Running 'tinytest.R' [10s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("statgenGWAS")
  + }
  
  Running test_GWAS.R...................    0 tests    
  Running test_GWAS.R...................    0 tests    
  Running test_GWAS.R...................    0 tests    
  Running test_GWAS.R...................    0 tests    
  Running test_GWAS.R...................    1 tests [0;32mOK[0m 
  Running test_GWAS.R...................    2 tests [0;32mOK[0m 
  Running test_GWAS.R...................    2 tests [0;32mOK[0m 
  Running test_GWAS.R...................    3 tests [0;32mOK[0m 
  Running test_GWAS.R...................    4 tests [0;32mOK[0m 
  Running test_GWAS.R...................    5 tests [0;32mOK[0m 
  Running test_GWAS.R...................    6 tests [0;32mOK[0m 
  Running test_GWAS.R...................    7 tests [0;32mOK[0m 
  Running test_GWAS.R...................    8 tests [0;32mOK[0m 
  Running test_GWAS.R...................    9 tests [0;32mOK[0m 
  Running test_GWAS.R...................   10 tests [0;32mOK[0m 
  Running test_GWAS.R...................   11 tests [0;32mOK[0m 
  Running test_GWAS.R...................   11 tests [0;32mOK[0m 
  Running test_GWAS.R...................   12 tests [0;32mOK[0m 
  Running test_GWAS.R...................   13 tests [0;32mOK[0m 
  Running test_GWAS.R...................   14 tests [0;32mOK[0m 
  Running test_GWAS.R...................   15 tests [0;32mOK[0m 
  Running test_GWAS.R...................   15 tests [0;32mOK[0m 
  Running test_GWAS.R...................   16 tests [0;32mOK[0m 
  Running test_GWAS.R...................   17 tests [0;32mOK[0m 
  
  Running test_STG.R....................    0 tests    
  Running test_STG.R....................    0 tests    
  Running test_STG.R....................    0 tests    
  Running test_STG.R....................    0 tests    
  Running test_STG.R....................    0 tests    
  Running test_STG.R....................    0 tests    
  Running test_STG.R....................    0 tests    
  Running test_STG.R....................    0 tests    
  Running test_STG.R....................    1 tests [0;32mOK[0m 
  Running test_STG.R....................    2 tests [0;32mOK[0m 
  Running test_STG.R....................    3 tests [0;32mOK[0m 
  Running test_STG.R....................    4 tests [0;32mOK[0m 
  Running test_STG.R....................    5 tests [0;32mOK[0m 
  Running test_STG.R....................    6 tests [0;32mOK[0m 
  Running test_STG.R....................    7 tests [0;32mOK[0m 
  Running test_STG.R....................    8 tests [0;32mOK[0m 
  Running test_STG.R....................    9 tests [0;32mOK[0m 
  Running test_STG.R....................   10 tests [0;32mOK[0m 
  Running test_STG.R....................   11 tests [0;32mOK[0m 
  Running test_STG.R....................   12 tests [0;32mOK[0m 
  Running test_STG.R....................   13 tests [0;32mOK[0m 
  Running test_STG.R....................   14 tests [0;32mOK[0m 
  Running test_STG.R....................   15 tests [0;32mOK[0m 
  Running test_STG.R....................   16 tests [0;32mOK[0m 
  Running test_STG.R....................   17 tests [0;32mOK[0m 
  Running test_STG.R....................   18 tests [0;32mOK[0m 
  Running test_STG.R....................   19 tests [0;32mOK[0m 
  Running test_STG.R....................   20 tests [0;32mOK[0m 
  Running test_STG.R....................   21 tests [0;32mOK[0m 
  Running test_STG.R....................   22 tests [0;32mOK[0m 
  Running test_STG.R....................   22 tests [0;32mOK[0m 
  Running test_STG.R....................   22 tests [0;32mOK[0m 
  Running test_STG.R....................   22 tests [0;32mOK[0m 
  Running test_STG.R....................   22 tests [0;32mOK[0m 
  Running test_STG.R....................   22 tests [0;32mOK[0m 
  Running test_STG.R....................   23 tests [0;32mOK[0m 
  Running test_STG.R....................   24 tests [0;32mOK[0m 
  Running test_STG.R....................   25 tests [0;32mOK[0m 
  Running test_STG.R....................   26 tests [0;32mOK[0m 
  Running test_STG.R....................   27 tests [0;32mOK[0m 
  Running test_STG.R....................   28 tests [0;32mOK[0m 
  Running test_STG.R....................   29 tests [0;32mOK[0m 
  Running test_STG.R....................   30 tests [0;32mOK[0m 
  Running test_STG.R....................   31 tests [0;32mOK[0m 
  Running test_STG.R....................   32 tests [0;32mOK[0m 
  Running test_STG.R....................   33 tests [0;32mOK[0m 
  Running test_STG.R....................   34 tests [0;32mOK[0m 
  Running test_STG.R....................   35 tests [0;32mOK[0m 
  Running test_STG.R....................   36 tests [0;32mOK[0m 
  Running test_STG.R....................   37 tests [0;32mOK[0m 
  Running test_STG.R....................   38 tests [0;32mOK[0m 
  Running test_STG.R....................   39 tests [0;32mOK[0m 
  Running test_STG.R....................   40 tests [0;32mOK[0m 
  Running test_STG.R....................   41 tests [0;32mOK[0m 
  Running test_STG.R....................   42 tests [0;32mOK[0m 
  Running test_STG.R....................   43 tests [0;32mOK[0m 
  Running test_STG.R....................   44 tests [0;32mOK[0m 
  Running test_STG.R....................   45 tests [0;32mOK[0m 
  Running test_STG.R....................   46 tests [0;32mOK[0m 
  Running test_STG.R....................   47 tests [0;32mOK[0m 
  
