Running 'testthat.R' [11m]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(amregtest)
  Loading required package: allelematch
  Loading required package: dynamicTreeCut
  > 
  > test_check("amregtest")
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=1) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=2) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=4) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=1) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=2) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=4) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample2, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=2) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample2, runUntilSingletons=TRUE, cutHeight=0.95, missingMethod=1, consensusMethod=2) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample2, runUntilSingletons=TRUE, cutHeight=0.99, missingMethod=1, consensusMethod=2) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.7, missingMethod=2, consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=4) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.95, missingMethod=1, consensusMethod=4) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.95, missingMethod=2, consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.99, missingMethod=1, consensusMethod=4) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_4-amCluster 
    Rejected :  amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.99, missingMethod=2, consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataMini, cutHeight=1, doPsib="missing", consensusMethod=1) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataMini, cutHeight=1, doPsib="missing", consensusMethod=2) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataMini, cutHeight=1, doPsib="missing", consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataMini, cutHeight=1, doPsib="missing", consensusMethod=4) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataMini, cutHeight=1, doPsib="all", consensusMethod=1) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataMini, cutHeight=1, doPsib="all", consensusMethod=2) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataMini, cutHeight=1, doPsib="all", consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataMini, cutHeight=1, doPsib="all", consensusMethod=4) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample1, cutHeight=0.9, doPsib="missing", consensusMethod=1) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample1, cutHeight=0.9, doPsib="missing", consensusMethod=2) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample1, cutHeight=0.9, doPsib="missing", consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample1, cutHeight=0.9, doPsib="missing", consensusMethod=4) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample1, cutHeight=0.9, doPsib="all", consensusMethod=1) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample1, cutHeight=0.9, doPsib="all", consensusMethod=2) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample1, cutHeight=0.9, doPsib="all", consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample1, cutHeight=0.9, doPsib="all", consensusMethod=4) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample4, cutHeight=0.7, doPsib="missing", consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample4, cutHeight=0.7, doPsib="all", consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample4, cutHeight=0.9, doPsib="missing", consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample4, cutHeight=0.9, doPsib="all", consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample4, cutHeight=0.95, doPsib="missing", consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample4, cutHeight=0.95, doPsib="all", consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample4, cutHeight=0.99, doPsib="missing", consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample4, cutHeight=0.99, doPsib="all", consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample4, cutHeight=1, doPsib="missing", consensusMethod=3) 
  
  
    
    Error    :  allelematch: amCluster: no clusters formed. 
    Test     :  test-allelematch_6-amUnique 
    Rejected :  amUnique(amdataExample4, cutHeight=1, doPsib="all", consensusMethod=3) 
  
  Cleaning up 1 leaked TEMP file(s):
    D:\temp\2026_07_08_01_50_00_3490\Rtmp6x84E2/pdfa41c1a874fe8
  Cleaning up 1 leaked TEMP file(s):
    D:\temp\2026_07_08_01_50_00_3490\Rtmp6x84E2/pdfa41c47a9d89
  Cleaning up 1 leaked TEMP file(s):
    D:\temp\2026_07_08_01_50_00_3490\Rtmp6x84E2/pdfa41c66206309
  Cleaning up 1 leaked TEMP file(s):
    D:\temp\2026_07_08_01_50_00_3490\Rtmp6x84E2/pdfa41c1fe388e
  Cleaning up 1 leaked TEMP file(s):
    D:\temp\2026_07_08_01_50_00_3490\Rtmp6x84E2/pdfa41c55197213
  [ FAIL 9 | WARN 0 | SKIP 20 | PASS 146 ]
  
