Last updated on 2026-05-01 20:49:33 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.12.0 | 1063.89 | 4.98 | 1068.87 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.12.0 | 43.94 | 4.04 | 47.98 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.12.0 | 1200.00 | -23.18 | 1176.82 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 2.12.0 | 132.00 | 6.56 | 138.56 | ERROR | |
| r-devel-windows-x86_64 | 2.12.0 | 79.00 | 13.00 | 92.00 | ERROR | |
| r-patched-linux-x86_64 | 2.12.0 | 60.04 | 3.03 | 63.07 | ERROR | |
| r-release-linux-x86_64 | 2.12.0 | 61.37 | 2.94 | 64.31 | ERROR | |
| r-release-macos-arm64 | 2.12.0 | ERROR | ||||
| r-release-macos-x86_64 | 2.12.0 | 540.00 | 999.00 | 1539.00 | ERROR | |
| r-release-windows-x86_64 | 2.12.0 | 68.00 | 8.00 | 76.00 | ERROR | |
| r-oldrel-macos-arm64 | 2.12.0 | 15.00 | 60.00 | 75.00 | OK | |
| r-oldrel-macos-x86_64 | 2.12.0 | 59.00 | 358.00 | 417.00 | OK | |
| r-oldrel-windows-x86_64 | 2.12.0 | 89.00 | 8.00 | 97.00 | ERROR |
Version: 2.12.0
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 2.12.0
Check: R code for possible problems
Result: NOTE
COMCLUST: no visible binding for global variable ‘_TreeDist_COMCLUST’
EHMI_xptr: no visible binding for global variable ‘_TreeDist_EHMI_xptr’
HH_xptr: no visible binding for global variable ‘_TreeDist_HH_xptr’
HMI_xptr: no visible binding for global variable ‘_TreeDist_HMI_xptr’
binary_entropy_counts: no visible binding for global variable
‘_TreeDist_binary_entropy_counts’
build_hpart_from_list: no visible binding for global variable
‘_TreeDist_build_hpart_from_list’
build_hpart_from_phylo: no visible binding for global variable
‘_TreeDist_build_hpart_from_phylo’
clone_hpart: no visible binding for global variable
‘_TreeDist_clone_hpart’
confusion: no visible binding for global variable ‘_TreeDist_confusion’
consensus_info: no visible binding for global variable
‘_TreeDist_consensus_info’
cpp_jaccard_similarity: no visible binding for global variable
‘_TreeDist_cpp_jaccard_similarity’
cpp_mast: no visible binding for global variable ‘_TreeDist_cpp_mast’
cpp_matching_split_distance: no visible binding for global variable
‘_TreeDist_cpp_matching_split_distance’
cpp_msi_distance: no visible binding for global variable
‘_TreeDist_cpp_msi_distance’
cpp_mutual_clustering: no visible binding for global variable
‘_TreeDist_cpp_mutual_clustering’
cpp_nni_distance: no visible binding for global variable
‘_TreeDist_cpp_nni_distance’
cpp_robinson_foulds_distance: no visible binding for global variable
‘_TreeDist_cpp_robinson_foulds_distance’
cpp_robinson_foulds_info: no visible binding for global variable
‘_TreeDist_cpp_robinson_foulds_info’
cpp_shared_phylo: no visible binding for global variable
‘_TreeDist_cpp_shared_phylo’
entropy_int: no visible binding for global variable
‘_TreeDist_entropy_int’
expected_mi: no visible binding for global variable
‘_TreeDist_expected_mi’
hpart_to_edge: no visible binding for global variable
‘_TreeDist_hpart_to_edge’
keep_and_reduce: no visible binding for global variable
‘_TreeDist_keep_and_reduce’
keep_and_reroot: no visible binding for global variable
‘_TreeDist_keep_and_reroot’
lapjv: no visible binding for global variable ‘_TreeDist_lapjv’
mismatch_size: no visible binding for global variable
‘_TreeDist_mismatch_size’
pair_diff_euclidean: no visible binding for global variable
‘_TreeDist_pair_diff_euclidean’
path_vector: no visible binding for global variable
‘_TreeDist_path_vector’
reduce_trees: no visible binding for global variable
‘_TreeDist_reduce_trees’
relabel_hpart: no visible binding for global variable
‘_TreeDist_relabel_hpart’
robinson_foulds_all_pairs: no visible binding for global variable
‘_TreeDist_robinson_foulds_all_pairs’
spr_table_7: no visible binding for global variable
‘_TreeDist_spr_table_7’
vec_diff_euclidean: no visible binding for global variable
‘_TreeDist_vec_diff_euclidean’
Undefined global functions or variables:
_TreeDist_COMCLUST _TreeDist_EHMI_xptr _TreeDist_HH_xptr
_TreeDist_HMI_xptr _TreeDist_binary_entropy_counts
_TreeDist_build_hpart_from_list _TreeDist_build_hpart_from_phylo
_TreeDist_clone_hpart _TreeDist_confusion _TreeDist_consensus_info
_TreeDist_cpp_jaccard_similarity _TreeDist_cpp_mast
_TreeDist_cpp_matching_split_distance _TreeDist_cpp_msi_distance
_TreeDist_cpp_mutual_clustering _TreeDist_cpp_nni_distance
_TreeDist_cpp_robinson_foulds_distance
_TreeDist_cpp_robinson_foulds_info _TreeDist_cpp_shared_phylo
_TreeDist_entropy_int _TreeDist_expected_mi _TreeDist_hpart_to_edge
_TreeDist_keep_and_reduce _TreeDist_keep_and_reroot _TreeDist_lapjv
_TreeDist_mismatch_size _TreeDist_pair_diff_euclidean
_TreeDist_path_vector _TreeDist_reduce_trees _TreeDist_relabel_hpart
_TreeDist_robinson_foulds_all_pairs _TreeDist_spr_table_7
_TreeDist_vec_diff_euclidean
Flavor: r-release-macos-x86_64
Version: 2.12.0
Check: examples
Result: ERROR
Running examples in ‘TreeDist-Ex.R’ failed
The error most likely occurred in:
> ### Name: CompareAll
> ### Title: Distances between each pair of trees
> ### Aliases: CompareAll
>
> ### ** Examples
>
> # Generate a list of trees to compare
> library("TreeTools", quietly = TRUE)
> trees <- list(bal1 = BalancedTree(1:8),
+ pec1 = PectinateTree(1:8),
+ pec2 = PectinateTree(c(4:1, 5:8)))
>
> # Compare each tree with each other tree
> CompareAll(trees, NNIDist)
Error in cpp_nni_distance(edge1, edge2, nTip) :
object '_TreeDist_cpp_nni_distance' not found
Calls: CompareAll ... vapply -> Func -> .TreeDistance -> Func -> cpp_nni_distance
Execution halted
Flavor: r-release-macos-x86_64
Version: 2.12.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [21s/62s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library("testthat", warn.conflicts = FALSE)
> library("TreeDist")
>
> test_check("TreeDist")
Saving _problems/test-64-4.R
Loading required package: ape
Saving _problems/test-HPart-4.R
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Saving _problems/test-Islands-4.R
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Saving _problems/test-Reduce-14.R
Saving _problems/test-VisualizeMatching-24.R
Saving _problems/test-VisualizeMatching-144.R
Saving _problems/test-binary_entropy_counts-2.R
Saving _problems/test-day_1985.cpp-4.R
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[ FAIL 94 | WARN 0 | SKIP 7 | PASS 307 ]
══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• #TODO (1): 'test-tree_distance_spr.R:247:3'
• On CRAN (3): 'test-MSTSegments.R:1:1', 'test-Plot3.R:1:1', 'test-plot.R:12:1'
• getOption("slowMode", FALSE) is not TRUE (3):
'test-tree_distance_spr.R:96:3', 'test-tree_distance_spr.R:117:3',
'test-tree_distance_spr.R:154:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-64.R:2:10'): 64-bit splits handled ok ──────────────────────────
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_shared_phylo' not found
Backtrace:
▆
1. ├─testthat::expect_gt(SPI(64), SPI(63)) at test-64.R:5:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist (local) SPI(64)
5. └─TreeDist::SharedPhylogeneticInfo(...) at test-64.R:2:10
6. └─TreeDist::CalculateTreeDistance(...)
