* using log directory 'd:/Rcompile/CRANpkg/local/3.5/statgenGWAS.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'statgenGWAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'statgenGWAS' version '1.0.4'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'statgenGWAS' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.1Mb
* checking package directory ... 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
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
** checking use of S3 registration ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... 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 ... [12s] OK
* checking Rd files ... OK
* checking Rd metadata ... 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [5s] OK
** running examples for arch 'x64' ... [4s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ... [17s] ERROR
  Running 'tinytest.R' [15s]
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 OK 
  Running test_GWAS.R...................    2 tests OK 
  Running test_GWAS.R...................    2 tests OK 
  Running test_GWAS.R...................    3 tests OK 
  Running test_GWAS.R...................    4 tests OK 
  Running test_GWAS.R...................    5 tests OK 
  Running test_GWAS.R...................    6 tests OK 
  Running test_GWAS.R...................    7 tests OK 
  Running test_GWAS.R...................    8 tests OK 
  Running test_GWAS.R...................    9 tests OK 
  Running test_GWAS.R...................   10 tests OK 
  Running test_GWAS.R...................   11 tests OK 
  Running test_GWAS.R...................   11 tests OK 
  Running test_GWAS.R...................   12 tests OK 
  Running test_GWAS.R...................   13 tests OK 
  Running test_GWAS.R...................   14 tests OK 
  Running test_GWAS.R...................   15 tests OK 
  Running test_GWAS.R...................   15 tests OK 
  Running test_GWAS.R...................   16 tests OK 
  Running test_GWAS.R...................   17 tests OK 
  
  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 OK 
  Running test_STG.R....................    2 tests OK 
  Running test_STG.R....................    3 tests OK 
  Running test_STG.R....................    4 tests OK 
  Running test_STG.R....................    5 tests OK 
  Running test_STG.R....................    6 tests OK 
  Running test_STG.R....................    7 tests OK 
  Running test_STG.R....................    8 tests OK 
  Running test_STG.R....................    9 tests OK 
  Running test_STG.R....................   10 tests OK 
  Running test_STG.R....................   11 tests OK 
  Running test_STG.R....................   12 tests OK 
  Running test_STG.R....................   13 tests OK 
  Running test_STG.R....................   14 tests OK 
  Running test_STG.R....................   15 tests OK 
  Running test_STG.R....................   16 tests OK 
  Running test_STG.R....................   17 tests OK 
  Running test_STG.R....................   18 tests OK 
  Running test_STG.R....................   19 tests OK 
  Running test_STG.R....................   20 tests OK 
  Running test_STG.R....................   21 tests OK 
  Running test_STG.R....................   22 tests OK 
  Running test_STG.R....................   22 tests OK 
  Running test_STG.R....................   22 tests OK 
  Running test_STG.R....................   22 tests OK 
  Running test_STG.R....................   22 tests OK 
  Running test_STG.R....................   22 tests OK 
  Running test_STG.R....................   23 tests OK 
  Running test_STG.R....................   24 tests OK 
  Running test_STG.R....................   25 tests OK 
  Running test_STG.R....................   26 tests OK 
  Running test_STG.R....................   27 tests OK 
  Running test_STG.R....................   28 tests OK 
  Running test_STG.R....................   29 tests OK 
  Running test_STG.R....................   30 tests OK 
  Running test_STG.R....................   31 tests OK 
  Running test_STG.R....................   32 tests OK 
  Running test_STG.R....................   33 tests OK 
  Running test_STG.R....................   34 tests OK 
  Running test_STG.R....................   35 tests OK 
  Running test_STG.R....................   36 tests OK 
  Running test_STG.R....................   37 tests OK 
  Running test_STG.R....................   38 tests OK 
  Running test_STG.R....................   39 tests OK 
  Running test_STG.R....................   40 tests OK 
  Running test_STG.R....................   41 tests OK 
  Running test_STG.R....................   42 tests OK 
  Running test_STG.R....................   43 tests OK 
  Running test_STG.R....................   44 tests OK 
  Running test_STG.R....................   45 tests OK 
  Running test_STG.R....................   46 tests OK 
  Running test_STG.R....................   47 tests OK 
  
  Running test_STGHelper.R..............    0 tests    
  Running test_STGHelper.R..............    0 tests    
  Running test_STGHelper.R..............    0 tests    
  Running test_STGHelper.R..............    1 tests OK 
  Running test_STGHelper.R..............    2 tests OK 
  Running test_STGHelper.R..............    3 tests OK 
  Running test_STGHelper.R..............    3 tests OK 
  Running test_STGHelper.R..............    4 tests OK 
  Running test_STGHelper.R..............    5 tests OK 
  Running test_STGHelper.R..............    6 tests OK 
  Running test_STGHelper.R..............    7 tests OK 
  Running test_STGHelper.R..............    8 tests OK 
  Running test_STGHelper.R..............    9 tests OK 
  Running test_STGHelper.R..............   10 tests OK 
  Running test_STGHelper.R..............   11 tests OK 
  Running test_STGHelper.R..............   12 tests OK 
  Running test_STGHelper.R..............   13 tests OK 
  Running test_STGHelper.R..............   14 tests OK 
  Running test_STGHelper.R..............   14 tests OK 
  Running test_STGHelper.R..............   15 tests OK 
  Running test_STGHelper.R..............   16 tests OK 
  Running test_STGHelper.R..............   17 tests OK 
  Running test_STGHelper.R..............   18 tests OK 
  Running test_STGHelper.R..............   18 tests OK 
  Running test_STGHelper.R..............   19 tests OK 
  Running test_STGHelper.R..............   20 tests OK 
  Running test_STGHelper.R..............   20 tests OK 
  Running test_STGHelper.R..............   20 tests OK 
  Running test_STGHelper.R..............   21 tests OK 
  Running test_STGHelper.R..............   22 tests OK 
  Running test_STGHelper.R..............   23 tests OK 
  Running test_STGHelper.R..............   24 tests OK 
  Running test_STGHelper.R..............   25 tests OK 
  Running test_STGHelper.R..............   26 tests OK 
  Running test_STGHelper.R..............   27 tests OK 
  Running test_STGHelper.R..............   28 tests OK 
  Running test_STGHelper.R..............   29 tests OK 
  Running test_STGHelper.R..............   30 tests OK 
  Running test_STGHelper.R..............   31 tests OK 
  
