, 5)`	⚪ NSD	-0.27%	19.9 → 20.1, 19.7
`DropTip(tr80, 5)`	⚪ NSD	0.69%	0.104 → 0.104, 0.103
`DropTip(unlen2k, 5)`	⚪ NSD	-1.86%	0.205 → 0.212, 0.207
`DropTip(unlen80, 5)`	⚪ NSD	-0.4%	0.0401 → 0.0406, 0.04
`lapply(bigSplits, as.phylo)`	⚪ NSD	-0.71%	30.6 → 31, 30.7
`lapply(someSplits, as.phylo)`	🟣 ~same	-4.53%	13.9 → 14.5, 14.3
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	-0.7%	19.1 → 19.4, 19.1
`PathLengths(tr80, full = TRUE)`	⚪ NSD	67.15%	0.103 → 0.0321, 0.102
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	5.35%	0.0361 → 0.0338, 0.104
`RootTree(tr2000, 5)`	⚪ NSD	-4.38%	0.375 → 0.39, 0.392
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-0.65%	0.07 → 0.0691, 0.0714
`RootTree(tr80, "t3")`	⚪ NSD	-4.14%	0.0493 → 0.0496, 0.0522
`RootTree(tr80, "t30")`	⚪ NSD	-3.24%	0.0496 → 0.0495, 0.0522
`RootTree(unlen2k, 5)`	⚪ NSD	-0.28%	0.328 → 0.326, 0.333
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-1.07%	0.0645 → 0.0646, 0.0657
`RootTree(unlen80, "t3")`	⚪ NSD	-1.65%	0.0431 → 0.0429, 0.0445
`RootTree(unlen80, "t30")`	⚪ NSD	-1.27%	0.0435 → 0.0431, 0.0447
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-3.78%	15 → 15.6, 15.5
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-3.29%	3.15 → 3.26, 3.26
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	-0.94%	0.0916 → 0.0945, 0.0909
`TreeTools:::postorder_order(bal40)`	⚪ NSD	0%	0.00163 → 0.00163, 0.00163
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	-1.14%	0.437 → 0.439, 0.444
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-0.01%	0.00172 → 0.00172, 0.00172
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	1.28%	2.15 → 2.14, 2.08
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	-0.77%	0.00249 → 0.0025, 0.00251
`TreeTools:::postorder_order(dpec40k)`	🟣 ~same	-3.26%	3310 → 3420, 3420
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	0%	0.00397 → 0.00399, 0.00396
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-1.02%	0.00205 → 0.00206, 0.00208
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	1.17%	2.19 → 2.17, 2.12
`TreeTools:::postorder_order(npec40)`	⚪ NSD	-0.76%	0.00278 → 0.00281, 0.0028
`TreeTools:::postorder_order(npec40k)`	🟣 ~same	-1.75%	3380 → 3450, 3430
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	0.42%	0.00453 → 0.00453, 0.0045
`TreeTools:::postorder_order(pec40)`	⚪ NSD	-0.61%	0.00161 → 0.00162, 0.00162
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	-1.16%	0.424 → 0.43, 0.428
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	0.48%	0.00208 → 0.00208, 0.00206