  ══ Skipped tests (20) ══════════════════════════════════════════════════════════
  • On CRAN (20): 'test-allelematch_1-amDataset.R:47:1',
    'test-allelematch_1-amDataset.R:147:1', 'test-allelematch_2-amMatrix.R:2:1',
    'test-allelematch_2-amMatrix.R:90:1',
    'test-allelematch_2-amMatrix_negative.R:2:1',
    'test-allelematch_3-amPairwise.R:2:1',
    'test-allelematch_3-amPairwise.R:68:1',
    'test-allelematch_3-amPairwise_negative.R:2:1',
    'test-allelematch_3-amPairwise_print.R:2:1',
    'test-allelematch_4-amCluster.R:2:1',
    'test-allelematch_4-amCluster_print.R:2:1',
    'test-allelematch_5-amAlleleFreq.R:2:1', 'test-allelematch_6-amUnique.R:2:1',
    'test-allelematch_6-amUnique_print.R:2:1',
    'test-allelematch_7-amUniqueProfile.R:2:1', 'test-amExample1.R:10:1',
    'test-amExample2.R:6:1', 'test-amExample3.R:11:1', 'test-amExample4.R:10:1',
    'test-ggData.R:11:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-allelematch_6-amUnique_negative.R:31:5'): Validation of arguments to amUnique() is working ──
  Error: allelematch: multilocusMap length mismatch.
  Backtrace:
      ▆
   1. ├─testthat::expect_error(...) at test-allelematch_6-amUnique_negative.R:31:5
   2. │ └─testthat:::expect_condition_matching_(...)
   3. │   └─testthat:::quasi_capture(...)
   4. │     ├─testthat (local) .capture(...)
   5. │     │ └─base::withCallingHandlers(...)
   6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   7. └─allelematch::amUnique(amdata, multilocusMap = NA)
  ── Failure ('test-amExample1.R:33:9'): amExample1 from pg 5 in allelematchSuppDoc.pdf is 2.5.3 compatible ──
  Expected some element of `output` to match string "missing data load for input dataset is 0.005 ".
  Actual text:
  x | allelematch: assuming genotype columns are in pairs, representing 10 loci
  x | allelematch: running amUnique() at 9 different values of alleleMismatch
  x | allelematch: 1 of 9 (matchThreshold=1, cutHeight=0, alleleMismatch=0)
  x | allelematch: 2 of 9 (matchThreshold=0.95, cutHeight=0.05, alleleMismatch=1)
  x | allelematch: 3 of 9 (matchThreshold=0.9, cutHeight=0.1, alleleMismatch=2)
  x | allelematch: 4 of 9 (matchThreshold=0.85, cutHeight=0.15, alleleMismatch=3)
  x | allelematch: 5 of 9 (matchThreshold=0.8, cutHeight=0.2, alleleMismatch=4)
  x | allelematch: 6 of 9 (matchThreshold=0.75, cutHeight=0.25, alleleMismatch=5)
  x | allelematch: 7 of 9 (matchThreshold=0.7, cutHeight=0.3, alleleMismatch=6)
  x | allelematch: 8 of 9 (matchThreshold=0.65, cutHeight=0.35, alleleMismatch=7)
  x | allelematch: 9 of 9 (matchThreshold=0.6, cutHeight=0.4, alleleMismatch=8)
  x | allelematch: missing data load for input dataset is 0.005
  x | allelematch: allelic diversity for input dataset is 6.1
  x | allelematch: Best guess for optimal parameter at alleleMismatch=2 OR matchThreshold=0.9 OR cutHeight=0.1
  x | allelematch: Best guess for unique profile morphology: ZeroSecondMinimum
  x |   matchThreshold cutHeight alleleMismatch samples unique unclassified multipleMatch guessOptimum missingDataLoad allelicDiversity   guessMorphology
  x | 1           1.00      0.00              0      20     13            0             0        FALSE           0.005              6.1 ZeroSecondMinimum
  x | 2           0.95      0.05              1      20     13            0             2        FALSE           0.005              6.1 ZeroSecondMinimum
  x | 3           0.90      0.10              2      20     12            0             0         TRUE           0.005              6.1 ZeroSecondMinimum
  x | 4           0.85      0.15              3      20     12            0             0        FALSE           0.005              6.1 ZeroSecondMinimum
  ... and 5 more.
  