  Running test_STGHelper.R..............    0 tests    
  Running test_STGHelper.R..............    0 tests    
  Running test_STGHelper.R..............    0 tests    
  Running test_STGHelper.R..............    1 tests [0;32mOK[0m 
  Running test_STGHelper.R..............    2 tests [0;32mOK[0m 
  Running test_STGHelper.R..............    3 tests [0;32mOK[0m 
  Running test_STGHelper.R..............    3 tests [0;32mOK[0m 
  Running test_STGHelper.R..............    4 tests [0;32mOK[0m 
  Running test_STGHelper.R..............    5 tests [0;32mOK[0m 
  Running test_STGHelper.R..............    6 tests [0;32mOK[0m 
  Running test_STGHelper.R..............    7 tests [0;32mOK[0m 
  Running test_STGHelper.R..............    8 tests [0;32mOK[0m 
  Running test_STGHelper.R..............    9 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   10 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   11 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   12 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   13 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   14 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   14 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   15 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   16 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   17 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   18 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   18 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   19 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   20 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   20 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   20 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   21 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   22 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   23 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   24 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   25 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   26 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   27 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   28 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   29 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   30 tests [0;32mOK[0m 
  Running test_STGHelper.R..............   31 tests [0;32mOK[0m 
  
  Running test_STGoptions.R.............    0 tests    
  Running test_STGoptions.R.............    1 tests [0;32mOK[0m 
  Running test_STGoptions.R.............    1 tests [0;32mOK[0m 
  Running test_STGoptions.R.............    1 tests [0;32mOK[0m 
  Running test_STGoptions.R.............    2 tests [0;32mOK[0m 
  Running test_STGoptions.R.............    3 tests [0;32mOK[0m 
  Running test_STGoptions.R.............    4 tests [0;32mOK[0m 
  Running test_STGoptions.R.............    5 tests [0;32mOK[0m 
  Running test_STGoptions.R.............    6 tests [0;32mOK[0m 
  Running test_STGoptions.R.............    6 tests [0;32mOK[0m 
  Running test_STGoptions.R.............    6 tests [0;32mOK[0m 
  Running test_STGoptions.R.............    7 tests [0;32mOK[0m 
  Running test_STGoptions.R.............    8 tests [0;32mOK[0m 
  Running test_STGoptions.R.............    9 tests [0;32mOK[0m 
  Running test_STGoptions.R.............   10 tests [0;32mOK[0m 
  Running test_STGoptions.R.............   11 tests [0;32mOK[0m 
  Running test_STGoptions.R.............   11 tests [0;32mOK[0m 
  Running test_STGoptions.R.............   12 tests [0;32mOK[0m 
  Running test_STGoptions.R.............   13 tests [0;32mOK[0m 
  Running test_STGoptions.R.............   14 tests [0;32mOK[0m 
  Running test_STGoptions.R.............   14 tests [0;32mOK[0m 
  Running test_STGoptions.R.............   15 tests [0;32mOK[0m 
  Running test_STGoptions.R.............   16 tests [0;32mOK[0m 
  Running test_STGoptions.R.............   16 tests [0;32mOK[0m 
  Running test_STGoptions.R.............   17 tests [0;32mOK[0m 
  Running test_STGoptions.R.............   18 tests [0;32mOK[0m 
  
