• using R Under development (unstable) (2023-03-25 r84062)
• using platform: x86_64-pc-linux-gnu (64-bit)
• R was compiled by
      gcc-12 (Debian 12.2.0-14) 12.2.0
      GNU Fortran (Debian 12.2.0-14) 12.2.0
• running under: Debian GNU/Linux 12 (bookworm)
• using session charset: UTF-8
• checking for file ‘TreeSearch/DESCRIPTION’ ... OK
• this is package ‘TreeSearch’ version ‘1.3.0’
• 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
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘TreeSearch’ can be installed ... OK
• used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
• used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
• checking C++ specification ... OK
    Not all R platforms support C++17
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [4s/6s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/6s] OK
• checking whether the package can be unloaded cleanly ... [3s/5s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/5s] OK
• checking whether the namespace can be unloaded cleanly ... [4s/7s] OK
• checking loading without being on the library search path ... [4s/6s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [28s/46s] OK
• checking Rd files ... [6s/9s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [1s/2s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [4s/7s] ERROR
  Running examples in ‘TreeSearch-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: AdditionTree
  > ### Title: Addition tree
  > ### Aliases: AdditionTree
  >
  > ### ** Examples
  >
  > data("Lobo", package = "TreeTools")
  > AdditionTree(Lobo.phy, concavity = 10)
  Error in mpl_new_Morphy() : DLL requires the use of native symbols
  Calls: AdditionTree ... TreeLength -> TreeLength.list -> lapply -> FUN -> mpl_new_Morphy
  Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [40s/62s] ERROR
    Running ‘spelling.R’ [0s/1s]
    Running ‘testthat.R’ [39s/60s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library("testthat")
    > library("TreeSearch")
    >
    > test_check("TreeSearch")
    [ FAIL 42 | WARN 0 | SKIP 3 | PASS 6990 ]
    
    ══ Skipped tests ═══════════════════════════════════════════════════════════════
    • On CRAN (3)
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-AdditionTree.R:8:3'): Addition tree is more parsimonious ───────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch::AdditionTree(Lobo.phy) at test-AdditionTree.R:8:2
     2. ├─TreeSearch::TreeLength(candidates, theseData, concavity)
     3. └─TreeSearch:::TreeLength.list(candidates, theseData, concavity)
     4. └─TreeSearch::PhyDat2Morphy(dataset)
     5. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     6. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-AdditionTree.R:30:3'): Addition tree obeys constraints ─────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. ├─testthat::expect_true(...) at test-AdditionTree.R:30:2
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─as.Splits(c(F, F, F, F, T, T), letters[1:6]) %in% ...
     5. ├─TreeTools::as.Splits(...)
     6. └─TreeSearch::AdditionTree(dataset, constraint = MatrixToPhyDat(constraint))
     7. └─TreeSearch::PhyDat2Morphy(thisConstr)
     8. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     9. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-AdditionTree.R:57:3'): AdditionTree() handles edge cases ───────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
         ▆
      1. ├─testthat::expect_equal(...) at test-AdditionTree.R:57:2
      2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
      3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
      4. ├─TreeTools::UnrootTree(AdditionTree(dataset[1:4], conc = "pr"))
      5. └─TreeSearch::AdditionTree(dataset[1:4], conc = "pr")
      6. ├─TreeSearch::TreeLength(candidates, theseData, concavity)
      7. └─TreeSearch:::TreeLength.list(candidates, theseData, concavity)
      8. └─base::lapply(characters, SingleCharMorphy)
      9. └─TreeSearch (local) FUN(X[[i]], ...)
     10. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-Concordance.R:111:1'): (code run outside of `test_that()`) ─────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch::ConcordantInformation(tree, dataset) at test-Concordance.R:111:0
     2. └─TreeSearch::CharacterLength(tree, dataset, compress = TRUE)
     3. └─TreeSearch:::FastCharacterLength(tree, dataset)
     4. └─base::lapply(characters, SingleCharMorphy)
     5. └─TreeSearch (local) FUN(X[[i]], ...)
     6. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-CustomSearch.R:17:3'): Tree can be found ───────────────────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. ├─testthat::expect_equal(...) at test-CustomSearch.R:17:2
     2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. └─TreeSearch::TreeSearch(...)