7. └─TreeDist:::.SplitDistanceOneOne(...)
8. └─TreeDist (local) Func(...)
9. └─TreeDist::GeneralizedRF(...)
10. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-HPart.R:4:3'): is.HPart() succeeds ─────────────────────────────
Error in `build_hpart_from_phylo(tree)`: object '_TreeDist_build_hpart_from_phylo' not found
Backtrace:
▆
1. ├─testthat::expect_true(is.HPart(as.HPart(TreeTools::BalancedTree(7)))) at test-HPart.R:4:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─TreeDist::is.HPart(as.HPart(TreeTools::BalancedTree(7)))
5. ├─TreeDist::as.HPart(TreeTools::BalancedTree(7))
6. └─TreeDist:::as.HPart.phylo(TreeTools::BalancedTree(7))
7. ├─base::structure(...)
8. └─TreeDist:::build_hpart_from_phylo(tree)
── Error ('test-HPart.R:13:3'): as.phylo.HPart ─────────────────────────────────
Error in `build_hpart_from_phylo(tree)`: object '_TreeDist_build_hpart_from_phylo' not found
Backtrace:
▆
1. ├─TreeDist::as.HPart(bal7) at test-HPart.R:13:3
2. └─TreeDist:::as.HPart.phylo(bal7)
3. ├─base::structure(...)
4. └─TreeDist:::build_hpart_from_phylo(tree)
── Error ('test-HPart.R:22:3'): as.HPart.numeric ───────────────────────────────
Error in `build_hpart_from_list(tree, n_tip)`: object '_TreeDist_build_hpart_from_list' not found
Backtrace:
▆
1. ├─TreeDist::as.HPart(...) at test-HPart.R:22:3
2. └─TreeDist:::as.HPart.list(...)
3. └─TreeDist:::build_hpart_from_list(tree, n_tip)
── Error ('test-HPart.R:50:3'): HParts are relabelled correctly ────────────────
Error in `build_hpart_from_phylo(tree)`: object '_TreeDist_build_hpart_from_phylo' not found
Backtrace:
▆
1. ├─TreeDist::as.HPart(bal7) at test-HPart.R:50:3
2. └─TreeDist:::as.HPart.phylo(bal7)
3. ├─base::structure(...)
4. └─TreeDist:::build_hpart_from_phylo(tree)
── Error ('test-HPart.R:67:45'): plot.HPart ────────────────────────────────────
Error in `build_hpart_from_list(tree, n_tip)`: object '_TreeDist_build_hpart_from_list' not found
Backtrace:
▆
1. └─vdiffr::expect_doppelganger(...) at test-HPart.R:67:3
2. └─vdiffr (local) writer(fig, testcase, title)
3. ├─vdiffr:::print_plot(plot, title)
4. └─vdiffr:::print_plot.function(plot, title)
5. └─TreeDist (local) p()
6. ├─base::plot(as.HPart(list(list(1, 2, 3), list(4, list(5, 6))))) at test-HPart.R:67:45
7. ├─TreeDist::as.HPart(list(list(1, 2, 3), list(4, list(5, 6))))
8. └─TreeDist:::as.HPart.list(...)
9. └─TreeDist:::build_hpart_from_list(tree, n_tip)
── Error ('test-HPart.R:73:3'): Renumber.HPart ─────────────────────────────────
Error in `build_hpart_from_list(tree, n_tip)`: object '_TreeDist_build_hpart_from_list' not found
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-HPart.R:73:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─TreeTools::RenumberTips(as.HPart(list(1, 2, 4, 3)), 4:2)
8. ├─TreeDist::as.HPart(list(1, 2, 4, 3))
9. └─TreeDist:::as.HPart.list(list(1, 2, 4, 3))
10. └─TreeDist:::build_hpart_from_list(tree, n_tip)
── Error ('test-Islands.R:4:3'): Islands() works ───────────────────────────────
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_mutual_clustering' not found
Backtrace:
▆
1. └─TreeDist::ClusteringInfoDist(trees) at test-Islands.R:4:3
2. └─TreeDist::MutualClusteringInfo(...)
3. └─TreeDist::CalculateTreeDistance(...)
4. └─TreeDist:::.SplitDistanceAllPairs(...)
5. ├─base::structure(...)
6. └─base::apply(is, 2, .CliPairDist)
7. └─TreeDist (local) FUN(newX[, i], ...)
8. └─TreeDist (local) .PairDist(i)
9. └─TreeDist (local) Func(...)
10. └─TreeDist::GeneralizedRF(...)
11. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-Reduce.R:7:3'): ReduceTrees() handles invalid input ────────────
Error in `reduce_trees(BalancedTree(3)$edge, PectinateTree(3)$edge, letters[1:3])`: object '_TreeDist_reduce_trees' not found
Backtrace:
▆
1. ├─testthat::expect_null(...) at test-Reduce.R:7:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist:::reduce_trees(...)
── Error ('test-Reduce.R:14:3'): ReduceTrees() ─────────────────────────────────
Error in `reduce_trees(tree1$edge[PostorderOrder(tree1), ], tree2$edge[PostorderOrder(tree2), ], tree1[["tip.label"]])`: object '_TreeDist_reduce_trees' not found
Backtrace:
▆
1. ├─testthat::expect_null(ReduceTrees(bal9, bal9)) at test-Reduce.R:14:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::ReduceTrees(bal9, bal9)
5. └─TreeDist:::reduce_trees(...)
── Error ('test-VisualizeMatching.R:22:5'): VisualizeMatching() works ──────────
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_mutual_clustering' not found
Backtrace:
▆
1. └─vdiffr::expect_doppelganger(...) at test-VisualizeMatching.R:21:3
2. └─vdiffr (local) writer(fig, testcase, title)
3. ├─vdiffr:::print_plot(plot, title)
4. └─vdiffr:::print_plot.function(plot, title)
5. └─TreeDist (local) p()
6. └─TreeDist::VisualizeMatching(...) at test-VisualizeMatching.R:22:5
7. └─TreeDist (local) Func(tree1, tree2, reportMatching = TRUE)
8. └─TreeDist::CalculateTreeDistance(...)
9. └─TreeDist:::.SplitDistanceOneOne(...)
10. └─TreeDist (local) Func(...)
11. └─TreeDist::GeneralizedRF(...)
12. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-VisualizeMatching.R:141:5'): VisualizeMatching() handles unrooted trees ──
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_robinson_foulds_distance' not found
Backtrace:
▆
1. └─vdiffr::expect_doppelganger(...) at test-VisualizeMatching.R:137:3
2. └─vdiffr (local) writer(fig, testcase, title)
3. ├─vdiffr:::print_plot(plot, title)
4. └─vdiffr:::print_plot.function(plot, title)
5. └─TreeDist (local) p()
6. └─TreeDist::VisualizeMatching(...) at test-VisualizeMatching.R:141:5
7. └─TreeDist (local) Func(tree1, tree2, reportMatching = TRUE)
8. └─TreeDist::CalculateTreeDistance(...)
9. └─TreeDist:::.SplitDistanceOneOne(...)
10. └─TreeDist (local) Func(...)
11. └─TreeDist::GeneralizedRF(...)
12. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-binary_entropy_counts.R:2:3'): binary_entropy_counts() fails gracefully ──
Error in `binary_entropy_counts(integer(0), 0)`: object '_TreeDist_binary_entropy_counts' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-binary_entropy_counts.R:2:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist:::binary_entropy_counts(integer(0), 0)
── Error ('test-day_1985.cpp.r:4:3'): Day 1985 does not overflow ───────────────
Error in `robinson_foulds_all_pairs(if (is.list(ct)) ct else list(ct))`: object '_TreeDist_robinson_foulds_all_pairs' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-day_1985.cpp.r:4:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::RobinsonFoulds(list(bigTree, bigTree))
5. └─TreeDist:::robinson_foulds_all_pairs(if (is.list(ct)) ct else list(ct))
── Error ('test-day_1985.cpp.r:32:3'): Day 1985 examples ───────────────────────
Error in `robinson_foulds_all_pairs(list(c1, c2))`: object '_TreeDist_robinson_foulds_all_pairs' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-day_1985.cpp.r:32:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist:::robinson_foulds_all_pairs(list(c1, c2))
── Error ('test-day_1985.cpp.r:75:3'): RobinsonFoulds() with realistic trees ───
Error in `robinson_foulds_all_pairs(if (is.list(ct)) ct else list(ct))`: object '_TreeDist_robinson_foulds_all_pairs' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-day_1985.cpp.r:75:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::RobinsonFoulds(r4)
5. └─TreeDist:::robinson_foulds_all_pairs(if (is.list(ct)) ct else list(ct))
── Error ('test-different-tips.R:12:3'): Non-identical tips are handled okay ───
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_mutual_clustering' not found
Backtrace:
▆
1. └─TreeDist::TreeDistance(bal8, pec8) at test-different-tips.R:12:3
2. └─TreeDist::ClusteringInfoDistance(...)
3. └─TreeDist::MutualClusteringInfo(...)
4. └─TreeDist::CalculateTreeDistance(...)
5. └─TreeDist:::.SplitDistanceOneOne(...)
6. └─TreeDist (local) Func(...)
7. └─TreeDist::GeneralizedRF(...)
8. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Failure ('test-hierarchical_mutual_information.R:11:3'): Hierarchical Mutual Information ──
Expected `HierarchicalMutualInfo(tree1, tree2)` not to throw any errors.
Actually got a <simpleError> with message:
object '_TreeDist_build_hpart_from_phylo' not found
── Error ('test-hierarchical_mutual_information.R:14:3'): Hierarchical Mutual Information ──
Error in `build_hpart_from_phylo(tree)`: object '_TreeDist_build_hpart_from_phylo' not found
Backtrace:
▆
1. └─TreeDist::HierarchicalMutualInfo(tree1, tree2) at test-hierarchical_mutual_information.R:14:3
2. ├─TreeDist::as.HPart(tree1)
3. └─TreeDist:::as.HPart.phylo(tree1)
4. ├─base::structure(...)
5. └─TreeDist:::build_hpart_from_phylo(tree)
── Error ('test-hierarchical_mutual_information.R:55:3'): HMI edge cases ───────
Error in `build_hpart_from_phylo(tree)`: object '_TreeDist_build_hpart_from_phylo' not found
Backtrace:
▆
1. ├─testthat::expect_lt(HMI(bal9, bal9b), HMI(bal9, bal9)) at test-hierarchical_mutual_information.R:55:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::HMI(bal9, bal9b)
5. ├─TreeDist::as.HPart(tree1)
6. └─TreeDist:::as.HPart.phylo(tree1)
7. ├─base::structure(...)
8. └─TreeDist:::build_hpart_from_phylo(tree)
── Error ('test-hmi.cpp.R:4:3'): HMI fails nicely ──────────────────────────────
Error in `build_hpart_from_phylo(tree)`: object '_TreeDist_build_hpart_from_phylo' not found
Backtrace:
▆
1. ├─TreeDist::as.HPart(BalancedTree(5)) at test-hmi.cpp.R:4:3
2. └─TreeDist:::as.HPart.phylo(BalancedTree(5))
3. ├─base::structure(...)
4. └─TreeDist:::build_hpart_from_phylo(tree)
── Error ('test-hmi.cpp.R:18:3'): HMI examples from Perotti et al. 2015 ────────
Error in `build_hpart_from_list(tree, n_tip)`: object '_TreeDist_build_hpart_from_list' not found
Backtrace:
▆
1. ├─testthat::expect_equal(SelfHMI(p1), 1.011/log(2), tolerance = 0.01) at test-hmi.cpp.R:18:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::SelfHMI(p1)
5. ├─TreeDist::as.HPart(tree)
6. └─TreeDist:::as.HPart.list(tree)
7. └─TreeDist:::build_hpart_from_list(tree, n_tip)
── Error ('test-hmi.cpp.R:26:3'): HMI is dependent on root position ────────────
Error in `build_hpart_from_phylo(tree)`: object '_TreeDist_build_hpart_from_phylo' not found
Backtrace:
▆
1. ├─testthat::expect_lt(...) at test-hmi.cpp.R:26:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::HMI(RootTree(bal9, 1), RootTree(bal9, 9), normalize = TRUE)
5. ├─TreeDist::as.HPart(tree1)
6. └─TreeDist:::as.HPart.phylo(tree1)
7. ├─base::structure(...)
8. └─TreeDist:::build_hpart_from_phylo(tree)
── Error ('test-hmi.cpp.R:34:3'): HMI results match hmi.pynb ───────────────────
Error in `build_hpart_from_list(tree, n_tip)`: object '_TreeDist_build_hpart_from_list' not found
Backtrace:
▆
1. ├─testthat::expect_equal(HMI(p1, p2), 0.941098035724547/log(2)) at test-hmi.cpp.R:34:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::HMI(p1, p2)
5. ├─TreeDist::as.HPart(tree1)
6. └─TreeDist:::as.HPart.list(tree1)
7. └─TreeDist:::build_hpart_from_list(tree, n_tip)
── Error ('test-hmi.cpp.R:102:3'): HMI calculated correctly ────────────────────
Error in `build_hpart_from_phylo(tree)`: object '_TreeDist_build_hpart_from_phylo' not found
Backtrace:
▆
1. ├─TreeDist::as.HPart(BalancedTree(6)) at test-hmi.cpp.R:102:3
2. └─TreeDist:::as.HPart.phylo(BalancedTree(6))
3. ├─base::structure(...)
4. └─TreeDist:::build_hpart_from_phylo(tree)
── Error ('test-hmi.cpp.R:126:3'): HMI_cpp equals SelfHMI for same partition ───
Error in `build_hpart_from_phylo(tree)`: object '_TreeDist_build_hpart_from_phylo' not found
Backtrace:
▆
1. ├─TreeDist::as.HPart(tr) at test-hmi.cpp.R:126:3
2. └─TreeDist:::as.HPart.phylo(tr)
3. ├─base::structure(...)
4. └─TreeDist:::build_hpart_from_phylo(tree)
── Error ('test-hmi.cpp.R:141:3'): HMI works with real dataset ─────────────────
Error in `build_hpart_from_list(lapply(unique(tree), function(x) as.list(which(tree == x))), length(tree))`: object '_TreeDist_build_hpart_from_list' not found
Backtrace:
▆
1. ├─TreeDist::as.HPart(ch) at test-hmi.cpp.R:141:3
2. └─TreeDist:::as.HPart.default(ch)
3. ├─base::structure(...)
4. └─TreeDist:::build_hpart_from_list(...)
── Error ('test-information.R:6:3'): Entropy is calculated correctly ───────────
Error in `entropy_int(as.integer(c(1, 1, 0, 1, 1)))`: object '_TreeDist_entropy_int' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-information.R:6:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::entropy_int(as.integer(c(1, 1, 0, 1, 1)))
── Error ('test-information.R:37:5'): Removing contradictions improves scores ──
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_shared_phylo' not found
Backtrace:
▆
1. └─TreeDist (local) Test(200, 2) at test-information.R:44:3
2. ├─testthat::expect_true(...) at test-information.R:37:5
3. │ └─testthat::quasi_label(enquo(object), label)
4. │ └─rlang::eval_bare(expr, quo_get_env(quo))
5. └─TreeDist::SharedPhylogeneticInfoSplits(...)
6. └─TreeDist::GeneralizedRF(...)
7. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-lap.R:8:3'): LAP example1 ──────────────────────────────────────
Error in `lapjv(x, max(x))`: object '_TreeDist_lapjv' not found
Backtrace:
▆
1. └─TreeDist::LAPJV(problem) at test-lap.R:8:3
2. └─TreeDist:::lapjv(x, max(x))
── Error ('test-lap.R:21:3'): LAP example2 ─────────────────────────────────────
Error in `lapjv(x, max(x))`: object '_TreeDist_lapjv' not found
Backtrace:
▆
1. └─TreeDist::LAPJV(problem) at test-lap.R:21:3
2. └─TreeDist:::lapjv(x, max(x))
── Error ('test-lap.R:33:3'): LAP example3 ─────────────────────────────────────
Error in `lapjv(x, max(x))`: object '_TreeDist_lapjv' not found
Backtrace:
▆
1. └─TreeDist::LAPJV(problem) at test-lap.R:33:3
2. └─TreeDist:::lapjv(x, max(x))
── Error ('test-lap.R:44:3'): LAP handles non-square matrices ──────────────────
Error in `lapjv(x, max(x))`: object '_TreeDist_lapjv' not found
Backtrace:
▆
1. ├─testthat::expect_equal(LAPJV(problem), LAPJV(problem[, -5])) at test-lap.R:44:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::LAPJV(problem)
5. └─TreeDist:::lapjv(x, max(x))
── Error ('test-lap.R:60:3'): LAP handles tiny matrices ────────────────────────
Error in `lapjv(x, max(x))`: object '_TreeDist_lapjv' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-lap.R:60:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::LAPJV(matrix(8, 1, 1))
5. └─TreeDist:::lapjv(x, max(x))
── Error ('test-lap.R:313:3'): Precision avoids interminable loop in LAP ───────
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_mutual_clustering' not found
Backtrace:
▆
1. ├─testthat::expect_gt(...) at test-lap.R:313:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::MutualClusteringInfoSplits(spl2180, spl2180)
5. └─TreeDist::GeneralizedRF(...)
6. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-lap.R:326:3'): LAPJV doesn't crash ─────────────────────────────
Error in `lapjv(x, max(x))`: object '_TreeDist_lapjv' not found
Backtrace:
▆
1. └─TreeDist::LAPJV(matrix(c(2, 1, 1, 2), 2, 2)) at test-lap.R:326:3
2. └─TreeDist:::lapjv(x, max(x))
── Error ('test-lap.R:347:3'): Avoid infinite loop in LAP ──────────────────────
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_mutual_clustering' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-lap.R:347:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::ClusteringInfoDistance(...)
5. └─TreeDist::MutualClusteringInfo(...)
6. └─TreeDist::CalculateTreeDistance(...)
7. └─TreeDist:::.SplitDistanceOneOne(...)
8. └─TreeDist (local) Func(...)
9. └─TreeDist::GeneralizedRF(...)
10. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-mast.R:13:3'): MAST works ──────────────────────────────────────
Error in `cpp_mast(edge1 - 1L, Postorder(edge2) - 1L, nTip)`: object '_TreeDist_cpp_mast' not found
Backtrace:
▆
1. ├─testthat::expect_equal(8L, MASTSize(tree1, tree1, rooted = TRUE)) at test-mast.R:13:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::MASTSize(tree1, tree1, rooted = TRUE)
5. └─TreeDist::.TreeDistance(...)
6. └─TreeDist (local) Func(tree1, tree2, tipLabels = labels1, nTip = nTip, ...)
7. └─TreeDist:::.MASTSizeEdges(...)
8. └─TreeDist:::cpp_mast(edge1 - 1L, Postorder(edge2) - 1L, nTip)
── Error ('test-mast.R:37:3'): MAST supports funnily-ordered edges ─────────────
Error in `cpp_mast(edge1 - 1L, Postorder(edge2) - 1L, nTip)`: object '_TreeDist_cpp_mast' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-mast.R:37:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::MASTSize(Postorder(tree1), Postorder(tree2), rooted = FALSE)
5. └─TreeDist::.TreeDistance(...)
6. └─TreeDist (local) Func(tree1, tree2, tipLabels = labels1, nTip = nTip, ...)
7. └─base::vapply(...)
8. └─TreeDist (local) FUN(X[[i]], ...)
9. └─TreeDist:::.MASTSizeEdges(...)
10. └─TreeDist:::cpp_mast(edge1 - 1L, Postorder(edge2) - 1L, nTip)
── Error ('test-mast.R:60:5'): MAST size calculated correctly on small trees ───
Error in `cpp_mast(edge1 - 1L, Postorder(edge2) - 1L, nTip)`: object '_TreeDist_cpp_mast' not found
Backtrace:
▆
1. └─TreeDist (local) ME(2L, 1) at test-mast.R:66:3
2. ├─testthat::expect_equal(...) at test-mast.R:60:5
3. │ └─testthat::quasi_label(enquo(expected), expected.label)
4. │ └─rlang::eval_bare(expr, quo_get_env(quo))
5. └─TreeDist:::.MASTSizeEdges(...)
6. └─TreeDist:::cpp_mast(edge1 - 1L, Postorder(edge2) - 1L, nTip)
── Error ('test-median.R:4:3'): Median is calculated ───────────────────────────
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_mutual_clustering' not found
Backtrace:
▆
1. ├─testthat::expect_equal(4, median(tenTrees, index = TRUE)) at test-median.R:4:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─stats::median(tenTrees, index = TRUE)
5. └─TreeDist:::median.multiPhylo(tenTrees, index = TRUE)
6. ├─base::unname(colSums(as.matrix(Distance(x))))
7. ├─base::colSums(as.matrix(Distance(x)))
8. │ └─base::is.data.frame(x)
9. ├─base::as.matrix(Distance(x))
10. └─TreeDist (local) Distance(x)
11. └─TreeDist::MutualClusteringInfo(...)
12. └─TreeDist::CalculateTreeDistance(...)
13. └─TreeDist:::.SplitDistanceAllPairs(...)
14. ├─base::structure(...)
15. └─base::apply(is, 2, .CliPairDist)
16. └─TreeDist (local) FUN(newX[, i], ...)
17. └─TreeDist (local) .PairDist(i)
18. └─TreeDist (local) Func(...)
19. └─TreeDist::GeneralizedRF(...)
20. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-parallel.R:9:3'): Parallelization works ────────────────────────
Error in `checkForRemoteErrors(val)`: 2 nodes produced errors; first error: object '_TreeDist_cpp_mutual_clustering' not found
Backtrace:
▆
1. ├─base::suppressMessages(...) at test-parallel.R:5:3
2. │ └─base::withCallingHandlers(...)
3. └─TreeDist::ClusteringInfoDistance(trees) at test-parallel.R:9:3
4. └─TreeDist::MutualClusteringInfo(...)
5. └─TreeDist::CalculateTreeDistance(...)
6. └─TreeDist:::.SplitDistanceAllPairs(...)
7. ├─base::structure(...)
8. └─parallel::parCapply(cluster, is, .PairDist)
9. └─parallel::clusterApply(...)
10. └─parallel:::staticClusterApply(cl, fun, length(x), argfun)
11. └─parallel:::checkForRemoteErrors(val)
── Error ('test-split_info.R:13:3'): Split info calculated ─────────────────────
Error in `consensus_info(trees, TRUE, 1)`: object '_TreeDist_consensus_info' not found
Backtrace:
▆
1. ├─testthat::expect_equal(consensus_info(trees, TRUE, 1), 0) at test-split_info.R:13:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist:::consensus_info(trees, TRUE, 1)
── Error ('test-tree_distance.R:95:10'): Metrics handle polytomies ─────────────
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_shared_phylo' not found
Backtrace:
▆
1. └─base::lapply(...) at test-tree_distance.R:93:3
2. └─TreeDist (local) FUN(X[[i]], ...)
3. ├─testthat::expect_equal(0, Func(treeSym8, polytomy8)) at test-tree_distance.R:95:10
4. │ └─testthat::quasi_label(enquo(expected), expected.label)
5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
6. └─TreeDist (local) Func(treeSym8, polytomy8)
7. └─TreeDist::CalculateTreeDistance(...)
8. └─TreeDist:::.SplitDistanceOneOne(...)
9. └─TreeDist (local) Func(...)
10. └─TreeDist::GeneralizedRF(...)
11. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance.R:135:3'): .MaxValue() succeeds ──────────────────
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_mutual_clustering' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance.R:135:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::MutualClusteringInfo(list1, list2[[2]], normalize = FALSE)
5. └─TreeDist::CalculateTreeDistance(...)
6. └─TreeDist:::.SplitDistanceOneMany(...)
7. └─base::vapply(...)