  ── Failure ('test-amExample1.R:34:9'): amExample1 from pg 5 in allelematchSuppDoc.pdf is 2.5.3 compatible ──
  Expected some element of `output` to match string "allelic diversity for input dataset is 6.1 ".
  Actual text:
  x | allelematch: assuming genotype columns are in pairs, representing 10 loci
  x | allelematch: running amUnique() at 9 different values of alleleMismatch
  x | allelematch: 1 of 9 (matchThreshold=1, cutHeight=0, alleleMismatch=0)
  x | allelematch: 2 of 9 (matchThreshold=0.95, cutHeight=0.05, alleleMismatch=1)
  x | allelematch: 3 of 9 (matchThreshold=0.9, cutHeight=0.1, alleleMismatch=2)
  x | allelematch: 4 of 9 (matchThreshold=0.85, cutHeight=0.15, alleleMismatch=3)
  x | allelematch: 5 of 9 (matchThreshold=0.8, cutHeight=0.2, alleleMismatch=4)
  x | allelematch: 6 of 9 (matchThreshold=0.75, cutHeight=0.25, alleleMismatch=5)
  x | allelematch: 7 of 9 (matchThreshold=0.7, cutHeight=0.3, alleleMismatch=6)
  x | allelematch: 8 of 9 (matchThreshold=0.65, cutHeight=0.35, alleleMismatch=7)
  x | allelematch: 9 of 9 (matchThreshold=0.6, cutHeight=0.4, alleleMismatch=8)
  x | allelematch: missing data load for input dataset is 0.005
  x | allelematch: allelic diversity for input dataset is 6.1
  x | allelematch: Best guess for optimal parameter at alleleMismatch=2 OR matchThreshold=0.9 OR cutHeight=0.1
  x | allelematch: Best guess for unique profile morphology: ZeroSecondMinimum
  x |   matchThreshold cutHeight alleleMismatch samples unique unclassified multipleMatch guessOptimum missingDataLoad allelicDiversity   guessMorphology
  x | 1           1.00      0.00              0      20     13            0             0        FALSE           0.005              6.1 ZeroSecondMinimum
  x | 2           0.95      0.05              1      20     13            0             2        FALSE           0.005              6.1 ZeroSecondMinimum
  x | 3           0.90      0.10              2      20     12            0             0         TRUE           0.005              6.1 ZeroSecondMinimum
  x | 4           0.85      0.15              3      20     12            0             0        FALSE           0.005              6.1 ZeroSecondMinimum
  ... and 5 more.
  
  ── Failure ('test-amExample2.R:25:9'): amExample2 results from pg 8 in allelematchSuppDoc.pdf 2.5.3 compatible ──
  Expected some element of `output` to match string "missing data load for input dataset is 0.046 ".
  Actual text:
  x | allelematch: assuming genotype columns are in pairs, representing 10 loci
  x | allelematch: running amUnique() at 9 different values of alleleMismatch
  x | allelematch: 1 of 9 (matchThreshold=1, cutHeight=0, alleleMismatch=0)
  x | allelematch: 2 of 9 (matchThreshold=0.95, cutHeight=0.05, alleleMismatch=1)
  x | allelematch: 3 of 9 (matchThreshold=0.9, cutHeight=0.1, alleleMismatch=2)
  x | allelematch: 4 of 9 (matchThreshold=0.85, cutHeight=0.15, alleleMismatch=3)
  x | allelematch: 5 of 9 (matchThreshold=0.8, cutHeight=0.2, alleleMismatch=4)
  x | allelematch: 6 of 9 (matchThreshold=0.75, cutHeight=0.25, alleleMismatch=5)
  x | allelematch: 7 of 9 (matchThreshold=0.7, cutHeight=0.3, alleleMismatch=6)
  x | allelematch: 8 of 9 (matchThreshold=0.65, cutHeight=0.35, alleleMismatch=7)
  x | allelematch: 9 of 9 (matchThreshold=0.6, cutHeight=0.4, alleleMismatch=8)
  x | allelematch: missing data load for input dataset is 0.046
  x | allelematch: allelic diversity for input dataset is 7.9
  x | allelematch: Best guess for optimal parameter at alleleMismatch=3 OR matchThreshold=0.85 OR cutHeight=0.15
  x | allelematch: Best guess for unique profile morphology: ZeroSecondMinimum
  x |   matchThreshold cutHeight alleleMismatch samples unique unclassified multipleMatch guessOptimum missingDataLoad allelicDiversity   guessMorphology
  x | 1           1.00      0.00              0     148    140            0             0        FALSE           0.046              7.9 ZeroSecondMinimum
  x | 2           0.95      0.05              1     148    136            0            25        FALSE           0.046              7.9 ZeroSecondMinimum
  x | 3           0.90      0.10              2     148    122            0            33        FALSE           0.046              7.9 ZeroSecondMinimum
  x | 4           0.85      0.15              3     148    100            0             0         TRUE           0.046              7.9 ZeroSecondMinimum
  ... and 5 more.
  