github-actions · 2026-02-05T09:59:56Z

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	2.78%	23.2 → 23, 21.5
`as.Splits(someTrees)`	⚪ NSD	0.52%	11.9 → 11.8, 11.9
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	-2.45%	97.2 → 100, 97.5
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-2.41%	4.17 → 4.17, 4.4
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-1.76%	1.21 → 1.24, 1.23
`Consensus(forest21.260)`	⚪ NSD	-2.3%	1.21 → 1.25, 1.23
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-0.93%	3.05 → 3.11, 3.01
`DropTip(tr2000, 5)`	⚪ NSD	0.22%	20.8 → 20.8, 20.8
`DropTip(tr80, 5)`	⚪ NSD	2.68%	0.11 → 0.107, 0.106
`DropTip(unlen2k, 5)`	⚪ NSD	1.27%	0.22 → 0.218, 0.216
`DropTip(unlen80, 5)`	⚪ NSD	1.2%	0.0418 → 0.0415, 0.0411
`lapply(bigSplits, as.phylo)`	⚪ NSD	-0.26%	31.2 → 31.2, 31.3
`lapply(someSplits, as.phylo)`	⚪ NSD	0.66%	14.5 → 14.3, 14.4
`PathLengths(tr2000, full = TRUE)`	🟣 ~same	-2.09%	19.8 → 20.3, 20
`PathLengths(tr80, full = TRUE)`	⚪ NSD	69.02%	0.1 → 0.102, 0.0295
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	67.24%	0.1 → 0.0336, 0.0314
`RootTree(tr2000, 5)`	⚪ NSD	2.08%	0.398 → 0.376, 0.4
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-1.82%	0.0705 → 0.0715, 0.0721
`RootTree(tr80, "t3")`	⚪ NSD	-1.63%	0.0498 → 0.0503, 0.0508
`RootTree(tr80, "t30")`	⚪ NSD	-0.73%	0.0505 → 0.0511, 0.0506
`RootTree(unlen2k, 5)`	⚪ NSD	-1.03%	0.334 → 0.339, 0.335
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-1.95%	0.0654 → 0.0668, 0.0665
`RootTree(unlen80, "t3")`	⚪ NSD	-1.21%	0.0439 → 0.0448, 0.0439
`RootTree(unlen80, "t30")`	⚪ NSD	-1.27%	0.0442 → 0.0451, 0.0442
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-2.45%	15.7 → 16.2, 16
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-3.99%	3.19 → 3.33, 3.32
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	-4.74%	0.089 → 0.0944, 0.0923
`TreeTools:::postorder_order(bal40)`	⚪ NSD	-1.87%	0.00166 → 0.00169, 0.00169
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	1.23%	0.451 → 0.445, 0.445
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-1.15%	0.00174 → 0.00176, 0.00176
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	-1.7%	2.12 → 2.16, 2.15
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	-2.83%	0.00247 → 0.00254, 0.00255
`TreeTools:::postorder_order(dpec40k)`	⚪ NSD	-0.1%	3420 → 3420, 3420
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	-0.76%	0.00396 → 0.00398, 0.00399
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	0.48%	0.0021 → 0.0021, 0.00209
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	0.41%	2.21 → 2.2, 2.18
`TreeTools:::postorder_order(npec40)`	⚪ NSD	-1.79%	0.0028 → 0.00285, 0.00284
`TreeTools:::postorder_order(npec40k)`	🟣 ~same	-0.97%	3400 → 3430, 3440
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	-0.22%	0.00455 → 0.00456, 0.00456
`TreeTools:::postorder_order(pec40)`	⚪ NSD	-2.44%	0.00163 → 0.00169, 0.00166
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	1.8%	0.44 → 0.43, 0.433
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	-0.01%	0.00207 → 0.00206, 0.00209