8. └─TreeDist (local) FUN(X[[i]], ...)
9. └─TreeDist (local) Func(...)
10. └─TreeDist::GeneralizedRF(...)
11. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance.R:176:5'): Output dimensions are correct ─────────
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_shared_phylo' not found
Backtrace:
▆
1. └─base::lapply(methodsToTest, Test) at test-tree_distance.R:191:3
2. └─TreeDist (local) FUN(X[[i]], ...)
3. ├─base::matrix(...) at test-tree_distance.R:176:5
4. └─TreeDist (local) Func(treeSym8, treeSym8)
5. └─TreeDist::CalculateTreeDistance(...)
6. └─TreeDist:::.SplitDistanceOneOne(...)
7. └─TreeDist (local) Func(...)
8. └─TreeDist::GeneralizedRF(...)
9. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance.R:199:5'): RF Distance is correctly calculated ───
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_robinson_foulds_distance' not found
Backtrace:
▆
1. └─TreeDist (local) RFTest(treeSym8, treeSym8) at test-tree_distance.R:206:3
2. ├─testthat::expect_equal(...) at test-tree_distance.R:199:5
3. │ └─testthat::quasi_label(enquo(expected), expected.label)
4. │ └─rlang::eval_bare(expr, quo_get_env(quo))
5. └─TreeDist::RobinsonFoulds(t1, t2)
6. └─TreeDist::CalculateTreeDistance(...)
7. └─TreeDist:::.SplitDistanceOneOne(...)
8. └─TreeDist (local) Func(...)
9. └─TreeDist::GeneralizedRF(...)
10. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance.R:229:3'): Shared Phylogenetic Info is correctly calculated ──
Error in `cpp_shared_phylo(as.Splits(as.logical(c(1, 1, 1, 1, 0, 0, 0, 0))), as.Splits(as.logical(c(1, 1, 1, 1, 0, 0, 0, 0))), 8L)`: object '_TreeDist_cpp_shared_phylo' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance.R:229:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist:::cpp_shared_phylo(...)
── Error ('test-tree_distance.R:335:3'): MatchingSplitInfo() is correctly calculated ──
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_msi_distance' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance.R:335:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::MatchingSplitInfoSplits(...)
5. └─TreeDist::GeneralizedRF(...)
6. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance.R:375:3'): Shared Phylogenetic Information is correctly estimated ──
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_shared_phylo' not found
Backtrace:
▆
1. └─TreeDist::ExpectedVariation(treeSym8, treeAbc.Defgh, samples = 1000L) at test-tree_distance.R:375:3
2. └─base::vapply(...)
3. └─TreeDist (local) FUN(X[[i]], ...)
4. └─TreeDist::SharedPhylogeneticInfoSplits(splits1, resampled2)
5. └─TreeDist::GeneralizedRF(...)
6. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance.R:390:3'): Clustering information is correctly calculated ──
Error in `cpp_mutual_clustering(as.Splits(as.logical(c(1, 1, 1, 0, 0, 0, 0, 0))), as.Splits(as.logical(c(1, 1, 1, 0, 0, 0, 0, 0))), 8L)`: object '_TreeDist_cpp_mutual_clustering' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance.R:390:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist:::cpp_mutual_clustering(...)
── Error ('test-tree_distance.R:562:3'): Matchings are correct ─────────────────
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_mutual_clustering' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance.R:562:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::MutualClusteringInfo(threeAwayPoly, randomBif20)
5. └─TreeDist::CalculateTreeDistance(...)
6. └─TreeDist:::.SplitDistanceOneOne(...)
7. └─TreeDist (local) Func(...)
8. └─TreeDist::GeneralizedRF(...)
9. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance.R:660:3'): Matching Split Distance is correctly calculated ──
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_matching_split_distance' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance.R:660:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::MatchingSplitDistance(treeSym8, treeSym8)
5. └─TreeDist::CalculateTreeDistance(...)
6. └─TreeDist:::.SplitDistanceOneOne(...)
7. └─TreeDist (local) Func(...)
8. └─TreeDist::GeneralizedRF(...)
9. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance.R:705:3'): NyeSimilarity is correctly calculated, and matches JRF ──
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_jaccard_similarity' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance.R:705:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::NyeSimilarity(as.Splits(treeSym8), treeSym8)
5. └─TreeDist::CalculateTreeDistance(...)
6. └─TreeDist:::.SplitDistanceOneOne(...)
7. └─TreeDist (local) Func(...)
8. └─TreeDist::GeneralizedRF(...)
9. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance.R:743:3'): Jaccard RF extremes tend to equivalent functions ──
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_jaccard_similarity' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance.R:743:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::JaccardRobinsonFoulds(...)
5. └─TreeDist::CalculateTreeDistance(...)
6. └─TreeDist:::.SplitDistanceOneMany(...)
7. └─base::vapply(...)
8. └─TreeDist (local) FUN(X[[i]], ...)
9. └─TreeDist (local) Func(...)
10. └─TreeDist::GeneralizedRF(...)
11. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance.R:758:3'): Jaccard RF is correctly calculated ────
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_jaccard_similarity' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance.R:758:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::JaccardRobinsonFoulds(treeSym8, treeSym8, k = 2, similarity = TRUE)
5. └─TreeDist::CalculateTreeDistance(...)
6. └─TreeDist:::.SplitDistanceOneOne(...)
7. └─TreeDist (local) Func(...)
8. └─TreeDist::GeneralizedRF(...)
9. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance.R:797:5'): RobinsonFoulds() is correctly calculated ──
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_robinson_foulds_distance' not found
Backtrace:
▆
1. └─TreeDist (local) RFTest(treeSym8, treeSym8) at test-tree_distance.R:800:3
2. ├─testthat::expect_equal(...) at test-tree_distance.R:797:5
3. │ └─testthat::quasi_label(enquo(expected), expected.label)
4. │ └─rlang::eval_bare(expr, quo_get_env(quo))
5. └─TreeDist::RobinsonFoulds(tree1, tree2)
6. └─TreeDist::CalculateTreeDistance(...)
7. └─TreeDist:::.SplitDistanceOneOne(...)
8. └─TreeDist (local) Func(...)
9. └─TreeDist::GeneralizedRF(...)
10. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance.R:834:3'): RobinsonFoulds() supports large lists ──
Error in `robinson_foulds_all_pairs(if (is.list(ct)) ct else list(ct))`: object '_TreeDist_robinson_foulds_all_pairs' not found
Backtrace:
▆
1. ├─base::as.matrix(RobinsonFoulds(trees)) at test-tree_distance.R:834:3
2. └─TreeDist::RobinsonFoulds(trees)
3. └─TreeDist:::robinson_foulds_all_pairs(if (is.list(ct)) ct else list(ct))
── Error ('test-tree_distance.R:848:3'): Robinson Foulds Info is correctly calculated ──
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_robinson_foulds_info' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance.R:848:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::InfoRobinsonFoulds(...)
5. └─TreeDist::CalculateTreeDistance(...)
6. └─TreeDist:::.SplitDistanceOneOne(...)
7. └─TreeDist (local) Func(...)
8. └─TreeDist::GeneralizedRF(...)
9. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance.R:922:3'): Multiple comparisons are correctly ordered ──
Error in `robinson_foulds_all_pairs(if (is.list(ct)) ct else list(ct))`: object '_TreeDist_robinson_foulds_all_pairs' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance.R:922:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::RobinsonFoulds(trees)
5. └─TreeDist:::robinson_foulds_all_pairs(if (is.list(ct)) ct else list(ct))
── Error ('test-tree_distance.R:949:3'): Normalization occurs as documented ────
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_shared_phylo' not found
Backtrace:
▆
1. └─TreeDist::SharedPhylogeneticInfo(tree1, tree2, normalize = FALSE) at test-tree_distance.R:949:3
2. └─TreeDist::CalculateTreeDistance(...)
3. └─TreeDist:::.SplitDistanceOneOne(...)
4. └─TreeDist (local) Func(...)
5. └─TreeDist::GeneralizedRF(...)
6. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance.R:992:5'): Independent of root position ──────────
Error in `checkForRemoteErrors(val)`: 2 nodes produced errors; first error: object '_TreeDist_cpp_shared_phylo' not found
Backtrace:
▆
1. └─base::lapply(...) at test-tree_distance.R:991:3
2. └─TreeDist (local) FUN(X[[i]], ...)
3. ├─base::as.matrix(Method(trees)) at test-tree_distance.R:992:5
4. └─TreeDist (local) Method(trees)
5. └─TreeDist::CalculateTreeDistance(...)
6. └─TreeDist:::.SplitDistanceAllPairs(...)
7. ├─base::structure(...)
8. └─parallel::parCapply(cluster, is, .PairDist)
9. └─parallel::clusterApply(...)
10. └─parallel:::staticClusterApply(cl, fun, length(x), argfun)
11. └─parallel:::checkForRemoteErrors(val)
── Error ('test-tree_distance.R:1016:3'): Matchings are correctly reported ─────
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_mutual_clustering' not found
Backtrace:
▆
1. └─TreeDist (local) expect_matching_score(MutualClusteringInfo) at test-tree_distance.R:1016:3
2. └─TreeDist (local) Func(BalancedTree(33), PectinateTree(33), reportMatching = TRUE) at test-tree_distance.R:26:5
3. └─TreeDist::CalculateTreeDistance(...)
4. └─TreeDist:::.SplitDistanceOneOne(...)
5. └─TreeDist (local) Func(...)
6. └─TreeDist::GeneralizedRF(...)
7. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance_kc.R:13:3'): KC vector calculations ──────────────
Error in `path_vector(edge)`: object '_TreeDist_path_vector' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance_kc.R:13:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::PathVector(UnrootTree(bal7))
5. ├─base::structure(path_vector(edge), Size = NTip(tree), class = "dist")
6. └─TreeDist:::path_vector(edge)
── Error ('test-tree_distance_kc.R:40:3'): KC distances with special vectors ───
Error in `path_vector(edge)`: object '_TreeDist_path_vector' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance_kc.R:40:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::PathDist(trees)
5. └─TreeDist:::.PathDistManySelf(tree1)
6. └─base::vapply(...)
7. └─TreeDist (local) FUN(X[[i]], ...)
8. ├─base::structure(path_vector(edge), Size = NTip(tree), class = "dist")
9. └─TreeDist:::path_vector(edge)
── Error ('test-tree_distance_nni.R:11:3'): NNIDist() handles exceptions ───────
Error in `cpp_nni_distance(PectinateTree(40000)$edge, BalancedTree(40000)$edge, 40000)`: object '_TreeDist_cpp_nni_distance' not found
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-tree_distance_nni.R:11:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─TreeDist:::cpp_nni_distance(...)
── Error ('test-tree_distance_nni.R:22:3'): NNIDist() at NNI_MAX_TIPS ──────────
Error in `cpp_nni_distance(edge1, edge2, nTip)`: object '_TreeDist_cpp_nni_distance' not found
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-tree_distance_nni.R:22:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─TreeDist:::.NNIDistSingle(...)
8. └─TreeDist:::cpp_nni_distance(edge1, edge2, nTip)
── Error ('test-tree_distance_nni.R:97:3'): Simple NNI approximations ──────────
Error in `cpp_nni_distance(edge1, edge2, nTip)`: object '_TreeDist_cpp_nni_distance' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance_nni.R:97:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::NNIDist(BalancedTree(2), PectinateTree(2))
5. └─TreeDist::.TreeDistance(.NNIDistSingle, tree1, tree2)
6. └─TreeDist (local) Func(tree1, tree2, tipLabels = labels1, nTip = nTip, ...)
7. └─TreeDist:::cpp_nni_distance(edge1, edge2, nTip)
── Error ('test-tree_distance_nni.R:153:3'): NNI with lists of trees ───────────
Error in `cpp_nni_distance(edge1, edge2, nTip)`: object '_TreeDist_cpp_nni_distance' not found
Backtrace:
▆
1. └─TreeDist::NNIDist(tree1, list1) at test-tree_distance_nni.R:153:3
2. └─TreeDist::.TreeDistance(.NNIDistSingle, tree1, tree2)
3. └─TreeDist:::.TreeDistanceOneMany(...)
4. ├─base::vapply(...)
5. └─TreeDist (local) Func(...)
6. └─TreeDist:::cpp_nni_distance(edge1, edge2, nTip)
── Error ('test-tree_distance_path.R:5:3'): PathDist() ─────────────────────────
Error in `path_vector(edge)`: object '_TreeDist_path_vector' not found
Backtrace:
▆
1. └─TreeDist::PathVector(RenumberTips(bal6, t05)) at test-tree_distance_path.R:5:3
2. ├─base::structure(path_vector(edge), Size = NTip(tree), class = "dist")
3. └─TreeDist:::path_vector(edge)
── Error ('test-tree_distance_path.R:26:3'): PathDist() equivalent to path.dist() ──
Error in `path_vector(edge)`: object '_TreeDist_path_vector' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance_path.R:26:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::PathDist(UnrootTree(t1), UnrootTree(t2))
5. └─TreeDist:::.PathDist1Many(tree2, tree1)
6. └─TreeDist::PathVector(tree1)
7. ├─base::structure(path_vector(edge), Size = NTip(tree), class = "dist")
8. └─TreeDist:::path_vector(edge)
── Error ('test-tree_distance_spr.R:8:3'): SPR: keep_and_reroot() ──────────────
Error in `keep_and_reroot(tree1, tree2, keep)`: object '_TreeDist_keep_and_reroot' not found
Backtrace:
▆
1. └─TreeDist:::keep_and_reroot(tree1, tree2, keep) at test-tree_distance_spr.R:8:3
── Error ('test-tree_distance_spr.R:30:3'): SPRDist() handles different inputs ──
Error in `mismatch_size(as.Splits(c(T, T, F)), as.Splits(c(T, T, T, T)))`: object '_TreeDist_mismatch_size' not found
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-tree_distance_spr.R:30:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─TreeDist:::mismatch_size(...)
── Error ('test-tree_distance_spr.R:72:5'): confusion() ────────────────────────
Error in `confusion(a, b)`: object '_TreeDist_confusion' not found
Backtrace:
▆
1. └─TreeDist (local) TestConfusion(...) at test-tree_distance_spr.R:86:3
2. ├─testthat::expect_equal(...) at test-tree_distance_spr.R:72:5
3. │ └─testthat::quasi_label(enquo(object), label)
4. │ └─rlang::eval_bare(expr, quo_get_env(quo))
5. └─TreeDist:::confusion(a, b)
── Error ('test-tree_distance_spr.R:190:3'): SPR calculated correctly ──────────
Error in `reduce_trees(tree1$edge[PostorderOrder(tree1), ], tree2$edge[PostorderOrder(tree2), ], tree1[["tip.label"]])`: object '_TreeDist_reduce_trees' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance_spr.R:190:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist:::.SPRRogue(...)
5. └─TreeDist::ReduceTrees(tree1, tree2, check = check)
6. └─TreeDist:::reduce_trees(...)
── Error ('test-tree_distance_spr.R:277:3'): SPR deOliveira2008 calculation looks valid ──
Error in `reduce_trees(tree1$edge[PostorderOrder(tree1), ], tree2$edge[PostorderOrder(tree2), ], tree1[["tip.label"]])`: object '_TreeDist_reduce_trees' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance_spr.R:277:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─TreeDist::SPRDist(...)
5. └─TreeDist:::SPRDist.phylo(...)
6. └─.SPRFunc(method)(tree1, tree2)
7. └─TreeDist::ReduceTrees(tree1, tree2, check = check)
8. └─TreeDist:::reduce_trees(...)
── Error ('test-tree_distance_spr.R:285:3'): SPR: Under the hood ───────────────
Error in `mismatch_size(as.Splits(c(T, T, F)), as.Splits(c(T, T, T, T)))`: object '_TreeDist_mismatch_size' not found
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-tree_distance_spr.R:285:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─TreeDist:::mismatch_size(...)