  ── Failure ('test-amExample2.R:26:9'): amExample2 results from pg 8 in allelematchSuppDoc.pdf 2.5.3 compatible ──
  Expected some element of `output` to match string "allelic diversity for input dataset is 7.9 ".
  Actual text:
  x | allelematch: assuming genotype columns are in pairs, representing 10 loci
  x | allelematch: running amUnique() at 9 different values of alleleMismatch
  x | allelematch: 1 of 9 (matchThreshold=1, cutHeight=0, alleleMismatch=0)
  x | allelematch: 2 of 9 (matchThreshold=0.95, cutHeight=0.05, alleleMismatch=1)
  x | allelematch: 3 of 9 (matchThreshold=0.9, cutHeight=0.1, alleleMismatch=2)
  x | allelematch: 4 of 9 (matchThreshold=0.85, cutHeight=0.15, alleleMismatch=3)
  x | allelematch: 5 of 9 (matchThreshold=0.8, cutHeight=0.2, alleleMismatch=4)
  x | allelematch: 6 of 9 (matchThreshold=0.75, cutHeight=0.25, alleleMismatch=5)
  x | allelematch: 7 of 9 (matchThreshold=0.7, cutHeight=0.3, alleleMismatch=6)
  x | allelematch: 8 of 9 (matchThreshold=0.65, cutHeight=0.35, alleleMismatch=7)
  x | allelematch: 9 of 9 (matchThreshold=0.6, cutHeight=0.4, alleleMismatch=8)
  x | allelematch: missing data load for input dataset is 0.046
  x | allelematch: allelic diversity for input dataset is 7.9
  x | allelematch: Best guess for optimal parameter at alleleMismatch=3 OR matchThreshold=0.85 OR cutHeight=0.15
  x | allelematch: Best guess for unique profile morphology: ZeroSecondMinimum
  x |   matchThreshold cutHeight alleleMismatch samples unique unclassified multipleMatch guessOptimum missingDataLoad allelicDiversity   guessMorphology
  x | 1           1.00      0.00              0     148    140            0             0        FALSE           0.046              7.9 ZeroSecondMinimum
  x | 2           0.95      0.05              1     148    136            0            25        FALSE           0.046              7.9 ZeroSecondMinimum
  x | 3           0.90      0.10              2     148    122            0            33        FALSE           0.046              7.9 ZeroSecondMinimum
  x | 4           0.85      0.15              3     148    100            0             0         TRUE           0.046              7.9 ZeroSecondMinimum
  ... and 5 more.
  
  ── Failure ('test-amExample3.R:32:9'): amExample3 results from pg 10 in allelematchSuppDoc.pdf are 2.5.3 compatible ──
  Expected some element of `output` to match string "missing data load for input dataset is 0.097 ".
  Actual text:
  x | allelematch: assuming genotype columns are in pairs, representing 10 loci
  x | allelematch: running amUnique() at 9 different values of alleleMismatch
  x | allelematch: 1 of 9 (matchThreshold=1, cutHeight=0, alleleMismatch=0)
  x | allelematch: 2 of 9 (matchThreshold=0.95, cutHeight=0.05, alleleMismatch=1)
  x | allelematch: 3 of 9 (matchThreshold=0.9, cutHeight=0.1, alleleMismatch=2)
  x | allelematch: 4 of 9 (matchThreshold=0.85, cutHeight=0.15, alleleMismatch=3)
  x | allelematch: 5 of 9 (matchThreshold=0.8, cutHeight=0.2, alleleMismatch=4)
  x | allelematch: 6 of 9 (matchThreshold=0.75, cutHeight=0.25, alleleMismatch=5)
  x | allelematch: 7 of 9 (matchThreshold=0.7, cutHeight=0.3, alleleMismatch=6)
  x | allelematch: 8 of 9 (matchThreshold=0.65, cutHeight=0.35, alleleMismatch=7)
  x | allelematch: 9 of 9 (matchThreshold=0.6, cutHeight=0.4, alleleMismatch=8)
  x | allelematch: missing data load for input dataset is 0.097
  x | allelematch: allelic diversity for input dataset is 8.2
  x | allelematch: Best guess for optimal parameter at alleleMismatch=6 OR matchThreshold=0.7 OR cutHeight=0.3
  x | allelematch: Best guess for unique profile morphology: NonZeroSecondMinimum
  x | allelematch: Use extra caution. Detection of optimal parameter is more error prone with this morphology.
  x |   matchThreshold cutHeight alleleMismatch samples unique unclassified multipleMatch guessOptimum missingDataLoad allelicDiversity      guessMorphology
  x | 1           1.00      0.00              0     319    291            0             0        FALSE           0.097              8.2 NonZeroSecondMinimum
  x | 2           0.95      0.05              1     319    281            0            97        FALSE           0.097              8.2 NonZeroSecondMinimum
  x | 3           0.90      0.10              2     319    212            0           103        FALSE           0.097              8.2 NonZeroSecondMinimum
  ... and 6 more.
  