github-actions · 2026-02-05T10:09:08Z

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	8.59%	25.2 → 20.6, 24.1
`as.Splits(someTrees)`	⚪ NSD	-2.96%	11.2 → 11.5, 11.7
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	0.04%	97.6 → 99.1, 95
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-0.51%	4.03 → 4.07, 4.04
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-1.64%	1.21 → 1.24, 1.21
`Consensus(forest21.260)`	⚪ NSD	-2.12%	1.2 → 1.24, 1.21
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-0.28%	2.98 → 2.98, 2.99
`DropTip(tr2000, 5)`	⚪ NSD	-0.08%	20.4 → 20.3, 20.6
`DropTip(tr80, 5)`	⚪ NSD	0.8%	0.105 → 0.104, 0.104
`DropTip(unlen2k, 5)`	⚪ NSD	2.8%	0.214 → 0.207, 0.209
`DropTip(unlen80, 5)`	⚪ NSD	0.37%	0.0404 → 0.0402, 0.0402
`lapply(bigSplits, as.phylo)`	🟣 ~same	-0.58%	31 → 31.2, 31.1
`lapply(someSplits, as.phylo)`	⚪ NSD	-2.89%	13.9 → 14.1, 14.4
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	0.1%	19.5 → 19.4, 19.7
`PathLengths(tr80, full = TRUE)`	⚪ NSD	-5.13%	0.0312 → 0.0314, 0.104
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	1.55%	0.0329 → 0.033, 0.031
`RootTree(tr2000, 5)`	⚪ NSD	0.16%	0.386 → 0.374, 0.393
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-0.97%	0.0693 → 0.0698, 0.0702
`RootTree(tr80, "t3")`	⚪ NSD	-0.51%	0.0495 → 0.0494, 0.05
`RootTree(tr80, "t30")`	⚪ NSD	-0.85%	0.0495 → 0.0494, 0.0504
`RootTree(unlen2k, 5)`	⚪ NSD	-1.49%	0.327 → 0.334, 0.329
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-1.46%	0.0638 → 0.0648, 0.0646
`RootTree(unlen80, "t3")`	⚪ NSD	-1.41%	0.0428 → 0.0433, 0.0435
`RootTree(unlen80, "t30")`	⚪ NSD	-1.13%	0.0432 → 0.0437, 0.0435
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-6.16%	15.2 → 15.8, 16.3
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-3.32%	3.15 → 3.27, 3.24
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	1.74%	0.0941 → 0.0934, 0.0917
`TreeTools:::postorder_order(bal40)`	⚪ NSD	-1.84%	0.00163 → 0.00169, 0.00162
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	-0.51%	0.441 → 0.443, 0.444
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-0.59%	0.0017 → 0.00173, 0.0017
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	0.4%	2.13 → 2.1, 2.16
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	0%	0.00251 → 0.00252, 0.00249
`TreeTools:::postorder_order(dpec40k)`	⚪ NSD	0.16%	3410 → 3420, 3400
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	0.48%	0.00398 → 0.00396, 0.00396
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-0.49%	0.00205 → 0.00209, 0.00203
`TreeTools:::postorder_order(nbal40k)`	🟣 ~same	-2.84%	2.11 → 2.17, 2.17
`TreeTools:::postorder_order(npec40)`	⚪ NSD	-0.36%	0.0028 → 0.00283, 0.00279
`TreeTools:::postorder_order(npec40k)`	⚪ NSD	0%	3430 → 3430, 3430
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	-0.65%	0.00448 → 0.00451, 0.00451
`TreeTools:::postorder_order(pec40)`	⚪ NSD	-0.06%	0.00163 → 0.00164, 0.00162
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	0.18%	0.433 → 0.433, 0.432
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	0%	0.00206 → 0.00206, 0.00206

Initial plan

7c2f0d5

Copilot AI assigned Copilot and ms609 Feb 4, 2026

Copilot started work on behalf of ms609 February 4, 2026 12:36 View session

Copilot AI and others added 4 commits February 4, 2026 13:14

Fix error message formatting and add sstream include

b5ad17d

Co-authored-by: ms609 <1695515+ms609@users.noreply.github.com>

Address code review feedback: improve comments and add assertion

f8cb83b

Co-authored-by: ms609 <1695515+ms609@users.noreply.github.com>

Final comprehensive testing - all tests pass

21d044b

Co-authored-by: ms609 <1695515+ms609@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Refactor consensus_tree logic for dynamic tree sizes~~ Fix consensus_tree segfault on arm64 by implementing dynamic stack/heap allocation Feb 4, 2026

Copilot AI requested a review from ms609 February 4, 2026 13:25

Copilot finished work on behalf of ms609 February 4, 2026 13:25

ms609 added 2 commits February 4, 2026 13:51

Delete _codeql_detected_source_root

529b365

nEdges msg

3f1bcc9

rm comments

c699052

ms609 added 6 commits February 4, 2026 14:20

Use int32 & char, not int16 & bool

e3cb5c2

Guard against stack overflow

4627540

int32 in splits_to_edge

22aecf1

Extra ASSERTions

ca26ee4

Support >13k tips

bf2de6c

Skip on CRAN

5327217

ms609 marked this pull request as ready for review February 4, 2026 16:50

Copilot started work on behalf of ms609 February 4, 2026 16:53 View session

Copilot finished work on behalf of ms609 February 4, 2026 17:03

Copilot started work on behalf of ms609 February 5, 2026 08:33 View session

Copilot finished work on behalf of ms609 February 5, 2026 08:41

Version: 2.0.0.9002

3075526

Pass by value, not address

4f00a22

spell out int

f8fc019

ms609 merged commit d1103f5 into main Feb 5, 2026
16 of 19 checks passed

ms609 deleted the copilot/update-clustertable-logic branch February 5, 2026 10:36

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