── Error ('test-tree_distance_spr.R:320:3'): confusion() fails gracefully ──────
Error in `confusion(x, xx)`: object '_TreeDist_confusion' not found
Backtrace:
▆
1. ├─testthat::expect_error(confusion(x, xx), "differ in `nTip`") at test-tree_distance_spr.R:320:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─TreeDist:::confusion(x, xx)
── Error ('test-tree_distance_spr.R:331:5'): confusion() ───────────────────────
Error in `confusion(a, b)`: object '_TreeDist_confusion' not found
Backtrace:
▆
1. └─TreeDist (local) TestConfusion(...) at test-tree_distance_spr.R:341:3
2. ├─testthat::expect_equal(...) at test-tree_distance_spr.R:331:5
3. │ └─testthat::quasi_label(enquo(object), label)
4. │ └─rlang::eval_bare(expr, quo_get_env(quo))
5. └─TreeDist:::confusion(a, b)
── Error ('test-tree_distance_spr.R:355:3'): SPRDist handles input formats ─────
Error in `reduce_trees(tree1$edge[PostorderOrder(tree1), ], tree2$edge[PostorderOrder(tree2), ], tree1[["tip.label"]])`: object '_TreeDist_reduce_trees' not found
Backtrace:
▆
1. ├─testthat::expect_equal(SPRDist(bal9, bal9), 0) at test-tree_distance_spr.R:355:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─TreeDist::SPRDist(bal9, bal9)
5. └─TreeDist:::SPRDist.phylo(bal9, bal9)
6. └─.SPRFunc(method)(tree1, tree2)
7. └─TreeDist::ReduceTrees(tree1, tree2, check = check)
8. └─TreeDist:::reduce_trees(...)
── Error ('test-tree_distance_spr.R:382:3'): SPR deOliveira2008 calculation looks valid ──
Error in `reduce_trees(tree1$edge[PostorderOrder(tree1), ], tree2$edge[PostorderOrder(tree2), ], tree1[["tip.label"]])`: object '_TreeDist_reduce_trees' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance_spr.R:382:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─TreeDist::SPRDist(...)
5. └─TreeDist:::SPRDist.phylo(...)
6. └─.SPRFunc(method)(tree1, tree2)
7. └─TreeDist::ReduceTrees(tree1, tree2, check = check)
8. └─TreeDist:::reduce_trees(...)
── Error ('test-tree_distance_utilities.R:50:3'): CalculateTreeDistance() handles splits appropriately ──
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_robinson_foulds_distance' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance_utilities.R:50:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::CalculateTreeDistance(...)
5. └─TreeDist:::.SplitDistanceOneOne(...)
6. └─TreeDist (local) Func(...)
7. └─TreeDist::GeneralizedRF(...)
8. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance_utilities.R:114:3'): Matches are reported ────────
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_shared_phylo' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance_utilities.R:114:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::GeneralizedRF(...)
5. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance_utilities.R:209:5'): Matchings are calculated in both directions ──
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_shared_phylo' not found
Backtrace:
▆
1. └─TreeDist (local) Test(SharedPhylogeneticInfo) at test-tree_distance_utilities.R:216:3
2. └─TreeDist (local) Func(tree1, tree2, reportMatching = TRUE, ...) at test-tree_distance_utilities.R:209:5
3. └─TreeDist::CalculateTreeDistance(...)
4. └─TreeDist:::.SplitDistanceOneOne(...)
5. └─TreeDist (local) Func(...)
6. └─TreeDist::GeneralizedRF(...)
7. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-tree_distance_utilities.R:235:3'): .TreeDistance() supports all sizes ──
Error in `cpp_mast(edge1 - 1L, Postorder(edge2) - 1L, nTip)`: object '_TreeDist_cpp_mast' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance_utilities.R:235:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::rbind(...)
5. └─TreeDist::MASTSize(BalancedTree(7), as.phylo(0:3, 7))
6. └─TreeDist::.TreeDistance(...)
7. └─TreeDist:::.TreeDistanceOneMany(...)
8. ├─base::vapply(...)
9. └─TreeDist (local) Func(...)
10. └─TreeDist:::.MASTSizeEdges(...)
11. └─TreeDist:::cpp_mast(edge1 - 1L, Postorder(edge2) - 1L, nTip)
── Error ('test-tree_distance_utilities.R:249:3'): Unrooteds are handled by MAST ──
Error in `checkForRemoteErrors(val)`: one node produced an error: Both trees must be rooted if rooted = TRUE
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_distance_utilities.R:249:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::MASTSize(trees, rooted = FALSE)
5. └─TreeDist::.TreeDistance(...)
6. └─TreeDist:::.TreeDistanceManyMany(...)
7. └─TreeDist::CompareAll(...)
8. ├─base::do.call(...)
9. └─parallel::parLapply(...)
10. ├─base::do.call(...)
11. └─parallel::clusterApply(...)
12. └─parallel:::staticClusterApply(cl, fun, length(x), argfun)
13. └─parallel:::checkForRemoteErrors(val)
── Failure ('test-tree_information.R:43:3'): SplitwiseInfo() / ClusteringInfo() handle probabilities ──
Expected `1/3` to equal `Clust(tree, 60 * 3)`.
Differences:
`actual`: 0.33
`expected`: 0.23
── Failure ('test-tree_information.R:47:3'): SplitwiseInfo() / ClusteringInfo() handle probabilities ──
Expected 1 to equal `Clust(tree)`.
Differences:
`actual`: 1.00
`expected`: 0.69
── Failure ('test-tree_information.R:53:3'): SplitwiseInfo() / ClusteringInfo() handle probabilities ──
Expected 0.6 to equal `Clust(tree, 100)`.
Differences:
`actual`: 0.60
`expected`: 0.42
── Error ('test-tree_information.R:59:3'): SplitwiseInfo() / ClusteringInfo() handle probabilities ──
Error in `consensus_info(trees, mode == 1L, p = safeP)`: object '_TreeDist_consensus_info' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_information.R:59:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::ConsensusInfo(treeProfile, "p")
5. └─TreeDist:::consensus_info(trees, mode == 1L, p = safeP)
── Error ('test-tree_information.R:130:3'): ClusteringInfo() method works ──────
Error in `consensus_info(trees, mode == 1L, p = safeP)`: object '_TreeDist_consensus_info' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-tree_information.R:130:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::ConsensusInfo(trees, "spic")
5. └─TreeDist:::consensus_info(trees, mode == 1L, p = safeP)
── Error ('test-tree_information.R:139:3'): ConsensusInfo() is robust ──────────
Error in `consensus_info(trees, mode == 1L, p = safeP)`: object '_TreeDist_consensus_info' not found
Backtrace:
▆
1. ├─testthat::expect_equal(0, ConsensusInfo(trees, "cl")) at test-tree_information.R:139:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::ConsensusInfo(trees, "cl")
5. └─TreeDist:::consensus_info(trees, mode == 1L, p = safeP)
── Error ('test-tree_information.R:149:3'): ConsensusInfo() generates correct value ──
Error in `consensus_info(trees, mode == 1L, p = safeP)`: object '_TreeDist_consensus_info' not found
Backtrace:
▆
1. ├─testthat::expect_equal(0, ConsensusInfo(trees)) at test-tree_information.R:149:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TreeDist::ConsensusInfo(trees)
5. └─TreeDist:::consensus_info(trees, mode == 1L, p = safeP)
── Error ('test-trustworthiness.R:18:3'): Trustworthiness range ────────────────
Error in `checkForRemoteErrors(val)`: 2 nodes produced errors; first error: object '_TreeDist_cpp_mutual_clustering' not found
Backtrace:
▆
1. └─TreeDist::ClusteringInfoDist(trees) at test-trustworthiness.R:18:3
2. └─TreeDist::MutualClusteringInfo(...)
3. └─TreeDist::CalculateTreeDistance(...)
4. └─TreeDist:::.SplitDistanceAllPairs(...)
5. ├─base::structure(...)
6. └─parallel::parCapply(cluster, is, .PairDist)
7. └─parallel::clusterApply(...)