  ── Failure ('test-amExample3.R:33:9'): amExample3 results from pg 10 in allelematchSuppDoc.pdf are 2.5.3 compatible ──
  Expected some element of `output` to match string "allelic diversity for input dataset is 8.2 ".
  Actual text:
  x | allelematch: assuming genotype columns are in pairs, representing 10 loci
  x | allelematch: running amUnique() at 9 different values of alleleMismatch
  x | allelematch: 1 of 9 (matchThreshold=1, cutHeight=0, alleleMismatch=0)
  x | allelematch: 2 of 9 (matchThreshold=0.95, cutHeight=0.05, alleleMismatch=1)
  x | allelematch: 3 of 9 (matchThreshold=0.9, cutHeight=0.1, alleleMismatch=2)
  x | allelematch: 4 of 9 (matchThreshold=0.85, cutHeight=0.15, alleleMismatch=3)
  x | allelematch: 5 of 9 (matchThreshold=0.8, cutHeight=0.2, alleleMismatch=4)
  x | allelematch: 6 of 9 (matchThreshold=0.75, cutHeight=0.25, alleleMismatch=5)
  x | allelematch: 7 of 9 (matchThreshold=0.7, cutHeight=0.3, alleleMismatch=6)
  x | allelematch: 8 of 9 (matchThreshold=0.65, cutHeight=0.35, alleleMismatch=7)
  x | allelematch: 9 of 9 (matchThreshold=0.6, cutHeight=0.4, alleleMismatch=8)
  x | allelematch: missing data load for input dataset is 0.097
  x | allelematch: allelic diversity for input dataset is 8.2
  x | allelematch: Best guess for optimal parameter at alleleMismatch=6 OR matchThreshold=0.7 OR cutHeight=0.3
  x | allelematch: Best guess for unique profile morphology: NonZeroSecondMinimum
  x | allelematch: Use extra caution. Detection of optimal parameter is more error prone with this morphology.
  x |   matchThreshold cutHeight alleleMismatch samples unique unclassified multipleMatch guessOptimum missingDataLoad allelicDiversity      guessMorphology
  x | 1           1.00      0.00              0     319    291            0             0        FALSE           0.097              8.2 NonZeroSecondMinimum
  x | 2           0.95      0.05              1     319    281            0            97        FALSE           0.097              8.2 NonZeroSecondMinimum
  x | 3           0.90      0.10              2     319    212            0           103        FALSE           0.097              8.2 NonZeroSecondMinimum
  ... and 6 more.
  
