Check results for 'TreeSearch'

using R version 4.6.0 (2026-04-24)
using platform: x86_64-apple-darwin20
R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0
running under: macOS Ventura 13.3.1
using session charset: UTF-8 * current time: 2026-04-28 22:08:22 UTC
checking for file ‘TreeSearch/DESCRIPTION’ ... OK
this is package ‘TreeSearch’ version ‘1.7.0’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
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checking whether package ‘TreeSearch’ can be installed ... [60s/76s] OK See the install log for details.
used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
used SDK: ‘MacOSX11.3.1.sdk’
checking C++ specification ... INFO specified C++17
checking installed package size ... INFO installed size is 6.1Mb sub-directories of 1Mb or more: datasets 1.6Mb doc 1.3Mb libs 1.5Mb
checking package directory ... OK
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checking dependencies in R code ... OK
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checking compiled code ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [20s/33s] 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
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [56s/84s] 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
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [107s/163s] 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
checking PDF version of manual ... [11s/15s] OK
DONE Status: 3 ERRORs
using check arguments '--no-clean-on-error '