R Under development (unstable) (2026-06-23 r90186 ucrt) -- "Unsuffered Consequences"
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> # 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. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=1) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=2) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=4) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=1) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=2) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=4) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample2, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=2) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample2, runUntilSingletons=TRUE, cutHeight=0.95, missingMethod=1, consensusMethod=2) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample2, runUntilSingletons=TRUE, cutHeight=0.99, missingMethod=1, consensusMethod=2) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.7, missingMethod=2, consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=4) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.95, missingMethod=1, consensusMethod=4) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.95, missingMethod=2, consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.99, missingMethod=1, consensusMethod=4) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.99, missingMethod=2, consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataMini, cutHeight=1, doPsib="missing", consensusMethod=1) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataMini, cutHeight=1, doPsib="missing", consensusMethod=2) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataMini, cutHeight=1, doPsib="missing", consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataMini, cutHeight=1, doPsib="missing", consensusMethod=4) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataMini, cutHeight=1, doPsib="all", consensusMethod=1) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataMini, cutHeight=1, doPsib="all", consensusMethod=2) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataMini, cutHeight=1, doPsib="all", consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataMini, cutHeight=1, doPsib="all", consensusMethod=4) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample1, cutHeight=0.9, doPsib="missing", consensusMethod=1) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample1, cutHeight=0.9, doPsib="missing", consensusMethod=2) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample1, cutHeight=0.9, doPsib="missing", consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample1, cutHeight=0.9, doPsib="missing", consensusMethod=4) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample1, cutHeight=0.9, doPsib="all", consensusMethod=1) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample1, cutHeight=0.9, doPsib="all", consensusMethod=2) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample1, cutHeight=0.9, doPsib="all", consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample1, cutHeight=0.9, doPsib="all", consensusMethod=4) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample4, cutHeight=0.7, doPsib="missing", consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample4, cutHeight=0.7, doPsib="all", consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample4, cutHeight=0.9, doPsib="missing", consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample4, cutHeight=0.9, doPsib="all", consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample4, cutHeight=0.95, doPsib="missing", consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample4, cutHeight=0.95, doPsib="all", consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample4, cutHeight=0.99, doPsib="missing", consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample4, cutHeight=0.99, doPsib="all", consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample4, cutHeight=1, doPsib="missing", consensusMethod=3) 


  
  Error    :  allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again. 
  Rejected :  amUnique(amdataExample4, cutHeight=1, doPsib="all", consensusMethod=3) 

[ FAIL 1 | WARN 8 | SKIP 20 | PASS 164 ]

══ Skipped tests (20) ══════════════════════════════════════════════════════════
• On CRAN (20): 'test-allelematch_1-amDataset.R:32:1',
  'test-allelematch_1-amDataset.R:132:1', '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:47:5'): Validation of arguments to amUnique() is working ──
Error: allelematch:  amCluster: no clusters formed. Please set cutHeight lower and run again.
Backtrace:
    ▆
 1. ├─testthat::expect_error(...) at test-allelematch_6-amUnique_negative.R:47:5
 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, alleleMismatch = 5)
 8.   └─allelematch::amCluster(...)

[ FAIL 1 | WARN 8 | SKIP 20 | PASS 164 ]
Error:
! Test failures.

Cleaning up 4 leaked TEMP file(s):
  D:\temp\2026_06_24_11_30_17_999\RtmpKeemFz/amPairwise_Y8LUCKAH.htm
  D:\temp\2026_06_24_11_30_17_999\RtmpKeemFz/amCluster_7E3B9I4P.htm
  D:\temp\2026_06_24_11_30_17_999\RtmpKeemFz/amUnique_GVLEWBOF.htm
  D:\temp\2026_06_24_11_30_17_999\RtmpKeemFz/pdf4ddc5aff2c10
Execution halted
Warning message:
In file.remove(to_remove) :
  cannot remove file 'D:\temp\2026_06_24_11_30_17_999\RtmpKeemFz/pdf4ddc5aff2c10', reason 'Permission denied'