  Running test_chkFuncs.R...............    0 tests    
  Running test_chkFuncs.R...............    1 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............    2 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............    3 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............    3 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............    3 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............    4 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............    5 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............    6 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............    7 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............    8 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............    9 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   10 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   11 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   12 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   13 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   14 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   15 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   16 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   17 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   18 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   19 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   20 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   21 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   22 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   23 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   24 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   25 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   26 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   27 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   28 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   29 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   30 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   30 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   31 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   31 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   32 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   33 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   34 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   35 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   36 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   37 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   38 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   39 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   40 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   41 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   42 tests [0;32mOK[0m 
  Running test_chkFuncs.R...............   43 tests [0;32mOK[0m 
  
  Running test_codeMarkers.R............    0 tests    
  Running test_codeMarkers.R............    0 tests    
  Running test_codeMarkers.R............    0 tests    
  Running test_codeMarkers.R............    0 tests    
  Running test_codeMarkers.R............    0 tests    
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  Running test_codeMarkers.R............    0 tests    
  Running test_codeMarkers.R............    0 tests    
  Running test_codeMarkers.R............    0 tests    
  Running test_codeMarkers.R............    1 tests [0;31m1 fails[0m 
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  Running test_codeMarkers.R............    3 tests [0;31m1 fails[0m 
  Running test_codeMarkers.R............    4 tests [0;31m1 fails[0m 
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  Running test_codeMarkers.R............    6 tests [0;31m1 fails[0m 
  Running test_codeMarkers.R............    7 tests [0;31m1 fails[0m 
  Running test_codeMarkers.R............    8 tests [0;31m1 fails[0m 
  Running test_codeMarkers.R............    9 tests [0;31m1 fails[0m 
  Running test_codeMarkers.R............   10 tests [0;31m1 fails[0m 
  Running test_codeMarkers.R............   11 tests [0;31m1 fails[0m 
  Running test_codeMarkers.R............   12 tests [0;31m1 fails[0m 
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  Running test_codeMarkers.R............   14 tests [0;31m2 fails[0m 
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  Running test_codeMarkers.R............   16 tests [0;31m2 fails[0m 
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  Running test_codeMarkers.R............   18 tests [0;31m3 fails[0m 
  Running test_codeMarkers.R............   19 tests [0;31m3 fails[0m 
  Running test_codeMarkers.R............   19 tests [0;31m3 fails[0m 
  Running test_codeMarkers.R............   19 tests [0;31m3 fails[0m 
  Running test_codeMarkers.R............   20 tests [0;31m3 fails[0m 
  Running test_codeMarkers.R............   21 tests [0;31m3 fails[0m 
  Running test_codeMarkers.R............   22 tests [0;31m4 fails[0m 
  Running test_codeMarkers.R............   23 tests [0;31m4 fails[0m 
  Running test_codeMarkers.R............   24 tests [0;31m4 fails[0m 
  Running test_codeMarkers.R............   25 tests [0;31m4 fails[0m 
  Running test_codeMarkers.R............   26 tests [0;31m4 fails[0m 
  Running test_codeMarkers.R............   27 tests [0;31m4 fails[0m 
  Running test_codeMarkers.R............   28 tests [0;31m4 fails[0m 
  Running test_codeMarkers.R............   29 tests [0;31m4 fails[0m 
  Running test_codeMarkers.R............   30 tests [0;31m4 fails[0m 
  Running test_codeMarkers.R............   31 tests [0;31m4 fails[0m 
  Running test_codeMarkers.R............   32 tests [0;31m4 fails[0m 
  Running test_codeMarkers.R............   33 tests [0;31m4 fails[0m 
  Running test_codeMarkers.R............   34 tests [0;31m4 fails[0m 
  Running test_codeMarkers.R............   34 tests [0;31m4 fails[0m 
  Running test_codeMarkers.R............   34 tests [0;31m4 fails[0m 
  Running test_codeMarkers.R............   35 tests [0;31m5 fails[0m 
  Running test_codeMarkers.R............   35 tests [0;31m5 fails[0m 
  Running test_codeMarkers.R............   35 tests [0;31m5 fails[0m 
  Running test_codeMarkers.R............   36 tests [0;31m5 fails[0m 
  Running test_codeMarkers.R............   36 tests [0;31m5 fails[0m 
  Running test_codeMarkers.R............   37 tests [0;31m5 fails[0m 
  Running test_codeMarkers.R............   38 tests [0;31m5 fails[0m 
  Running test_codeMarkers.R............   39 tests [0;31m5 fails[0m 
  Running test_codeMarkers.R............   40 tests [0;31m5 fails[0m 
  Running test_codeMarkers.R............   41 tests [0;31m5 fails[0m 
  
