CRAN Package Check Results for Package TreeSearch

Last updated on 2026-05-20 23:50:29 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	1.7.0	29.81	274.21	304.02	OK
r-devel-linux-x86_64-debian-gcc	1.7.0	33.15	179.42	212.57	OK
r-devel-linux-x86_64-fedora-clang	1.7.0	43.00	437.36	480.36	OK
r-devel-linux-x86_64-fedora-gcc	1.7.0	59.00	423.86	482.86	OK
r-devel-windows-x86_64	1.7.0	42.00	294.00	336.00	OK
r-patched-linux-x86_64	1.7.0	31.37	259.43	290.80	OK
r-release-linux-x86_64	1.7.0	50.93	256.85	307.78	OK
r-release-macos-arm64	1.7.0	7.00	63.00	70.00	OK
r-release-macos-x86_64	1.7.0	60.00	758.00	818.00	ERROR
r-release-windows-x86_64	1.7.0	48.00	293.00	341.00	OK
r-oldrel-macos-arm64	1.7.0				OK
r-oldrel-macos-x86_64	1.7.0	21.00	265.00	286.00	OK
r-oldrel-windows-x86_64	1.7.0	57.00	383.00	440.00	OK

Check Details

Version: 1.7.0
Check: examples
Result: ERROR Running examples in ‘TreeSearch-Ex.R’ failed The error most likely occurred in: > ### Name: SiteConcordance > ### Title: Calculate site concordance factor > ### Aliases: SiteConcordance QuartetConcordance ClusteringConcordance > ### PhylogeneticConcordance MutualClusteringConcordance > ### SharedPhylogeneticConcordance > > ### ** Examples > > data("congreveLamsdellMatrices", package = "TreeSearch") > dataset <- congreveLamsdellMatrices[[1]][, 1:20] > tree <- referenceTree > qc <- QuartetConcordance(tree, dataset) > cc <- ClusteringConcordance(tree, dataset) > pc <- PhylogeneticConcordance(tree, dataset) > spc <- SharedPhylogeneticConcordance(tree, dataset) Error in PairScorer(splits1, splits2, nTip, ...) : object '_TreeDist_cpp_shared_phylo' not found Calls: SharedPhylogeneticConcordance ... vapply -> FUN -> Func -> GeneralizedRF -> PairScorer Execution halted Flavor: r-release-macos-x86_64

Version: 1.7.0
Check: tests
Result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [55s/83s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library("testthat") > library("TreeSearch") > > test_check("TreeSearch") Saving _problems/test-TaxonInfluence-9.R Saving _problems/test-TaxonInfluence-35.R 1 + 0 != 10 [ FAIL 2 | WARN 0 | SKIP 5 | PASS 7340 ] ══ Skipped tests (5) ═══════════════════════════════════════════════════════════ • On CRAN (4): 'test-Jackknife.R:27:1', 'test-PlotCharacter.R:1:1', 'test-PlotCharacter.R:141:1', 'test-PlotCharacter.R:151:1' • Sys.getenv("GITHUB_PAT") == "" is TRUE (1): 'test-MaximizeParsimony.R:71:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-TaxonInfluence.R:9:3'): TaxonInfluence() works ───────────────── Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_mutual_clustering' not found Backtrace: ▆ 1. └─TreeSearch::TaxonInfluence(...) at test-TaxonInfluence.R:9:3 2. ├─base::rowSums(as.matrix(Distance(tree))) 3. │ └─base::is.data.frame(x) 4. ├─base::as.matrix(Distance(tree)) 5. └─TreeDist (local) Distance(tree) 6. └─TreeDist::MutualClusteringInfo(...) 7. └─TreeDist::CalculateTreeDistance(...) 8. └─TreeDist:::.SplitDistanceAllPairs(...) 9. ├─base::structure(...) 10. └─base::apply(is, 2, .CliPairDist) 11. └─TreeDist (local) FUN(newX[, i], ...) 12. └─TreeDist (local) .PairDist(i) 13. └─TreeDist (local) Func(...) 14. └─TreeDist::GeneralizedRF(...) 15. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...) ── Error ('test-TaxonInfluence.R:34:3'): TaxonInfluence() saves intermediate trees ── Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_mutual_clustering' not found Backtrace: ▆ 1. └─TreeSearch::TaxonInfluence(...) at test-TaxonInfluence.R:34:3 2. └─base::vapply(...) 3. └─TreeSearch (local) FUN(X[[i]], ...) 4. ├─base::matrix(Distance(tree, result), length(result)) 5. └─TreeDist (local) Distance(tree, result) 6. └─TreeDist::MutualClusteringInfo(...) 7. └─TreeDist::CalculateTreeDistance(...) 8. └─TreeDist:::.SplitDistanceOneMany(...) 9. ├─stats::setNames(...) 10. ├─base::unlist(...) 11. └─base::.mapply(...) 12. └─TreeDist (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]]) 13. └─TreeDist (local) Func(...) 14. └─TreeDist::GeneralizedRF(...) 15. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...) [ FAIL 2 | WARN 0 | SKIP 5 | PASS 7340 ] Error: ! Test failures. Execution halted Flavor: r-release-macos-x86_64