     5. └─TreeSearch (local) InitializeData(dataset)
     6. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     7. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-CustomSearch.R:61:3'): Tree search finds shortest tree ─────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. ├─testthat::expect_equal(TreeLength(start_tree, dataset), 6) at test-CustomSearch.R:61:2
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─TreeSearch::TreeLength(start_tree, dataset)
     5. └─TreeSearch:::TreeLength.phylo(start_tree, dataset)
     6. └─TreeSearch::PhyDat2Morphy(dataset)
     7. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     8. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-CustomSearch.R:101:3'): Profile parsimony works in tree search ──
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. ├─testthat::expect_equal(...) at test-CustomSearch.R:101:2
     2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. └─TreeSearch::MaximizeParsimony(...)
     5. └─base::lapply(characters, SingleCharMorphy)
     6. └─TreeSearch (local) FUN(X[[i]], ...)
     7. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-Jackknife.R:17:3'): Jackknife supports are correct ─────────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch::TreeSearch(start_tree, dataset, verbosity = 0) at test-Jackknife.R:17:2
     2. └─TreeSearch (local) InitializeData(dataset)
     3. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     4. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-MaximizeParsimony.R:8:3'): Profile fails gracefully ────────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
         ▆
      1. ├─testthat::expect_warning(...) at test-MaximizeParsimony.R:8:2
      2. │ └─testthat:::quasi_capture(...)
      3. │ ├─testthat (local) .capture(...)
      4. │ │ └─base::withCallingHandlers(...)
      5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
      6. └─TreeSearch::MaximizeParsimony(dataset, concavity = "pr")
      7. └─TreeSearch::AdditionTree(dataset, constraint = constraint, concavity = concavity)
      8. ├─TreeSearch::TreeLength(candidates, theseData, concavity)
      9. └─TreeSearch:::TreeLength.list(candidates, theseData, concavity)
     10. └─base::lapply(characters, SingleCharMorphy)
     11. └─TreeSearch (local) FUN(X[[i]], ...)
     12. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-MaximizeParsimony.R:19:3'): Constraints work ───────────────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch::MaximizeParsimony(...) at test-MaximizeParsimony.R:19:2
     2. └─TreeSearch::PhyDat2Morphy(constraint)
     3. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     4. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-MaximizeParsimony.R:76:3'): MaximizeParsimony() times out ──────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch::MaximizeParsimony(...) at test-MaximizeParsimony.R:76:2
     2. └─TreeSearch::AdditionTree(dataset, constraint = constraint, concavity = concavity)
     3. ├─TreeSearch::TreeLength(candidates, theseData, concavity)
     4. └─TreeSearch:::TreeLength.list(candidates, theseData, concavity)
     5. └─TreeSearch::PhyDat2Morphy(dataset)
     6. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     7. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-MaximizeParsimony.R:87:3'): Seed trees retained ────────────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch::MaximizeParsimony(...) at test-MaximizeParsimony.R:87:2
     2. └─TreeSearch::PhyDat2Morphy(dataset)
     3. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     4. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-MaximizeParsimony.R:107:3'): Mismatched tree/dataset handled with warnings ──
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
         ▆
      1. ├─testthat::expect_equal(...) at test-MaximizeParsimony.R:107:2
      2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
      3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
      4. ├─base::unname(NTip(expect_warning(QP(datAf, treeBg))))
      5. ├─TreeTools::NTip(expect_warning(QP(datAf, treeBg)))
      6. ├─testthat::expect_warning(QP(datAf, treeBg))
      7. │ └─testthat:::quasi_capture(...)
      8. │ ├─testthat (local) .capture(...)
      9. │ │ └─base::withCallingHandlers(...)
     10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     11. └─TreeSearch (local) QP(datAf, treeBg)
     12. └─TreeSearch::MaximizeParsimony(...) at test-MaximizeParsimony.R:104:8
     13. └─TreeSearch::PhyDat2Morphy(dataset)
     14. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     15. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-MaximizeParsimony.R:120:3'): Root retained if not 1 ────────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch::MaximizeParsimony(dataset, tr) at test-MaximizeParsimony.R:120:2
     2. └─TreeSearch::PhyDat2Morphy(dataset)
     3. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     4. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-MaximizeParsimony.R:141:3'): Resample() fails and works ────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─base::replicate(nRep, Resample(dataset, NJTree(dataset), verbosity = 0L)) at test-MaximizeParsimony.R:141:2
     2. └─base::sapply(...)
     3. └─base::lapply(X = X, FUN = FUN, ...)
     4. └─TreeSearch (local) FUN(X[[i]], ...)
     5. └─TreeSearch::Resample(dataset, NJTree(dataset), verbosity = 0L)
     6. └─TreeSearch::MaximizeParsimony(...)