  Running test_STGoptions.R.............    0 tests    
  Running test_STGoptions.R.............    1 tests OK 
  Running test_STGoptions.R.............    1 tests OK 
  Running test_STGoptions.R.............    1 tests OK 
  Running test_STGoptions.R.............    2 tests OK 
  Running test_STGoptions.R.............    3 tests OK 
  Running test_STGoptions.R.............    4 tests OK 
  Running test_STGoptions.R.............    5 tests OK 
  Running test_STGoptions.R.............    6 tests OK 
  Running test_STGoptions.R.............    6 tests OK 
  Running test_STGoptions.R.............    6 tests OK 
  Running test_STGoptions.R.............    7 tests OK 
  Running test_STGoptions.R.............    8 tests OK 
  Running test_STGoptions.R.............    9 tests OK 
  Running test_STGoptions.R.............   10 tests OK 
  Running test_STGoptions.R.............   11 tests OK 
  Running test_STGoptions.R.............   11 tests OK 
  Running test_STGoptions.R.............   12 tests OK 
  Running test_STGoptions.R.............   13 tests OK 
  Running test_STGoptions.R.............   14 tests OK 
  Running test_STGoptions.R.............   14 tests OK 
  Running test_STGoptions.R.............   15 tests OK 
  Running test_STGoptions.R.............   16 tests OK 
  Running test_STGoptions.R.............   16 tests OK 
  Running test_STGoptions.R.............   17 tests OK 
  Running test_STGoptions.R.............   18 tests OK 
  
  Running test_chkFuncs.R...............    0 tests    
  Running test_chkFuncs.R...............    1 tests OK 
  Running test_chkFuncs.R...............    2 tests OK 
  Running test_chkFuncs.R...............    3 tests OK 
  Running test_chkFuncs.R...............    3 tests OK 
  Running test_chkFuncs.R...............    3 tests OK 
  Running test_chkFuncs.R...............    4 tests OK 
  Running test_chkFuncs.R...............    5 tests OK 
  Running test_chkFuncs.R...............    6 tests OK 
  Running test_chkFuncs.R...............    7 tests OK 
  Running test_chkFuncs.R...............    8 tests OK 
  Running test_chkFuncs.R...............    9 tests OK 
  Running test_chkFuncs.R...............   10 tests OK 
  Running test_chkFuncs.R...............   11 tests OK 
  Running test_chkFuncs.R...............   12 tests OK 
  Running test_chkFuncs.R...............   13 tests OK 
  Running test_chkFuncs.R...............   14 tests OK 
  Running test_chkFuncs.R...............   15 tests OK 
  Running test_chkFuncs.R...............   16 tests OK 
  Running test_chkFuncs.R...............   17 tests OK 
  Running test_chkFuncs.R...............   18 tests OK 
  Running test_chkFuncs.R...............   19 tests OK 
  Running test_chkFuncs.R...............   20 tests OK 
  Running test_chkFuncs.R...............   21 tests OK 
  Running test_chkFuncs.R...............   22 tests OK 
  Running test_chkFuncs.R...............   23 tests OK 
  Running test_chkFuncs.R...............   24 tests OK 
  Running test_chkFuncs.R...............   25 tests OK 
  Running test_chkFuncs.R...............   26 tests OK 
  Running test_chkFuncs.R...............   27 tests OK 
  Running test_chkFuncs.R...............   28 tests OK 
  Running test_chkFuncs.R...............   29 tests OK 
  Running test_chkFuncs.R...............   30 tests OK 
  Running test_chkFuncs.R...............   30 tests OK 
  Running test_chkFuncs.R...............   31 tests OK 
  Running test_chkFuncs.R...............   31 tests OK 
  Running test_chkFuncs.R...............   32 tests OK 
  Running test_chkFuncs.R...............   33 tests OK 
  Running test_chkFuncs.R...............   34 tests OK 
  Running test_chkFuncs.R...............   35 tests OK 
  Running test_chkFuncs.R...............   36 tests OK 
  Running test_chkFuncs.R...............   37 tests OK 
  Running test_chkFuncs.R...............   38 tests OK 
  Running test_chkFuncs.R...............   39 tests OK 
  Running test_chkFuncs.R...............   40 tests OK 
  Running test_chkFuncs.R...............   41 tests OK 
  Running test_chkFuncs.R...............   42 tests OK 
  Running test_chkFuncs.R...............   43 tests OK 
  
  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    
  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............    1 tests 1 fails 
  Running test_codeMarkers.R............    2 tests 1 fails 
  Running test_codeMarkers.R............    3 tests 1 fails 
  Running test_codeMarkers.R............    4 tests 1 fails 
  Running test_codeMarkers.R............    5 tests 1 fails 
  Running test_codeMarkers.R............    6 tests 1 fails 
  Running test_codeMarkers.R............    7 tests 1 fails 
  Running test_codeMarkers.R............    8 tests 1 fails 
  Running test_codeMarkers.R............    9 tests 1 fails 
  Running test_codeMarkers.R............   10 tests 1 fails 
  Running test_codeMarkers.R............   11 tests 1 fails 
  Running test_codeMarkers.R............   12 tests 1 fails 
  Running test_codeMarkers.R............   13 tests 1 fails 
  Running test_codeMarkers.R............   14 tests 2 fails 
  Running test_codeMarkers.R............   14 tests 2 fails 
  Running test_codeMarkers.R............   15 tests 2 fails 
  Running test_codeMarkers.R............   16 tests 2 fails 
  Running test_codeMarkers.R............   17 tests 3 fails 
  Running test_codeMarkers.R............   18 tests 3 fails 
  Running test_codeMarkers.R............   19 tests 3 fails 
  Running test_codeMarkers.R............   19 tests 3 fails 
  Running test_codeMarkers.R............   19 tests 3 fails 
  Running test_codeMarkers.R............   20 tests 3 fails 
  Running test_codeMarkers.R............   21 tests 3 fails 
  Running test_codeMarkers.R............   22 tests 4 fails 
  Running test_codeMarkers.R............   23 tests 4 fails 
  Running test_codeMarkers.R............   24 tests 4 fails 
  Running test_codeMarkers.R............   25 tests 4 fails 
  Running test_codeMarkers.R............   26 tests 4 fails 
  Running test_codeMarkers.R............   27 tests 4 fails 
  Running test_codeMarkers.R............   28 tests 4 fails 
  Running test_codeMarkers.R............   29 tests 4 fails 
  Running test_codeMarkers.R............   30 tests 4 fails 
  Running test_codeMarkers.R............   31 tests 4 fails 
  Running test_codeMarkers.R............   32 tests 4 fails 
  Running test_codeMarkers.R............   33 tests 4 fails 
  Running test_codeMarkers.R............   34 tests 4 fails 
  Running test_codeMarkers.R............   34 tests 4 fails 
  Running test_codeMarkers.R............   34 tests 4 fails 
  Running test_codeMarkers.R............   35 tests 5 fails 
  Running test_codeMarkers.R............   35 tests 5 fails 
  Running test_codeMarkers.R............   35 tests 5 fails 
  Running test_codeMarkers.R............   36 tests 5 fails 
  Running test_codeMarkers.R............   36 tests 5 fails 
  Running test_codeMarkers.R............   37 tests 5 fails 
  Running test_codeMarkers.R............   38 tests 5 fails 
  Running test_codeMarkers.R............   39 tests 5 fails 
  Running test_codeMarkers.R............   40 tests 5 fails 
  Running test_codeMarkers.R............   41 tests 5 fails 
  