  Running test_gData.R..................    0 tests    
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  Running test_gData.R..................    1 tests [0;32mOK[0m 
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  Running test_gData.R..................    4 tests [0;32mOK[0m 
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  Running test_gData.R..................    6 tests [0;32mOK[0m 
  Running test_gData.R..................    6 tests [0;32mOK[0m 
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  Running test_gData.R..................   17 tests [0;32mOK[0m 
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  Running test_gData.R..................   19 tests [0;32mOK[0m 
  Running test_gData.R..................   19 tests [0;32mOK[0m 
  Running test_gData.R..................   20 tests [0;32mOK[0m 
  Running test_gData.R..................   21 tests [0;32mOK[0m 
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  Running test_gData.R..................   23 tests [0;32mOK[0m 
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  Running test_gData.R..................   25 tests [0;32mOK[0m 
  Running test_gData.R..................   25 tests [0;32mOK[0m 
  Running test_gData.R..................   26 tests [0;32mOK[0m 
  Running test_gData.R..................   27 tests [0;32mOK[0m 
  Running test_gData.R..................   28 tests [0;32mOK[0m 
  Running test_gData.R..................   29 tests [0;32mOK[0m 
  Running test_gData.R..................   30 tests [0;32mOK[0m 
  Running test_gData.R..................   30 tests [0;32mOK[0m 
  Running test_gData.R..................   30 tests [0;32mOK[0m 
  Running test_gData.R..................   31 tests [0;32mOK[0m 
  Running test_gData.R..................   32 tests [0;32mOK[0m 
  Running test_gData.R..................   33 tests [0;32mOK[0m 
  Running test_gData.R..................   34 tests [0;32mOK[0m 
  Running test_gData.R..................   35 tests [0;32mOK[0m 
  Running test_gData.R..................   36 tests [0;32mOK[0m 
  Running test_gData.R..................   37 tests [0;32mOK[0m 
  Running test_gData.R..................   38 tests [0;32mOK[0m 
  Running test_gData.R..................   39 tests [0;32mOK[0m 
  Running test_gData.R..................   40 tests [0;32mOK[0m 
  Running test_gData.R..................   41 tests [0;32mOK[0m 
  Running test_gData.R..................   42 tests [0;32mOK[0m 
  Running test_gData.R..................   43 tests [0;32mOK[0m 
  Running test_gData.R..................   43 tests [0;32mOK[0m 
  Running test_gData.R..................   43 tests [0;32mOK[0m 
  Running test_gData.R..................   44 tests [0;32mOK[0m 
  Running test_gData.R..................   45 tests [0;32mOK[0m 
  Running test_gData.R..................   46 tests [0;32mOK[0m 
  Running test_gData.R..................   47 tests [0;32mOK[0m 
  Running test_gData.R..................   47 tests [0;32mOK[0m 
  Running test_gData.R..................   48 tests [0;32mOK[0m 
  Running test_gData.R..................   49 tests [0;32mOK[0m 
  Running test_gData.R..................   50 tests [0;32mOK[0m 
  Running test_gData.R..................   51 tests [0;32mOK[0m 
  Running test_gData.R..................   51 tests [0;32mOK[0m 
  Running test_gData.R..................   51 tests [0;32mOK[0m 
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  Error: ----- FAILED[data]: test_codeMarkers.R<26--27>
   call| expect_equivalent(codeMarkers(gData = gData, impute = FALSE)$markers, 
   call| matrix(c(0, NA, 0, 0, NA, 1, 1, 2, 0), nrow = 3))
   diff| 'is.NA' value mismatch: 2 in current 2 in target
  ----- FAILED[data]: test_codeMarkers.R<70--72>
   call| expect_equivalent(codeMarkers(gData = gData, removeDuplicates = FALSE, 
   call| impute = TRUE, imputeType = "random")$markers, matrix(c(0, 
   call| 0, 0, 1, 2, 0, 0, 0, 1, 1, 2, 0), nrow = 3))
   diff| Mean absolute difference: 1
  ----- FAILED[data]: test_codeMarkers.R<112--114>
   call| expect_equivalent(codeMarkers(gData = gData, MAF = 0.2, keep = "SNP1", 
   call| impute = FALSE)$markers, matrix(c(0, NA, 0, 0, NA, 1, 1, 
   call| 2, 0), nrow = 3))
   diff| 'is.NA' value mismatch: 2 in current 2 in target
  ----- FAILED[data]: test_codeMarkers.R<134--136>
   call| expect_equivalent(codeMarkers(gData = gData, refAll = "A", impute = FALSE)$markers, 
   call| matrix(c(2, NA, 2, 2, NA, 1, 1, 2, 0), nrow = 3))
   d
  Execution halted