     7. └─TreeSearch::PhyDat2Morphy(dataset)
     8. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     9. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-PolEscapa.R:26:3'): LengthAdded() ──────────────────────────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch::LengthAdded(trees, dataset[, 10]) at test-PolEscapa.R:26:2
     2. ├─TreeSearch::TreeLength(trees, char, concavity)
     3. └─TreeSearch:::TreeLength.multiPhylo(trees, char, concavity)
     4. └─TreeSearch::PhyDat2Morphy(dataset)
     5. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     6. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-QuartetResolution.R:2:3'): QuartetResolution() ─────────────────
    <<not available>/C++Error/error/condition>
    Error: Not compatible with requested type: [type=NULL; target=integer].
    Backtrace:
         ▆
      1. ├─testthat::expect_equal(...) at test-QuartetResolution.R:2:2
      2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
      3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
      4. └─TreeSearch::QuartetResolution(...)
      5. ├─base::vapply(...)
      6. ├─base::lapply(as.Splits(KeepTip(trees, tips), tips), PolarizeSplits)
      7. ├─TreeTools::as.Splits(KeepTip(trees, tips), tips)
      8. └─TreeTools::KeepTip(trees, tips)
      9. ├─TreeTools::DropTip(tree, keep, preorder, check)
     10. └─TreeTools:::DropTip.multiPhylo(tree, keep, preorder, check)
     11. └─base::lapply(tree, DropTip, tip, preorder)
     12. ├─TreeTools (local) FUN(X[[i]], ...)
     13. └─TreeTools:::DropTip.phylo(X[[i]], ...)
     14. ├─TreeTools::Preorder(tree)
     15. └─TreeTools:::Preorder.phylo(tree)
     16. └─TreeTools::RenumberTree(parent, child)
    ── Error ('test-RMorphy.R:4:3'): NULL pointers don't cause crash ───────────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch::mpl_new_Morphy() at test-RMorphy.R:4:2
    ── Error ('test-RMorphy.R:10:3'): Pointers survive garbage collection ──────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch::mpl_new_Morphy() at test-RMorphy.R:10:2
    ── Error ('test-RMorphy.R:21:3'): preorder_morphy() ────────────────────────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch::PhyDat2Morphy(dat) at test-RMorphy.R:21:2
     2. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     3. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-RandomTreeScore.R:8:3'): Two tip 'random' tree ─────────────────
    Error in `RandomMorphyTree(2)`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. ├─testthat::expect_equal(...) at test-RandomTreeScore.R:8:2
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. └─TreeSearch::RandomMorphyTree(2)
    ── Error ('test-RandomTreeScore.R:13:3'): RandomTreeScore() on small trees ─────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch::mpl_new_Morphy() at test-RandomTreeScore.R:13:2
    ── Error ('test-iw-scoring.R:27:3'): IW Scoring ────────────────────────────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─base::lapply(characters, SingleCharMorphy) at test-iw-scoring.R:27:2
     2. └─TreeSearch (local) FUN(X[[i]], ...)
     3. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-length_range.R:28:3'): Minimum step counts are correctly calculated ──
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch::SingleCharMorphy("{-1}{-2}{-3}2233") at test-length_range.R:28:2
     2. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-mpl_morphy_objects.R:15:3'): GapHandler() ──────────────────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch::PhyDat2Morphy(pd) at test-mpl_morphy_objects.R:15:2
     2. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     3. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-pp-fitch.R:24:3'): Profile score correct for small trees ───────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─base::lapply(characters, SingleCharMorphy) at test-pp-fitch.R:24:2
     2. └─TreeSearch (local) FUN(X[[i]], ...)
     3. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-pp-fitch.R:84:3'): Profile score can be calculated from real data ──
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. ├─testthat::expect_equal(...) at test-pp-fitch.R:84:2
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─TreeSearch::TreeLength(tree, dataset)
     5. └─TreeSearch:::TreeLength.phylo(tree, dataset)
     6. └─TreeSearch::PhyDat2Morphy(dataset)
     7. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     8. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-pp-random-tree.R:23:3'): four-tip trees are randomly distributed ──
    Error in `RandomMorphyTree(nTip)`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─base::vapply(...) at test-pp-random-tree.R:23:2
     2. └─TreeSearch (local) FUN(X[[i]], ...)