  Running test_gData.R..................    0 tests    
  Running test_gData.R..................    0 tests    
  Running test_gData.R..................    0 tests    
  Running test_gData.R..................    0 tests    
  Running test_gData.R..................    0 tests    
  Running test_gData.R..................    0 tests    
  Running test_gData.R..................    0 tests    
  Running test_gData.R..................    0 tests    
  Running test_gData.R..................    1 tests OK 
  Running test_gData.R..................    2 tests OK 
  Running test_gData.R..................    3 tests OK 
  Running test_gData.R..................    4 tests OK 
  Running test_gData.R..................    4 tests OK 
  Running test_gData.R..................    4 tests OK 
  Running test_gData.R..................    5 tests OK 
  Running test_gData.R..................    6 tests OK 
  Running test_gData.R..................    6 tests OK 
  Running test_gData.R..................    6 tests OK 
  Running test_gData.R..................    7 tests OK 
  Running test_gData.R..................    8 tests OK 
  Running test_gData.R..................    9 tests OK 
  Running test_gData.R..................    9 tests OK 
  Running test_gData.R..................   10 tests OK 
  Running test_gData.R..................   11 tests OK 
  Running test_gData.R..................   12 tests OK 
  Running test_gData.R..................   13 tests OK 
  Running test_gData.R..................   14 tests OK 
  Running test_gData.R..................   15 tests OK 
  Running test_gData.R..................   16 tests OK 
  Running test_gData.R..................   16 tests OK 
  Running test_gData.R..................   17 tests OK 
  Running test_gData.R..................   17 tests OK 
  Running test_gData.R..................   17 tests OK 
  Running test_gData.R..................   18 tests OK 
  Running test_gData.R..................   19 tests OK 
  Running test_gData.R..................   19 tests OK 
  Running test_gData.R..................   19 tests OK 
  Running test_gData.R..................   20 tests OK 
  Running test_gData.R..................   21 tests OK 
  Running test_gData.R..................   22 tests OK 
  Running test_gData.R..................   23 tests OK 
  Running test_gData.R..................   23 tests OK 
  Running test_gData.R..................   24 tests OK 
  Running test_gData.R..................   25 tests OK 
  Running test_gData.R..................   25 tests OK 
  Running test_gData.R..................   25 tests OK 
  Running test_gData.R..................   26 tests OK 
  Running test_gData.R..................   27 tests OK 
  Running test_gData.R..................   28 tests OK 
  Running test_gData.R..................   29 tests OK 
  Running test_gData.R..................   30 tests OK 
  Running test_gData.R..................   30 tests OK 
  Running test_gData.R..................   30 tests OK 
  Running test_gData.R..................   31 tests OK 
  Running test_gData.R..................   32 tests OK 
  Running test_gData.R..................   33 tests OK 
  Running test_gData.R..................   34 tests OK 
  Running test_gData.R..................   35 tests OK 
  Running test_gData.R..................   36 tests OK 
  Running test_gData.R..................   37 tests OK 
  Running test_gData.R..................   38 tests OK 
  Running test_gData.R..................   39 tests OK 
  Running test_gData.R..................   40 tests OK 
  Running test_gData.R..................   41 tests OK 
  Running test_gData.R..................   42 tests OK 
  Running test_gData.R..................   43 tests OK 
  Running test_gData.R..................   43 tests OK 
  Running test_gData.R..................   43 tests OK 
  Running test_gData.R..................   44 tests OK 
  Running test_gData.R..................   45 tests OK 
  Running test_gData.R..................   46 tests OK 
  Running test_gData.R..................   47 tests OK 
  Running test_gData.R..................   47 tests OK 
  Running test_gData.R..................   48 tests OK 
  Running test_gData.R..................   49 tests OK 
  Running test_gData.R..................   50 tests OK 
  Running test_gData.R..................   51 tests OK 
  Running test_gData.R..................   51 tests OK 
  Running test_gData.R..................   51 tests OK 
  Running test_gData.R..................   52 tests OK 
  Running test_gData.R..................   53 tests OK 
  Running test_gData.R..................   54 tests OK 
  Running test_gData.R..................   55 tests OK 
  Running test_gData.R..................   56 tests OK 
  Running test_gData.R..................   57 tests OK 
  Running test_gData.R..................   58 tests OK 
  Running test_gData.R..................   59 tests OK 
  Running test_gData.R..................   60 tests OK 
  
  Running test_kinship.R................    0 tests    
  Running test_kinship.R................    1 tests OK 
  Running test_kinship.R................    2 tests OK 
  Running test_kinship.R................    3 tests OK 
  Running test_kinship.R................    4 tests OK 
  Running test_kinship.R................    5 tests OK 
  Running test_kinship.R................    6 tests OK 
  Running test_kinship.R................    7 tests OK 
  Running test_kinship.R................    8 tests OK 
  Running test_kinship.R................    9 tests OK 
  
