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