     3. ├─base::unlist(RandomMorphyTree(nTip)) at test-pp-random-tree.R:23:36
     4. └─TreeSearch::RandomMorphyTree(nTip)
    ── Error ('test-pp-random-tree.R:48:3'): four-tip trees are randomly scored ────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch (local) MorphyWith("0011;") at test-pp-random-tree.R:48:2
     2. └─TreeSearch::mpl_new_Morphy() at test-pp-random-tree.R:5:2
    ── Error ('test-pp-random-tree.R:65:3'): five-tip trees are randomly scored ────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch (local) MorphyWith("00011;") at test-pp-random-tree.R:65:2
     2. └─TreeSearch::mpl_new_Morphy() at test-pp-random-tree.R:5:2
    ── Error ('test-pp-random-tree.R:85:3'): six-tip trees are randomly scored ─────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch (local) MorphyWith("000011;") at test-pp-random-tree.R:85:2
     2. └─TreeSearch::mpl_new_Morphy() at test-pp-random-tree.R:5:2
    ── Error ('test-pp-random-tree.R:126:3'): twelve-tip trees are randomly scored ──
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch (local) MorphyWith("000000011111;") at test-pp-random-tree.R:126:2
     2. └─TreeSearch::mpl_new_Morphy() at test-pp-random-tree.R:5:2
    ── Error ('test-tree_length.R:10:3'): Failures are graceful ────────────────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch::PhyDat2Morphy(dat) at test-tree_length.R:10:2
     2. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     3. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-tree_length.R:32:3'): Deprecations throw warning ───────────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. ├─testthat::expect_equal(...) at test-tree_length.R:32:2
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─TreeSearch::TreeLength(tree, dat)
     5. └─TreeSearch:::TreeLength.phylo(tree, dat)
     6. └─TreeSearch::PhyDat2Morphy(dataset)
     7. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     8. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-tree_length.R:97:5'): Morphy generates correct lengths ─────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch::SingleCharMorphy(characters[test]) at test-tree_length.R:97:4
     2. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-tree_length.R:173:3'): (random) lists of trees are scored ──────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
         ▆
      1. ├─testthat::expect_gt(...) at test-tree_length.R:173:2
      2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
      3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
      4. ├─stats::t.test(TreeLength(100, mat), mu = 318.5877)
      5. ├─TreeSearch::TreeLength(100, mat)
      6. └─TreeSearch:::TreeLength.numeric(100, mat)
      7. ├─TreeSearch::TreeLength(...)
      8. └─TreeSearch:::TreeLength.list(...)
      9. └─TreeSearch::PhyDat2Morphy(dataset)
     10. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     11. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-tree_length.R:185:3'): TreeLength() handles unrooted / non-preorder trees ──
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. ├─TreeSearch::TreeLength(c(rand, Postorder(rand)), mat) at test-tree_length.R:185:2
     2. └─TreeSearch:::TreeLength.multiPhylo(...)
     3. └─TreeSearch::PhyDat2Morphy(dataset)
     4. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     5. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-tree_length.R:210:3'): TreeLength() handles subsetted trees ────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. ├─testthat::expect_equal(4, length(TreeLength(t8, dat))) at test-tree_length.R:210:2
     2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─TreeSearch::TreeLength(t8, dat)
     5. └─TreeSearch:::TreeLength.multiPhylo(t8, dat)
     6. └─TreeSearch::PhyDat2Morphy(dataset)
     7. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     8. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-tree_length.R:226:3'): Profile scoring is reported correctly ───
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─base::lapply(characters, SingleCharMorphy) at test-tree_length.R:226:2
     2. └─TreeSearch (local) FUN(X[[i]], ...)
     3. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-tree_length.R:248:3'): CharacterLength() fails gracefully ──────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. ├─testthat::expect_equal(...) at test-tree_length.R:248:2
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. └─TreeSearch::CharacterLength(tMinus1, dataset[-1])
     5. └─TreeSearch:::FastCharacterLength(tree, dataset)
     6. └─base::lapply(characters, SingleCharMorphy)
     7. └─TreeSearch (local) FUN(X[[i]], ...)
     8. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-tree_length.R:269:3'): Character compression works ─────────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. ├─testthat::expect_equal(137, length(CharacterLength(tree, dataset))) at test-tree_length.R:269:2
     2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. └─TreeSearch::CharacterLength(tree, dataset)
     5. └─TreeSearch:::FastCharacterLength(tree, dataset)
     6. └─base::lapply(characters, SingleCharMorphy)
     7. └─TreeSearch (local) FUN(X[[i]], ...)