  Running test_plots.R..................    0 tests    
  Running test_plots.R..................    0 tests    
  Running test_plots.R..................    1 tests OK 
  Running test_plots.R..................    2 tests OK 
  Running test_plots.R..................    3 tests OK 
  Running test_plots.R..................    4 tests OK 
  Running test_plots.R..................    4 tests OK 
  Running test_plots.R..................    4 tests OK 
  Running test_plots.R..................    5 tests OK 
  Running test_plots.R..................    5 tests OK 
  Running test_plots.R..................    6 tests OK 
  Running test_plots.R..................    7 tests OK 
  Running test_plots.R..................    8 tests OK 
  Running test_plots.R..................    8 tests OK 
  Running test_plots.R..................    9 tests OK 
  Running test_plots.R..................    9 tests OK 
  Running test_plots.R..................   10 tests OK 
  Running test_plots.R..................   11 tests OK 
  Running test_plots.R..................   11 tests OK 
  Running test_plots.R..................   12 tests OK 
  Running test_plots.R..................   12 tests OK 
  Running test_plots.R..................   13 tests OK 
  Running test_plots.R..................   14 tests OK 
  Running test_plots.R..................   14 tests OK 
  Running test_plots.R..................   15 tests OK 
  Running test_plots.R..................   15 tests OK 
  Running test_plots.R..................   16 tests OK 
  Running test_plots.R..................   17 tests OK 
  Running test_plots.R..................   18 tests OK 
  Running test_plots.R..................   19 tests OK 
  Running test_plots.R..................   19 tests OK 
  Running test_plots.R..................   20 tests OK 
  Running test_plots.R..................   21 tests OK 
  Running test_plots.R..................   21 tests OK 
  Running test_plots.R..................   22 tests OK 
  Running test_plots.R..................   23 tests OK 
  Running test_plots.R..................   24 tests OK 
  Running test_plots.R..................   24 tests OK 
  Running test_plots.R..................   24 tests OK 
  Running test_plots.R..................   25 tests OK 
  Running test_plots.R..................   25 tests OK 
  Running test_plots.R..................   25 tests OK 
  Running test_plots.R..................   26 tests OK 
  Running test_plots.R..................   27 tests OK 
  Running test_plots.R..................   28 tests OK 
  Running test_plots.R..................   28 tests OK 
  Running test_plots.R..................   28 tests OK 
  Running test_plots.R..................   29 tests OK 
  Running test_plots.R..................   30 tests OK 
  Running test_plots.R..................   31 tests OK 
  Running test_plots.R..................   32 tests OK 
  Running test_plots.R..................   33 tests OK 
  Running test_plots.R..................   34 tests OK 
  Running test_plots.R..................   35 tests OK 
  Running test_plots.R..................   36 tests OK 
  Running test_plots.R..................   37 tests OK 
  Running test_plots.R..................   37 tests OK 
  Running test_plots.R..................   37 tests OK 
  Running test_plots.R..................   38 tests OK 
  Running test_plots.R..................   38 tests OK 
  Running test_plots.R..................   39 tests OK 
  Running test_plots.R..................   40 tests OK 
  Running test_plots.R..................   41 tests OK 
  Running test_plots.R..................   41 tests OK 
  Running test_plots.R..................   42 tests OK 
  Running test_plots.R..................   43 tests OK 
  Running test_plots.R..................   43 tests OK 
  Running test_plots.R..................   44 tests OK 
  Running test_plots.R..................   45 tests OK 
  Running test_plots.R..................   45 tests OK 
  Running test_plots.R..................   46 tests OK 
  Running test_plots.R..................   47 tests OK 
  Running test_plots.R..................   47 tests OK 
  Running test_plots.R..................   48 tests OK 
  Running test_plots.R..................   49 tests OK 
  Running test_plots.R..................   49 tests OK 
  Running test_plots.R..................   50 tests OK 
  Running test_plots.R..................   50 tests OK 
  Running test_plots.R..................   51 tests OK 
  Running test_plots.R..................   51 tests OK 
  Running test_plots.R..................   52 tests OK 
  Running test_plots.R..................   52 tests OK 
  Running test_plots.R..................   52 tests OK 
  
  Running test_utils.R..................    0 tests    
  Running test_utils.R..................    0 tests    
  Running test_utils.R..................    0 tests    
  Running test_utils.R..................    0 tests    
  Running test_utils.R..................    1 tests OK 
  Running test_utils.R..................    2 tests OK 
  Running test_utils.R..................    3 tests OK 
  Running test_utils.R..................    3 tests OK 
  Running test_utils.R..................    4 tests OK 
  Running test_utils.R..................    5 tests OK 
  Running test_utils.R..................    6 tests OK 
  Running test_utils.R..................    6 tests OK 
  Running test_utils.R..................    7 tests OK 
  Running test_utils.R..................    7 tests OK 
  Running test_utils.R..................    8 tests OK 
  Running test_utils.R..................    8 tests OK 
  Running test_utils.R..................    9 tests OK 
  Running test_utils.R..................    9 tests OK 
  Running test_utils.R..................   10 tests OK 
  Running test_utils.R..................   10 tests OK 
  Running test_utils.R..................   11 tests OK 
  Running test_utils.R..................   11 tests OK 
  Running test_utils.R..................   11 tests OK 
  Running test_utils.R..................   11 tests OK 
  Running test_utils.R..................   12 tests OK 
  Running test_utils.R..................   13 tests OK 
  Running test_utils.R..................   13 tests OK 
  Running test_utils.R..................   14 tests OK 
  Running test_utils.R..................   15 tests OK 
  Running test_utils.R..................   16 tests OK 
  Running test_utils.R..................   16 tests OK 
  Running test_utils.R..................   16 tests OK 
  Running test_utils.R..................   16 tests OK 
  Running test_utils.R..................   17 tests OK 
  Running test_utils.R..................   18 tests OK 
  Running test_utils.R..................   19 tests OK 
  Running test_utils.R..................   19 tests OK 
  Running test_utils.R..................   20 tests OK 
  Running test_utils.R..................   21 tests OK 
  Running test_utils.R..................   22 tests OK 
  Running test_utils.R..................   23 tests OK 
  Running test_utils.R..................   23 tests OK 
  Running test_utils.R..................   24 tests OK 
  Running test_utils.R..................   25 tests OK 
  Running test_utils.R..................   26 tests OK 
  Running test_utils.R..................   27 tests OK 
  Running test_utils.R..................   27 tests OK 
  Running test_utils.R..................   28 tests OK 
  Running test_utils.R..................   29 tests OK 
  Running test_utils.R..................   30 tests OK 
  Running test_utils.R..................   31 tests OK 
  Running test_utils.R..................   31 tests OK 
  Running test_utils.R..................   32 tests OK 
  Running test_utils.R..................   33 tests OK 
  Running test_utils.R..................   33 tests OK 
  Running test_utils.R..................   33 tests OK 
  Running test_utils.R..................   34 tests OK 
  Running test_utils.R..................   35 tests OK 
  Running test_utils.R..................   36 tests OK 
  Running test_utils.R..................   36 tests OK 
  Running test_utils.R..................   37 tests OK 
  Running test_utils.R..................   38 tests OK 
  Running test_utils.R..................   38 tests OK 
  Running test_utils.R..................   39 tests OK 
  Running test_utils.R..................   40 tests OK 
  Running test_utils.R..................   40 tests OK 
  Running test_utils.R..................   41 tests OK 
  Running test_utils.R..................   42 tests OK 
  Running test_utils.R..................   43 tests OK 
  Running test_utils.R..................   43 tests OK 
  Running test_utils.R..................   44 tests OK 
  Running test_utils.R..................   45 tests OK 
  Running test_utils.R..................   45 tests OK 
  Running test_utils.R..................   46 tests OK 
  Running test_utils.R..................   47 tests OK 
  Running test_utils.R..................   48 tests OK 
  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
  In addition: Warning messages:
  1: `expand_scale()` is deprecated; use `expansion()` instead. 
  2: `expand_scale()` is deprecated; use `expansion()` instead. 
  3: `expand_scale()` is deprecated; use `expansion()` instead. 
  4: `expand_scale()` is deprecated; use `expansion()` instead. 
  5: `expand_scale()` is deprecated; use `expansion()` instead. 
  6: `expand_scale()` is deprecated; use `expansion()` instead. 
  7: `expand_scale()` is deprecated; use `expansion()` instead. 
  8: `expand_scale()` is deprecated; use `expansion()` instead. 
  9: `expand_scale()` is deprecated; use `expansion()` instead. 
  Execution halted
** running tests for arch 'x64' ... [18s] ERROR
  Running 'tinytest.R' [17s]
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 OK 
  Running test_GWAS.R...................    2 tests OK 
  Running test_GWAS.R...................    2 tests OK 
  Running test_GWAS.R...................    3 tests OK 
  Running test_GWAS.R...................    4 tests OK 
  Running test_GWAS.R...................    5 tests OK 
  Running test_GWAS.R...................    6 tests OK 
  Running test_GWAS.R...................    7 tests OK 
  Running test_GWAS.R...................    8 tests OK 
  Running test_GWAS.R...................    9 tests OK 
  Running test_GWAS.R...................   10 tests OK 
  Running test_GWAS.R...................   11 tests OK 
  Running test_GWAS.R...................   11 tests OK 
  Running test_GWAS.R...................   12 tests OK 
  Running test_GWAS.R...................   13 tests OK 
  Running test_GWAS.R...................   14 tests OK 
  Running test_GWAS.R...................   15 tests OK 
  Running test_GWAS.R...................   15 tests OK 
  Running test_GWAS.R...................   16 tests OK 
  Running test_GWAS.R...................   17 tests OK 
  