  ── Failure ('test-amExample4.R:31:9'): amExample4 results from pg 14 in allelematchSuppDoc.pdf are 2.5.3 compatible ──
  Expected some element of `output` to match string "missing data load for input dataset is 0.199 ".
  Actual text:
  x | allelematch: assuming genotype columns are in pairs, representing 10 loci
  x | allelematch: running amUnique() at 9 different values of alleleMismatch
  x | allelematch: 1 of 9 (matchThreshold=1, cutHeight=0, alleleMismatch=0)
  x | allelematch: 2 of 9 (matchThreshold=0.95, cutHeight=0.05, alleleMismatch=1)
  x | allelematch: 3 of 9 (matchThreshold=0.9, cutHeight=0.1, alleleMismatch=2)
  x | allelematch: 4 of 9 (matchThreshold=0.85, cutHeight=0.15, alleleMismatch=3)
  x | allelematch: 5 of 9 (matchThreshold=0.8, cutHeight=0.2, alleleMismatch=4)
  x | allelematch: 6 of 9 (matchThreshold=0.75, cutHeight=0.25, alleleMismatch=5)
  x | allelematch: 7 of 9 (matchThreshold=0.7, cutHeight=0.3, alleleMismatch=6)
  x | allelematch: 8 of 9 (matchThreshold=0.65, cutHeight=0.35, alleleMismatch=7)
  x | allelematch: 9 of 9 (matchThreshold=0.6, cutHeight=0.4, alleleMismatch=8)
  x | allelematch: missing data load for input dataset is 0.199
  x | allelematch: allelic diversity for input dataset is 4.8
  x | allelematch: Best guess for optimal parameter at alleleMismatch=1 OR matchThreshold=0.95 OR cutHeight=0.05
  x | allelematch: Best guess for unique profile morphology: NoSecondMinimum
  x | allelematch: Use extra caution. Detection of optimal parameter is more error prone with this morphology.
  x |   matchThreshold cutHeight alleleMismatch samples unique unclassified multipleMatch guessOptimum missingDataLoad allelicDiversity guessMorphology
  x | 1           1.00      0.00              0     307    307            0             0        FALSE           0.199              4.8 NoSecondMinimum
  x | 2           0.95      0.05              1     307    307            0            42         TRUE           0.199              4.8 NoSecondMinimum
  x | 3           0.90      0.10              2     307    283            0            92        FALSE           0.199              4.8 NoSecondMinimum
  ... and 6 more.
  
  ── Failure ('test-amExample4.R:32:9'): amExample4 results from pg 14 in allelematchSuppDoc.pdf are 2.5.3 compatible ──
  Expected some element of `output` to match string "allelic diversity for input dataset is 4.8 ".
  Actual text:
  x | allelematch: assuming genotype columns are in pairs, representing 10 loci
  x | allelematch: running amUnique() at 9 different values of alleleMismatch
  x | allelematch: 1 of 9 (matchThreshold=1, cutHeight=0, alleleMismatch=0)
  x | allelematch: 2 of 9 (matchThreshold=0.95, cutHeight=0.05, alleleMismatch=1)
  x | allelematch: 3 of 9 (matchThreshold=0.9, cutHeight=0.1, alleleMismatch=2)
  x | allelematch: 4 of 9 (matchThreshold=0.85, cutHeight=0.15, alleleMismatch=3)
  x | allelematch: 5 of 9 (matchThreshold=0.8, cutHeight=0.2, alleleMismatch=4)
  x | allelematch: 6 of 9 (matchThreshold=0.75, cutHeight=0.25, alleleMismatch=5)
  x | allelematch: 7 of 9 (matchThreshold=0.7, cutHeight=0.3, alleleMismatch=6)
  x | allelematch: 8 of 9 (matchThreshold=0.65, cutHeight=0.35, alleleMismatch=7)
  x | allelematch: 9 of 9 (matchThreshold=0.6, cutHeight=0.4, alleleMismatch=8)
  x | allelematch: missing data load for input dataset is 0.199
  x | allelematch: allelic diversity for input dataset is 4.8
  x | allelematch: Best guess for optimal parameter at alleleMismatch=1 OR matchThreshold=0.95 OR cutHeight=0.05
  x | allelematch: Best guess for unique profile morphology: NoSecondMinimum
  x | allelematch: Use extra caution. Detection of optimal parameter is more error prone with this morphology.
  x |   matchThreshold cutHeight alleleMismatch samples unique unclassified multipleMatch guessOptimum missingDataLoad allelicDiversity guessMorphology
  x | 1           1.00      0.00              0     307    307            0             0        FALSE           0.199              4.8 NoSecondMinimum
  x | 2           0.95      0.05              1     307    307            0            42         TRUE           0.199              4.8 NoSecondMinimum
  x | 3           0.90      0.10              2     307    283            0            92        FALSE           0.199              4.8 NoSecondMinimum
  ... and 6 more.
  
  
  [ FAIL 9 | WARN 0 | SKIP 20 | PASS 146 ]
  Error:
  ! Test failures.
  Execution halted