     8. └─TreeSearch::mpl_new_Morphy()
    ── Error ('test-tree_length.R:279:3'): X_MorphyLength ──────────────────────────
    Error in `mpl_new_Morphy()`: DLL requires the use of native symbols
    Backtrace:
        ▆
     1. └─TreeSearch::PhyDat2Morphy(dataset) at test-tree_length.R:279:2
     2. ├─base::structure(mpl_new_Morphy(), class = "morphyPtr")
     3. └─TreeSearch::mpl_new_Morphy()
    
    [ FAIL 42 | WARN 0 | SKIP 3 | PASS 6990 ]
    Deleting unused snapshots:
    • PlotCharacter/plotchar-000011110000.svg
    • PlotCharacter/plotchar-000011qqqq00.svg
    • PlotCharacter/plotchar-011iiqii0011.svg
    • PlotCharacter/plotchar-01iii1010101.svg
    • PlotCharacter/plotchar-01iiii010101.svg
    • PlotCharacter/plotchar-01iiiiii0101.svg
    • PlotCharacter/plotchar-023iiqq1ii32.svg
    • PlotCharacter/plotchar-023iqqq1ii32.svg
    • PlotCharacter/plotchar-10101iiiii01.svg
    • PlotCharacter/plotchar-10iiii11iii1.svg
    • PlotCharacter/plotchar-1100iiii1100.svg
    • PlotCharacter/plotchar-110iiqiii100.svg
    • PlotCharacter/plotchar-110iiqqii100.svg
    • PlotCharacter/plotchar-11ii1000001i.svg
    • PlotCharacter/plotchar-11ii1qqii111.svg
    • PlotCharacter/plotchar-11iiii111111.svg
    • PlotCharacter/plotchar-11iiiiiii100.svg
    • PlotCharacter/plotchar-11iiqqqqii11.svg
    • PlotCharacter/plotchar-1234d45baacgttt.svg
    • PlotCharacter/plotchar-1iii1111iii1.svg
    • PlotCharacter/plotchar-1iiii1iiii1i.svg
    • PlotCharacter/plotchar-1qqiiqqii100.svg
    • PlotCharacter/plotchar-210210iiiiii.svg
    • PlotCharacter/plotchar-210ii100ii21.svg
    • PlotCharacter/plotchar-21ii1iiii012.svg
    • PlotCharacter/plotchar-21ii3qqii032.svg
    • PlotCharacter/plotchar-230iiqq1ii32.svg
    • PlotCharacter/plotchar-23ii1iiii032.svg
    • PlotCharacter/plotchar-23ii1q1ii023.svg
    • PlotCharacter/plotchar-23ii1qqdi0bid01b32.svg
    • PlotCharacter/plotchar-23qq1qqqq032.svg
    • PlotCharacter/plotchar-320iiqq3ii21.svg
    • PlotCharacter/plotchar-i1i1i1ii1i1i.svg
    • PlotCharacter/plotchar-iiii1010iiii.svg
    • PlotCharacter/plotchar-iiii1111iii1.svg
    • PlotCharacter/plotchar-iiii1111iiii.svg
    • PlotCharacter/plotchar-iiiiii11iii1.svg
    • PlotCharacter/plotchar-iiiiiiii0101.svg
    • PlotCharacter/plotchar-iiiiiiiiiiii.svg
    • PlotCharacter/plotchar-iiiiiiiqqqqq.svg
    • PlotCharacter/plotchar-qqqqiiii1qqq.svg
    • PlotCharacter/plotchar-qqqqqqqqqqqq.svg
    Error: Test failures
    Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking re-building of vignette outputs ... [26s/44s] ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘custom.Rmd’ using rmarkdown
  Quitting from lines 163-175 (custom.Rmd)
  Error: processing vignette ‘custom.Rmd’ failed with diagnostics:
  DLL requires the use of native symbols
  --- 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
  Quitting from lines 67-71 (profile.Rmd)
  Error: processing vignette ‘profile.Rmd’ failed with diagnostics:
  DLL requires the use of native symbols
  --- failed re-building ‘profile.Rmd’
  
  --- re-building ‘tree-search.Rmd’ using rmarkdown
  Quitting from lines 84-85 (tree-search.Rmd)
  Error: processing vignette ‘tree-search.Rmd’ failed with diagnostics:
  DLL requires the use of native symbols
  --- failed re-building ‘tree-search.Rmd’
  
  --- re-building ‘tree-space.Rmd’ using rmarkdown
  --- finished re-building ‘tree-space.Rmd’
  
  SUMMARY: processing the following files failed:
    ‘custom.Rmd’ ‘profile.Rmd’ ‘tree-search.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted
  
• checking PDF version of manual ... [9s/19s] OK
• checking HTML version of manual ... [4s/12s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs