Running ‘ci.balance.R’
  Running ‘makeGenotype_with_sep.R’
  Running ‘test.NA.R’
Running the tests in ‘tests/makeGenotype_with_sep.R’ failed.
Complete output:
  > library(genetics)
  Loading required package: combinat
  
  Attaching package: 'combinat'
  
  The following object is masked from 'package:utils':
  
      combn
  
  Loading required package: gdata
  gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
  
  gdata: Unable to load perl libaries needed by read.xls()
  gdata: to support 'XLSX' (Excel 2007+) files.
  
  gdata: Run the function 'installXLSXsupport()'
  gdata: to automatically download and install the perl
  gdata: libaries needed to support Excel XLS and XLSX formats.
  
  Attaching package: 'gdata'
  
  The following object is masked from 'package:stats':
  
      nobs
  
  The following object is masked from 'package:utils':
  
      object.size
  
  The following object is masked from 'package:base':
  
      startsWith
  
  Loading required package: gtools
  Loading required package: MASS
  Loading required package: mvtnorm
  
  
  NOTE: THIS PACKAGE IS NOW OBSOLETE.
  
  
  
    The R-Genetics project has developed an set of enhanced genetics
  
    packages to replace 'genetics'. Please visit the project homepage
  
    at http://rgenetics.org for informtion.
  
  
  
  
  Attaching package: 'genetics'
  
  The following objects are masked from 'package:base':
  
      %in%, as.factor, order
  
  > 
  > set.seed(12345)
  > 
  > # Create a test data set where there are several genotypes in columns
  > # of the form "A/T".
  > test1 <- data.frame(Tmt=sample(c("Control","Trt1","Trt2"),20, replace=TRUE),
  +                 G1=sample(c("A/T","T/T","T/A",NA),20, replace=TRUE),
  +                 N1=rnorm(20),
  +                 I1=sample(1:100,20,replace=TRUE),
  +                 G2=paste(sample(c("134","138","140","142","146"),20,
  +                                 replace=TRUE),
  +                          sample(c("134","138","140","142","146"),20,
  +                                 replace=TRUE),
  +                          sep=" / "),
  +                 G3=sample(c("A /T","T /T","T /A"),20, replace=TRUE),
  +                 comment=sample(c("Possible Bad Data/Lab Error",""),20,
  +                                rep=TRUE)
  +                 )
  > test1
         Tmt   G1           N1 I1        G2   G3                     comment
  1     Trt1  A/T  0.943560542 46 146 / 140 T /T Possible Bad Data/Lab Error
  2     Trt2  T/T -0.795967523 87 134 / 138 A /T                            
  3     Trt1  A/T -0.001902476 12 138 / 140 T /T Possible Bad Data/Lab Error
  4     Trt1 <NA> -1.402814741 90 138 / 146 A /T Possible Bad Data/Lab Error
  5  Control <NA> -0.717345556 88 134 / 134 A /T Possible Bad Data/Lab Error
  6     Trt2  T/T -0.647406880 99 142 / 134 T /A Possible Bad Data/Lab Error
  7     Trt1  T/A  0.696281587  5 134 / 142 A /T Possible Bad Data/Lab Error
  8     Trt1 <NA> -0.775751569 68 134 / 142 A /T Possible Bad Data/Lab Error
  9     Trt2 <NA> -1.038761036 11 140 / 142 T /T Possible Bad Data/Lab Error
  10    Trt1  T/T  1.611189208 49 138 / 142 T /A Possible Bad Data/Lab Error
  11    Trt2 <NA>  0.013871425 67 146 / 138 T /T Possible Bad Data/Lab Error
  12    Trt1  T/T -0.423939312 74 138 / 142 A /T                            
  13    Trt1 <NA>  0.302717823 15 134 / 146 T /T                            
  14 Control  T/A  0.398747884  7 138 / 146 T /T Possible Bad Data/Lab Error
  15    Trt2 <NA> -1.036012262 42 142 / 146 T /T Possible Bad Data/Lab Error
  16    Trt1  A/T  0.036207825 90 142 / 140 A /T Possible Bad Data/Lab Error
  17    Trt1 <NA> -2.070671332 55 138 / 140 T /T                            
  18 Control  A/T -0.509982788  4 142 / 142 A /T                            
  19    Trt1 <NA>  0.005877185 92 140 / 146 A /T                            
  20    Trt2 <NA> -1.549423415  4 142 / 142 T /A Possible Bad Data/Lab Error
  > 
  > 
  > # now automatically convert genotype columns
  > geno1 <- makeGenotypes(test1)
  > geno1
         Tmt   G1           N1 I1      G2  G3                  comment
  1     Trt1  A/T  0.943560542 46 146/140 T/T PossibleBadData/LabError
  2     Trt2  T/T -0.795967523 87 138/134 T/A                     <NA>
  3     Trt1  A/T -0.001902476 12 138/140 T/T PossibleBadData/LabError
  4     Trt1 <NA> -1.402814741 90 138/146 T/A PossibleBadData/LabError
  5  Control <NA> -0.717345556 88 134/134 T/A PossibleBadData/LabError
  6     Trt2  T/T -0.647406880 99 142/134 T/A PossibleBadData/LabError
  7     Trt1  T/A  0.696281587  5 142/134 T/A PossibleBadData/LabError
  8     Trt1 <NA> -0.775751569 68 142/134 T/A PossibleBadData/LabError
  9     Trt2 <NA> -1.038761036 11 142/140 T/T PossibleBadData/LabError
  10    Trt1  T/T  1.611189208 49 142/138 T/A PossibleBadData/LabError
  11    Trt2 <NA>  0.013871425 67 138/146 T/T PossibleBadData/LabError
  12    Trt1  T/T -0.423939312 74 142/138 T/A                     <NA>
  13    Trt1 <NA>  0.302717823 15 146/134 T/T                     <NA>
  14 Control  T/A  0.398747884  7 138/146 T/T PossibleBadData/LabError
  15    Trt2 <NA> -1.036012262 42 142/146 T/T PossibleBadData/LabError
  16    Trt1  A/T  0.036207825 90 142/140 T/A PossibleBadData/LabError
  17    Trt1 <NA> -2.070671332 55 138/140 T/T                     <NA>
  18 Control  A/T -0.509982788  4 142/142 T/A                     <NA>
  19    Trt1 <NA>  0.005877185 92 146/140 T/A                     <NA>
  20    Trt2 <NA> -1.549423415  4 142/142 T/A PossibleBadData/LabError
  > 
  > 
  > 
  > set.seed(12345)
  > 
  > # Create a test data set where there are several genotypes in columns
  > # of the form "A_T".
  > test1.b <- data.frame(Tmt=sample(c("Control","Trt1","Trt2"),20, replace=TRUE),
  +                 G1=sample(c("A_T","T_T","T_A",NA),20, replace=TRUE),
  +                 N1=rnorm(20),
  +                 I1=sample(1:100,20,replace=TRUE),
  +                 G2=paste(sample(c("134","138","140","142","146"),20,
  +                                 replace=TRUE),
  +                          sample(c("134","138","140","142","146"),20,
  +                                 replace=TRUE),
  +                          sep=" _ "),
  +                 G3=sample(c("A _T","T _T","T _A"),20, replace=TRUE),
  +                 comment=sample(c("Possible Bad Data/Lab Error",""),20,
  +                                rep=TRUE)
  +                 )
  > # now automatically convert genotype columns
  > geno1.b <- makeGenotypes(test1.b, sep="_")
  > 
  > stopifnot(identical(geno1,geno1.b))
  Error: identical(geno1, geno1.b) is not TRUE
  Execution halted