  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 OK 
  Running test_STG.R....................    2 tests OK 
  Running test_STG.R....................    3 tests OK 
  Running test_STG.R....................    4 tests OK 
  Running test_STG.R....................    5 tests OK 
  Running test_STG.R....................    6 tests OK 
  Running test_STG.R....................    7 tests OK 
  Running test_STG.R....................    8 tests OK 
  Running test_STG.R....................    9 tests OK 
  Running test_STG.R....................   10 tests OK 
  Running test_STG.R....................   11 tests OK 
  Running test_STG.R....................   12 tests OK 
  Running test_STG.R....................   13 tests OK 
  Running test_STG.R....................   14 tests OK 
  Running test_STG.R....................   15 tests OK 
  Running test_STG.R....................   16 tests OK 
  Running test_STG.R....................   17 tests OK 
  Running test_STG.R....................   18 tests OK 
  Running test_STG.R....................   19 tests OK 
  Running test_STG.R....................   20 tests OK 
  Running test_STG.R....................   21 tests OK 
  Running test_STG.R....................   22 tests OK 
  Running test_STG.R....................   22 tests OK 
  Running test_STG.R....................   22 tests OK 
  Running test_STG.R....................   22 tests OK 
  Running test_STG.R....................   22 tests OK 
  Running test_STG.R....................   22 tests OK 
  Running test_STG.R....................   23 tests OK 
  Running test_STG.R....................   24 tests OK 
  Running test_STG.R....................   25 tests OK 
  Running test_STG.R....................   26 tests OK 
  Running test_STG.R....................   27 tests OK 
  Running test_STG.R....................   28 tests OK 
  Running test_STG.R....................   29 tests OK 
  Running test_STG.R....................   30 tests OK 
  Running test_STG.R....................   31 tests OK 
  Running test_STG.R....................   32 tests OK 
  Running test_STG.R....................   33 tests OK 
  Running test_STG.R....................   34 tests OK 
  Running test_STG.R....................   35 tests OK 
  Running test_STG.R....................   36 tests OK 
  Running test_STG.R....................   37 tests OK 
  Running test_STG.R....................   38 tests OK 
  Running test_STG.R....................   39 tests OK 
  Running test_STG.R....................   40 tests OK 
  Running test_STG.R....................   41 tests OK 
  Running test_STG.R....................   42 tests OK 
  Running test_STG.R....................   43 tests OK 
  Running test_STG.R....................   44 tests OK 
  Running test_STG.R....................   45 tests OK 
  Running test_STG.R....................   46 tests OK 
  Running test_STG.R....................   47 tests OK 
  
  Running test_STGHelper.R..............    0 tests    
  Running test_STGHelper.R..............    0 tests    
  Running test_STGHelper.R..............    0 tests    
  Running test_STGHelper.R..............    1 tests OK 
  Running test_STGHelper.R..............    2 tests OK 
  Running test_STGHelper.R..............    3 tests OK 
  Running test_STGHelper.R..............    3 tests OK 
  Running test_STGHelper.R..............    4 tests OK 
  Running test_STGHelper.R..............    5 tests OK 
  Running test_STGHelper.R..............    6 tests OK 
  Running test_STGHelper.R..............    7 tests OK 
  Running test_STGHelper.R..............    8 tests OK 
  Running test_STGHelper.R..............    9 tests OK 
  Running test_STGHelper.R..............   10 tests OK 
  Running test_STGHelper.R..............   11 tests OK 
  Running test_STGHelper.R..............   12 tests OK 
  Running test_STGHelper.R..............   13 tests OK 
  Running test_STGHelper.R..............   14 tests OK 
  Running test_STGHelper.R..............   14 tests OK 
  Running test_STGHelper.R..............   15 tests OK 
  Running test_STGHelper.R..............   16 tests OK 
  Running test_STGHelper.R..............   17 tests OK 
  Running test_STGHelper.R..............   18 tests OK 
  Running test_STGHelper.R..............   18 tests OK 
  Running test_STGHelper.R..............   19 tests OK 
  Running test_STGHelper.R..............   20 tests OK 
  Running test_STGHelper.R..............   20 tests OK 
  Running test_STGHelper.R..............   20 tests OK 
  Running test_STGHelper.R..............   21 tests OK 
  Running test_STGHelper.R..............   22 tests OK 
  Running test_STGHelper.R..............   23 tests OK 
  Running test_STGHelper.R..............   24 tests OK 
  Running test_STGHelper.R..............   25 tests OK 
  Running test_STGHelper.R..............   26 tests OK 
  Running test_STGHelper.R..............   27 tests OK 
  Running test_STGHelper.R..............   28 tests OK 
  Running test_STGHelper.R..............   29 tests OK 
  Running test_STGHelper.R..............   30 tests OK 
  Running test_STGHelper.R..............   31 tests OK 
  
  Running test_STGoptions.R.............    0 tests    
  Running test_STGoptions.R.............    1 tests OK 
  Running test_STGoptions.R.............    1 tests OK 
  Running test_STGoptions.R.............    1 tests OK 
  Running test_STGoptions.R.............    2 tests OK 
  Running test_STGoptions.R.............    3 tests OK 
  Running test_STGoptions.R.............    4 tests OK 
  Running test_STGoptions.R.............    5 tests OK 
  Running test_STGoptions.R.............    6 tests OK 
  Running test_STGoptions.R.............    6 tests OK 
  Running test_STGoptions.R.............    6 tests OK 
  Running test_STGoptions.R.............    7 tests OK 
  Running test_STGoptions.R.............    8 tests OK 
  Running test_STGoptions.R.............    9 tests OK 
  Running test_STGoptions.R.............   10 tests OK 
  Running test_STGoptions.R.............   11 tests OK 
  Running test_STGoptions.R.............   11 tests OK 
  Running test_STGoptions.R.............   12 tests OK 
  Running test_STGoptions.R.............   13 tests OK 
  Running test_STGoptions.R.............   14 tests OK 
  Running test_STGoptions.R.............   14 tests OK 
  Running test_STGoptions.R.............   15 tests OK 
  Running test_STGoptions.R.............   16 tests OK 
  Running test_STGoptions.R.............   16 tests OK 
  Running test_STGoptions.R.............   17 tests OK 
  Running test_STGoptions.R.............   18 tests OK 
  
  Running test_chkFuncs.R...............    0 tests    
  Running test_chkFuncs.R...............    1 tests OK 
  Running test_chkFuncs.R...............    2 tests OK 
  Running test_chkFuncs.R...............    3 tests OK 
  Running test_chkFuncs.R...............    3 tests OK 
  Running test_chkFuncs.R...............    3 tests OK 
  Running test_chkFuncs.R...............    4 tests OK 
  Running test_chkFuncs.R...............    5 tests OK 
  Running test_chkFuncs.R...............    6 tests OK 
  Running test_chkFuncs.R...............    7 tests OK 
  Running test_chkFuncs.R...............    8 tests OK 
  Running test_chkFuncs.R...............    9 tests OK 
  Running test_chkFuncs.R...............   10 tests OK 
  Running test_chkFuncs.R...............   11 tests OK 
  Running test_chkFuncs.R...............   12 tests OK 
  Running test_chkFuncs.R...............   13 tests OK 
  Running test_chkFuncs.R...............   14 tests OK 
  Running test_chkFuncs.R...............   15 tests OK 
  Running test_chkFuncs.R...............   16 tests OK 
  Running test_chkFuncs.R...............   17 tests OK 
  Running test_chkFuncs.R...............   18 tests OK 
  Running test_chkFuncs.R...............   19 tests OK 
  Running test_chkFuncs.R...............   20 tests OK 
  Running test_chkFuncs.R...............   21 tests OK 
  Running test_chkFuncs.R...............   22 tests OK 
  Running test_chkFuncs.R...............   23 tests OK 
  Running test_chkFuncs.R...............   24 tests OK 
  Running test_chkFuncs.R...............   25 tests OK 
  Running test_chkFuncs.R...............   26 tests OK 
  Running test_chkFuncs.R...............   27 tests OK 
  Running test_chkFuncs.R...............   28 tests OK 
  Running test_chkFuncs.R...............   29 tests OK 
  Running test_chkFuncs.R...............   30 tests OK 
  Running test_chkFuncs.R...............   30 tests OK 
  Running test_chkFuncs.R...............   31 tests OK 
  Running test_chkFuncs.R...............   31 tests OK 
  Running test_chkFuncs.R...............   32 tests OK 
  Running test_chkFuncs.R...............   33 tests OK 
  Running test_chkFuncs.R...............   34 tests OK 
  Running test_chkFuncs.R...............   35 tests OK 
  Running test_chkFuncs.R...............   36 tests OK 
  Running test_chkFuncs.R...............   37 tests OK 
  Running test_chkFuncs.R...............   38 tests OK 
  Running test_chkFuncs.R...............   39 tests OK 
  Running test_chkFuncs.R...............   40 tests OK 
  Running test_chkFuncs.R...............   41 tests OK 
  Running test_chkFuncs.R...............   42 tests OK 
  Running test_chkFuncs.R...............   43 tests OK 
  
  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    
  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............    1 tests 1 fails 
  Running test_codeMarkers.R............    2 tests 1 fails 
  Running test_codeMarkers.R............    3 tests 1 fails 
  Running test_codeMarkers.R............    4 tests 1 fails 
  Running test_codeMarkers.R............    5 tests 1 fails 
  Running test_codeMarkers.R............    6 tests 1 fails 
  Running test_codeMarkers.R............    7 tests 1 fails 
  Running test_codeMarkers.R............    8 tests 1 fails 
  Running test_codeMarkers.R............    9 tests 1 fails 
  Running test_codeMarkers.R............   10 tests 1 fails 
  Running test_codeMarkers.R............   11 tests 1 fails 
  Running test_codeMarkers.R............   12 tests 1 fails 
  Running test_codeMarkers.R............   13 tests 1 fails 
  Running test_codeMarkers.R............   14 tests 2 fails 
  Running test_codeMarkers.R............   14 tests 2 fails 
  Running test_codeMarkers.R............   15 tests 2 fails 
  Running test_codeMarkers.R............   16 tests 2 fails 
  Running test_codeMarkers.R............   17 tests 3 fails 
  Running test_codeMarkers.R............   18 tests 3 fails 
  Running test_codeMarkers.R............   19 tests 3 fails 
  Running test_codeMarkers.R............   19 tests 3 fails 
  Running test_codeMarkers.R............   19 tests 3 fails 
  Running test_codeMarkers.R............   20 tests 3 fails 
  Running test_codeMarkers.R............   21 tests 3 fails 
  Running test_codeMarkers.R............   22 tests 4 fails 
  Running test_codeMarkers.R............   23 tests 4 fails 
  Running test_codeMarkers.R............   24 tests 4 fails 
  Running test_codeMarkers.R............   25 tests 4 fails 
  Running test_codeMarkers.R............   26 tests 4 fails 
  Running test_codeMarkers.R............   27 tests 4 fails 
  Running test_codeMarkers.R............   28 tests 4 fails 
  Running test_codeMarkers.R............   29 tests 4 fails 
  Running test_codeMarkers.R............   30 tests 4 fails 
  Running test_codeMarkers.R............   31 tests 4 fails 
  Running test_codeMarkers.R............   32 tests 4 fails 
  Running test_codeMarkers.R............   33 tests 4 fails 
  Running test_codeMarkers.R............   34 tests 4 fails 
  Running test_codeMarkers.R............   34 tests 4 fails 
  Running test_codeMarkers.R............   34 tests 4 fails 
  Running test_codeMarkers.R............   35 tests 5 fails 
  Running test_codeMarkers.R............   35 tests 5 fails 
  Running test_codeMarkers.R............   35 tests 5 fails 
  Running test_codeMarkers.R............   36 tests 5 fails 
  Running test_codeMarkers.R............   36 tests 5 fails 
  Running test_codeMarkers.R............   37 tests 5 fails 
  Running test_codeMarkers.R............   38 tests 5 fails 
  Running test_codeMarkers.R............   39 tests 5 fails 
  Running test_codeMarkers.R............   40 tests 5 fails 
  Running test_codeMarkers.R............   41 tests 5 fails 
  
  Running test_gData.R..................    0 tests    
  Running test_gData.R..................    0 tests    
  Running test_gData.R..................    0 tests    
  Running test_gData.R..................    0 tests    
  Running test_gData.R..................    0 tests    
  Running test_gData.R..................    0 tests    
  Running test_gData.R..................    0 tests    
  Running test_gData.R..................    0 tests    
  Running test_gData.R..................    1 tests OK 
  Running test_gData.R..................    2 tests OK 
  Running test_gData.R..................    3 tests OK 
  Running test_gData.R..................    4 tests OK 
  Running test_gData.R..................    4 tests OK 
  Running test_gData.R..................    4 tests OK 
  Running test_gData.R..................    5 tests OK 
  Running test_gData.R..................    6 tests OK 
  Running test_gData.R..................    6 tests OK 
  Running test_gData.R..................    6 tests OK 
  Running test_gData.R..................    7 tests OK 
  Running test_gData.R..................    8 tests OK 
  Running test_gData.R..................    9 tests OK 
  Running test_gData.R..................    9 tests OK 
  Running test_gData.R..................   10 tests OK 
  Running test_gData.R..................   11 tests OK 
  Running test_gData.R..................   12 tests OK 
  Running test_gData.R..................   13 tests OK 
  Running test_gData.R..................   14 tests OK 
  Running test_gData.R..................   15 tests OK 
  Running test_gData.R..................   16 tests OK 
  Running test_gData.R..................   16 tests OK 
  Running test_gData.R..................   17 tests OK 
  Running test_gData.R..................   17 tests OK 
  Running test_gData.R..................   17 tests OK 
  Running test_gData.R..................   18 tests OK 
  Running test_gData.R..................   19 tests OK 
  Running test_gData.R..................   19 tests OK 
  Running test_gData.R..................   19 tests OK 
  Running test_gData.R..................   20 tests OK 
  Running test_gData.R..................   21 tests OK 
  Running test_gData.R..................   22 tests OK 
  Running test_gData.R..................   23 tests OK 
  Running test_gData.R..................   23 tests OK 
  Running test_gData.R..................   24 tests OK 
  Running test_gData.R..................   25 tests OK 
  Running test_gData.R..................   25 tests OK 
  Running test_gData.R..................   25 tests OK 
  Running test_gData.R..................   26 tests OK 
  Running test_gData.R..................   27 tests OK 
  Running test_gData.R..................   28 tests OK 
  Running test_gData.R..................   29 tests OK 
  Running test_gData.R..................   30 tests OK 
  Running test_gData.R..................   30 tests OK 
  Running test_gData.R..................   30 tests OK 
  Running test_gData.R..................   31 tests OK 
  Running test_gData.R..................   32 tests OK 
  Running test_gData.R..................   33 tests OK 
  Running test_gData.R..................   34 tests OK 
  Running test_gData.R..................   35 tests OK 
  Running test_gData.R..................   36 tests OK 
  Running test_gData.R..................   37 tests OK 
  Running test_gData.R..................   38 tests OK 
  Running test_gData.R..................   39 tests OK 
  Running test_gData.R..................   40 tests OK 
  Running test_gData.R..................   41 tests OK 
  Running test_gData.R..................   42 tests OK 
  Running test_gData.R..................   43 tests OK 
  Running test_gData.R..................   43 tests OK 
  Running test_gData.R..................   43 tests OK 
  Running test_gData.R..................   44 tests OK 
  Running test_gData.R..................   45 tests OK 
  Running test_gData.R..................   46 tests OK 
  Running test_gData.R..................   47 tests OK 
  Running test_gData.R..................   47 tests OK 
  Running test_gData.R..................   48 tests OK 
  Running test_gData.R..................   49 tests OK 
  Running test_gData.R..................   50 tests OK 
  Running test_gData.R..................   51 tests OK 
  Running test_gData.R..................   51 tests OK 
  Running test_gData.R..................   51 tests OK 
  Running test_gData.R..................   52 tests OK 
  Running test_gData.R..................   53 tests OK 
  Running test_gData.R..................   54 tests OK 
  Running test_gData.R..................   55 tests OK 
  Running test_gData.R..................   56 tests OK 
  Running test_gData.R..................   57 tests OK 
  Running test_gData.R..................   58 tests OK 
  Running test_gData.R..................   59 tests OK 
  Running test_gData.R..................   60 tests OK 
  
  Running test_kinship.R................    0 tests    
  Running test_kinship.R................    1 tests OK 
  Running test_kinship.R................    2 tests OK 
  Running test_kinship.R................    3 tests OK 
  Running test_kinship.R................    4 tests OK 
  Running test_kinship.R................    5 tests OK 
  Running test_kinship.R................    6 tests OK 
  Running test_kinship.R................    7 tests OK 
  Running test_kinship.R................    8 tests OK 
  Running test_kinship.R................    9 tests OK 
  