8. └─parallel:::staticClusterApply(cl, fun, length(x), argfun)
9. └─parallel:::checkForRemoteErrors(val)
[ FAIL 94 | WARN 0 | SKIP 7 | PASS 307 ]
Deleting unused snapshots: 'VisualizeMatching/hidden-edge-labels.svg',
'VisualizeMatching/jrf-vm-matchzeros-false.svg',
'VisualizeMatching/rf-collapse-a-node.svg',
'VisualizeMatching/rf-collapse-and-change.svg',
'VisualizeMatching/rf-vm-single-splits-plainedges.svg',
'VisualizeMatching/test-vmr.svg',
'VisualizeMatching/visualize-mci-matching.svg', and
'VisualizeMatching/vm-one-rooted.svg'
Error:
! Test failures.
Execution halted
Flavor: r-release-macos-x86_64
Version: 2.12.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Generalized-RF.Rmd’ using rmarkdown
Quitting from Generalized-RF.Rmd:38-42 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `PairScorer()`:
! object '_TreeDist_cpp_shared_phylo' not found
---
Backtrace:
▆
1. └─TreeDist::VisualizeMatching(...)
2. └─TreeDist (local) Func(tree1, tree2, reportMatching = TRUE)
3. └─TreeDist::CalculateTreeDistance(...)
4. └─TreeDist:::.SplitDistanceOneOne(...)
5. └─TreeDist (local) Func(...)
6. └─TreeDist::GeneralizedRF(...)
7. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Generalized-RF.Rmd' failed with diagnostics:
object '_TreeDist_cpp_shared_phylo' not found
--- failed re-building ‘Generalized-RF.Rmd’
--- re-building ‘Robinson-Foulds.Rmd’ using rmarkdown
Quitting from Robinson-Foulds.Rmd:216-223 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `PairScorer()`:
! object '_TreeDist_cpp_robinson_foulds_info' not found
---
Backtrace:
▆
1. └─TreeDist::VisualizeMatching(...)
2. └─TreeDist (local) Func(tree1, tree2, reportMatching = TRUE)
3. └─TreeDist::CalculateTreeDistance(...)
4. └─TreeDist:::.SplitDistanceOneOne(...)
5. └─TreeDist (local) Func(...)
6. └─TreeDist::GeneralizedRF(...)
7. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Robinson-Foulds.Rmd' failed with diagnostics:
object '_TreeDist_cpp_robinson_foulds_info' not found
--- failed re-building ‘Robinson-Foulds.Rmd’
--- re-building ‘Using-TreeDist.Rmd’ using rmarkdown
Quitting from Using-TreeDist.Rmd:59-61 [measure-distance]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `PairScorer()`:
! object '_TreeDist_cpp_mutual_clustering' not found
---
Backtrace:
▆
1. └─TreeDist::TreeDistance(tree1, tree2)
2. └─TreeDist::ClusteringInfoDistance(...)
3. └─TreeDist::MutualClusteringInfo(...)
4. └─TreeDist::CalculateTreeDistance(...)
5. └─TreeDist:::.SplitDistanceOneOne(...)
6. └─TreeDist (local) Func(...)
7. └─TreeDist::GeneralizedRF(...)
8. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Using-TreeDist.Rmd' failed with diagnostics:
object '_TreeDist_cpp_mutual_clustering' not found
--- failed re-building ‘Using-TreeDist.Rmd’
--- re-building ‘compare-treesets.Rmd’ using rmarkdown
Quitting from compare-treesets.Rmd:48-62 [generate-trees]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `PairScorer()`:
! object '_TreeDist_cpp_mutual_clustering' not found
---
Backtrace:
▆
1. └─TreeDist::ClusteringInfoDistance(c(batch1, batch2))
2. └─TreeDist::MutualClusteringInfo(...)
3. └─TreeDist::CalculateTreeDistance(...)
4. └─TreeDist:::.SplitDistanceAllPairs(...)
5. ├─base::structure(...)
6. └─base::apply(is, 2, .CliPairDist)
7. └─TreeDist (local) FUN(newX[, i], ...)
8. └─TreeDist (local) .PairDist(i)
9. └─TreeDist (local) Func(...)
10. └─TreeDist::GeneralizedRF(...)
11. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'compare-treesets.Rmd' failed with diagnostics:
object '_TreeDist_cpp_mutual_clustering' not found
--- failed re-building ‘compare-treesets.Rmd’
--- re-building ‘different-leaves.Rmd’ using rmarkdown
Quitting from different-leaves.Rmd:62-73 [drop-some]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `PairScorer()`:
! object '_TreeDist_cpp_mutual_clustering' not found
---
Backtrace:
▆
1. └─TreeDist::MutualClusteringInfo(balCL, balAL)
2. └─TreeDist::CalculateTreeDistance(...)
3. └─TreeDist:::.SplitDistanceOneOne(...)
4. └─TreeDist (local) Func(...)
5. └─TreeDist::GeneralizedRF(...)
6. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'different-leaves.Rmd' failed with diagnostics:
object '_TreeDist_cpp_mutual_clustering' not found
--- failed re-building ‘different-leaves.Rmd’
--- re-building ‘information.Rmd’ using rmarkdown
--- finished re-building ‘information.Rmd’
--- re-building ‘landscapes.Rmd’ using rmarkdown
Quitting from landscapes.Rmd:32-74 [col-trees-by-score]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `PairScorer()`:
! object '_TreeDist_cpp_mutual_clustering' not found
---
Backtrace:
▆
1. └─TreeDist::ClusteringInfoDist(trees)
2. └─TreeDist::MutualClusteringInfo(...)
3. └─TreeDist::CalculateTreeDistance(...)
4. └─TreeDist:::.SplitDistanceAllPairs(...)
5. ├─base::structure(...)
6. └─base::apply(is, 2, .CliPairDist)
7. └─TreeDist (local) FUN(newX[, i], ...)
8. └─TreeDist (local) .PairDist(i)
9. └─TreeDist (local) Func(...)
10. └─TreeDist::GeneralizedRF(...)
11. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'landscapes.Rmd' failed with diagnostics:
object '_TreeDist_cpp_mutual_clustering' not found
--- failed re-building ‘landscapes.Rmd’
--- re-building ‘treespace.Rmd’ using rmarkdown
Quitting from treespace.Rmd:78-81 [calculate-distances]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `PairScorer()`:
! object '_TreeDist_cpp_mutual_clustering' not found
---
Backtrace:
▆
1. └─TreeDist::ClusteringInfoDistance(trees)
2. └─TreeDist::MutualClusteringInfo(...)
3. └─TreeDist::CalculateTreeDistance(...)
4. └─TreeDist:::.SplitDistanceAllPairs(...)
5. ├─base::structure(...)
6. └─base::apply(is, 2, .CliPairDist)
7. └─TreeDist (local) FUN(newX[, i], ...)
8. └─TreeDist (local) .PairDist(i)
9. └─TreeDist (local) Func(...)
10. └─TreeDist::GeneralizedRF(...)
11. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'treespace.Rmd' failed with diagnostics:
object '_TreeDist_cpp_mutual_clustering' not found
--- failed re-building ‘treespace.Rmd’
--- re-building ‘using-distances.Rmd’ using rmarkdown
Quitting from using-distances.Rmd:40-46 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `PairScorer()`:
! object '_TreeDist_cpp_jaccard_similarity' not found
---
Backtrace:
▆
1. └─TreeDist::VisualizeMatching(...)
2. └─TreeDist (local) Func(tree1, tree2, reportMatching = TRUE)
3. └─TreeDist::CalculateTreeDistance(...)
4. └─TreeDist:::.SplitDistanceOneOne(...)
5. └─TreeDist (local) Func(...)
6. └─TreeDist::GeneralizedRF(...)
7. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'using-distances.Rmd' failed with diagnostics:
object '_TreeDist_cpp_jaccard_similarity' not found
--- failed re-building ‘using-distances.Rmd’
SUMMARY: processing the following files failed:
‘Generalized-RF.Rmd’ ‘Robinson-Foulds.Rmd’ ‘Using-TreeDist.Rmd’
‘compare-treesets.Rmd’ ‘different-leaves.Rmd’ ‘landscapes.Rmd’
‘treespace.Rmd’ ‘using-distances.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-x86_64