Version: 1.7.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘custom.Rmd’ using rmarkdown Quitting from custom.Rmd:84-105 [cid] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `PairScorer()`: ! object '_TreeDist_cpp_mutual_clustering' not found --- Backtrace: ▆ 1. └─TreeSearch::TreeSearch(...) 2. └─TreeSearch::EdgeListSearch(...) 3. └─global TreeScorer(edgeList[[1]], edgeList[[2]], dataset, ...) 4. └─TreeDist::ClusteringInfoDistance(startTree, tmpTree) 5. └─TreeDist::MutualClusteringInfo(...) 6. └─TreeDist::CalculateTreeDistance(...) 7. └─TreeDist:::.SplitDistanceOneOne(...) 8. └─TreeDist (local) Func(...) 9. └─TreeDist::GeneralizedRF(...) 10. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'custom.Rmd' failed with diagnostics: object '_TreeDist_cpp_mutual_clustering' not found --- failed re-building ‘custom.Rmd’ --- re-building ‘getting-started.Rmd’ using rmarkdown --- finished re-building ‘getting-started.Rmd’ --- re-building ‘profile-scores.Rmd’ using rmarkdown --- finished re-building ‘profile-scores.Rmd’ --- re-building ‘profile.Rmd’ using rmarkdown --- finished re-building ‘profile.Rmd’ --- re-building ‘tree-search.Rmd’ using rmarkdown Quitting from tree-search.Rmd:102-115 [map-search] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `PairScorer()`: ! object '_TreeDist_cpp_mutual_clustering' not found --- Backtrace: ▆ 1. └─TreeDist::ClusteringInfoDistance(bestTrees) 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 'tree-search.Rmd' failed with diagnostics: object '_TreeDist_cpp_mutual_clustering' not found --- failed re-building ‘tree-search.Rmd’ --- re-building ‘tree-space.Rmd’ using rmarkdown Quitting from tree-space.Rmd:93-141 [exploring-consensus] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `consensus_info()`: ! object '_TreeDist_consensus_info' not found --- Backtrace: ▆ 1. └─Rogue::QuickRogue(trees, p = majority) 2. └─TreeDist::ConsensusInfo(trees, info = info, p = p, check.tips = FALSE) 3. └─TreeDist:::consensus_info(trees, mode == 1L, p = safeP) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'tree-space.Rmd' failed with diagnostics: object '_TreeDist_consensus_info' not found --- failed re-building ‘tree-space.Rmd’ SUMMARY: processing the following files failed: ‘custom.Rmd’ ‘tree-search.Rmd’ ‘tree-space.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-release-macos-x86_64