  Running test_plots.R..................    0 tests    
  Running test_plots.R..................    0 tests    
  Running test_plots.R..................    1 tests OK 
  Running test_plots.R..................    2 tests OK 
  Running test_plots.R..................    3 tests OK 
  Running test_plots.R..................    4 tests OK 
  Running test_plots.R..................    4 tests OK 
  Running test_plots.R..................    4 tests OK 
  Running test_plots.R..................    5 tests OK 
  Running test_plots.R..................    5 tests OK 
  Running test_plots.R..................    6 tests OK 
  Running test_plots.R..................    7 tests OK 
  Running test_plots.R..................    8 tests OK 
  Running test_plots.R..................    8 tests OK 
  Running test_plots.R..................    9 tests OK 
  Running test_plots.R..................    9 tests OK 
  Running test_plots.R..................   10 tests OK 
  Running test_plots.R..................   11 tests OK 
  Running test_plots.R..................   11 tests OK 
  Running test_plots.R..................   12 tests OK 
  Running test_plots.R..................   12 tests OK 
  Running test_plots.R..................   13 tests OK 
  Running test_plots.R..................   14 tests OK 
  Running test_plots.R..................   14 tests OK 
  Running test_plots.R..................   15 tests OK 
  Running test_plots.R..................   15 tests OK 
  Running test_plots.R..................   16 tests OK 
  Running test_plots.R..................   17 tests OK 
  Running test_plots.R..................   18 tests OK 
  Running test_plots.R..................   19 tests OK 
  Running test_plots.R..................   19 tests OK 
  Running test_plots.R..................   20 tests OK 
  Running test_plots.R..................   21 tests OK 
  Running test_plots.R..................   21 tests OK 
  Running test_plots.R..................   22 tests OK 
  Running test_plots.R..................   23 tests OK 
  Running test_plots.R..................   24 tests OK 
  Running test_plots.R..................   24 tests OK 
  Running test_plots.R..................   24 tests OK 
  Running test_plots.R..................   25 tests OK 
  Running test_plots.R..................   25 tests OK 
  Running test_plots.R..................   25 tests OK 
  Running test_plots.R..................   26 tests OK 
  Running test_plots.R..................   27 tests OK 
  Running test_plots.R..................   28 tests OK 
  Running test_plots.R..................   28 tests OK 
  Running test_plots.R..................   28 tests OK 
  Running test_plots.R..................   29 tests OK 
  Running test_plots.R..................   30 tests OK 
  Running test_plots.R..................   31 tests OK 
  Running test_plots.R..................   32 tests OK 
  Running test_plots.R..................   33 tests OK 
  Running test_plots.R..................   34 tests OK 
  Running test_plots.R..................   35 tests OK 
  Running test_plots.R..................   36 tests OK 
  Running test_plots.R..................   37 tests OK 
  Running test_plots.R..................   37 tests OK 
  Running test_plots.R..................   37 tests OK 
  Running test_plots.R..................   38 tests OK 
  Running test_plots.R..................   38 tests OK 
  Running test_plots.R..................   39 tests OK 
  Running test_plots.R..................   40 tests OK 
  Running test_plots.R..................   41 tests OK 
  Running test_plots.R..................   41 tests OK 
  Running test_plots.R..................   42 tests OK 
  Running test_plots.R..................   43 tests OK 
  Running test_plots.R..................   43 tests OK 
  Running test_plots.R..................   44 tests OK 
  Running test_plots.R..................   45 tests OK 
  Running test_plots.R..................   45 tests OK 
  Running test_plots.R..................   46 tests OK 
  Running test_plots.R..................   47 tests OK 
  Running test_plots.R..................   47 tests OK 
  Running test_plots.R..................   48 tests OK 
  Running test_plots.R..................   49 tests OK 
  Running test_plots.R..................   49 tests OK 
  Running test_plots.R..................   50 tests OK 
  Running test_plots.R..................   50 tests OK 
  Running test_plots.R..................   51 tests OK 
  Running test_plots.R..................   51 tests OK 
  Running test_plots.R..................   52 tests OK 
  Running test_plots.R..................   52 tests OK 
  Running test_plots.R..................   52 tests OK 
  
  Running test_utils.R..................    0 tests    
  Running test_utils.R..................    0 tests    
  Running test_utils.R..................    0 tests    
  Running test_utils.R..................    0 tests    
  Running test_utils.R..................    1 tests OK 
  Running test_utils.R..................    2 tests OK 
  Running test_utils.R..................    3 tests OK 
  Running test_utils.R..................    3 tests OK 
  Running test_utils.R..................    4 tests OK 
  Running test_utils.R..................    5 tests OK 
  Running test_utils.R..................    6 tests OK 
  Running test_utils.R..................    6 tests OK 
  Running test_utils.R..................    7 tests OK 
  Running test_utils.R..................    7 tests OK 
  Running test_utils.R..................    8 tests OK 
  Running test_utils.R..................    8 tests OK 
  Running test_utils.R..................    9 tests OK 
  Running test_utils.R..................    9 tests OK 
  Running test_utils.R..................   10 tests OK 
  Running test_utils.R..................   10 tests OK 
  Running test_utils.R..................   11 tests OK 
  Running test_utils.R..................   11 tests OK 
  Running test_utils.R..................   11 tests OK 
  Running test_utils.R..................   11 tests OK 
  Running test_utils.R..................   12 tests OK 
  Running test_utils.R..................   13 tests OK 
  Running test_utils.R..................   13 tests OK 
  Running test_utils.R..................   14 tests OK 
  Running test_utils.R..................   15 tests OK 
  Running test_utils.R..................   16 tests OK 
  Running test_utils.R..................   16 tests OK 
  Running test_utils.R..................   16 tests OK 
  Running test_utils.R..................   16 tests OK 
  Running test_utils.R..................   17 tests OK 
  Running test_utils.R..................   18 tests OK 
  Running test_utils.R..................   19 tests OK 
  Running test_utils.R..................   19 tests OK 
  Running test_utils.R..................   20 tests OK 
  Running test_utils.R..................   21 tests OK 
  Running test_utils.R..................   22 tests OK 
  Running test_utils.R..................   23 tests OK 
  Running test_utils.R..................   23 tests OK 
  Running test_utils.R..................   24 tests OK 
  Running test_utils.R..................   25 tests OK 
  Running test_utils.R..................   26 tests OK 
  Running test_utils.R..................   27 tests OK 
  Running test_utils.R..................   27 tests OK 
  Running test_utils.R..................   28 tests OK 
  Running test_utils.R..................   29 tests OK 
  Running test_utils.R..................   30 tests OK 
  Running test_utils.R..................   31 tests OK 
  Running test_utils.R..................   31 tests OK 
  Running test_utils.R..................   32 tests OK 
  Running test_utils.R..................   33 tests OK 
  Running test_utils.R..................   33 tests OK 
  Running test_utils.R..................   33 tests OK 
  Running test_utils.R..................   34 tests OK 
  Running test_utils.R..................   35 tests OK 
  Running test_utils.R..................   36 tests OK 
  Running test_utils.R..................   36 tests OK 
  Running test_utils.R..................   37 tests OK 
  Running test_utils.R..................   38 tests OK 
  Running test_utils.R..................   38 tests OK 
  Running test_utils.R..................   39 tests OK 
  Running test_utils.R..................   40 tests OK 
  Running test_utils.R..................   40 tests OK 
  Running test_utils.R..................   41 tests OK 
  Running test_utils.R..................   42 tests OK 
  Running test_utils.R..................   43 tests OK 
  Running test_utils.R..................   43 tests OK 
  Running test_utils.R..................   44 tests OK 
  Running test_utils.R..................   45 tests OK 
  Running test_utils.R..................   45 tests OK 
  Running test_utils.R..................   46 tests OK 
  Running test_utils.R..................   47 tests OK 
  Running test_utils.R..................   48 tests OK 
  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
  In addition: Warning messages:
  1: `expand_scale()` is deprecated; use `expansion()` instead. 
  2: `expand_scale()` is deprecated; use `expansion()` instead. 
  3: `expand_scale()` is deprecated; use `expansion()` instead. 
  4: `expand_scale()` is deprecated; use `expansion()` instead. 
  5: `expand_scale()` is deprecated; use `expansion()` instead. 
  6: `expand_scale()` is deprecated; use `expansion()` instead. 
  7: `expand_scale()` is deprecated; use `expansion()` instead. 
  8: `expand_scale()` is deprecated; use `expansion()` instead. 
  9: `expand_scale()` is deprecated; use `expansion()` instead. 
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [112s] OK
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 NOTE