TreeSearch

examples

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

re-building of vignette outputs

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' 
...[truncated]...
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

tests

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-T
...[truncated]...
_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