Running 'ci.balance.R' [169s]
  Running 'makeGenotype_with_sep.R' [160s]
  Running 'test.NA.R' [0s]
Running the tests in 'tests/ci.balance.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
  
  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(7981357)
  > x <- abs(rnorm(100,1))
  > ci.balance(x,1, minval=0)
  $ci
          2%        98% 
  0.05844961 3.08604216 
  
  $overflow.upper
  [1] 0
  
  $overflow.lower
  [1] 0
  
  $n.above
  [1] 50
  
  $n.below
  [1] 50
  
  $lower.n
  [1] 2
  
  $upper.n
  [1] 98
  
  > ci.balance(x,1)
  $ci
          2%        98% 
  0.05844961 3.08604216 
  
  $overflow.upper
  [1] 0
  
  $overflow.lower
  [1] 0
  
  $n.above
  [1] 50
  
  $n.below
  [1] 50
  
  $lower.n
  [1] 2
  
  $upper.n
  [1] 98
  
  > 
  > x <- rnorm(100,1)
  > x <- ifelse(x>1, 1, x)
  > ci.balance(x,1, maxval=1)
  $ci
              5% Upper Boundary 
      -0.6396774      1.0000000 
  
  $overflow.upper
  [1] 25.5
  
  $overflow.lower
  [1] 0
  
  $n.above
  [1] 22
  
  $n.below
  [1] 78
  
  $lower.n
  [1] 5
  
  $upper.n
  [1] "Upper Boundary"
  
  > ci.balance(x,1)
  $ci
          5%     max(x) 
  -0.6396774  1.0000000 
  
  $overflow.upper
  [1] 25.5
  
  $overflow.lower
  [1] 0
  
  $n.above
  [1] 22
  
  $n.below
  [1] 78
  
  $lower.n
  [1] 5
  
  $upper.n
  [1] "max(x)"
  
  > 
  > proc.time()
     user  system elapsed 
     0.31    0.09    0.39 
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
  
  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
  
  > 
  > suppressWarnings(RNGversion("3.5.0"))
  > 
  > 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     Trt2  T/T  0.77962192 88 138 / 140 T /T                            
  2     Trt2  T/T  1.45578508 52 142 / 140 T /A                            
  3     Trt2 <NA> -0.64432843  1 146 / 134 A /T                            
  4     Trt2  T/A -1.55313741  2 142 / 142 T /T                            
  5     Trt1  T/A -1.59770952 15 140 / 142 A /T Possible Bad Data/Lab Error
  6  Control  T/T  1.80509752 31 146 / 146 T /A Possible Bad Data/Lab Error
  7  Control  T/A -0.48164736 83 142 / 146 T /A                            
  8     Trt1  T/A  0.62037980 51 146 / 134 T /T Possible Bad Data/Lab Error
  9     Trt2  A/T  0.61212349 81 138 / 138 T /A                            
  10    Trt2  T/T -0.16231098  7 138 / 142 T /T Possible Bad Data/Lab Error
  11 Control <NA>  0.81187318 93 142 / 134 T /A                            
  12 Control  A/T  2.19683355 81 138 / 142 T /T Possible Bad Data/Lab Error
  13    Trt2  A/T  2.04919034  8 142 / 146 T /A                            
  14 Control  T/A  1.63244564 61 138 / 142 T /T Possible Bad Data/Lab Error
  15    Trt1  T/T  0.25427119 72 142 / 146 A /T Possible Bad Data/Lab Error
  16    Trt1  T/T  0.49118828 52 146 / 146 T /A                            
  17    Trt1 <NA> -0.32408658 73 146 / 142 T /A                            
  18    Trt1 <NA> -1.66205024 75 140 / 134 T /T                            
  19 Control  T/A  1.76773385 10 134 / 134 T /A                            
  20    Trt2  A/T  0.02580105 40 138 / 146 T /T                            
  > 
  > 
  > # now automatically convert genotype columns
  > geno1 <- makeGenotypes(test1)
  > geno1
         Tmt   G1          N1 I1      G2  G3                     comment
  1     Trt2  T/T  0.77962192 88 138/140 T/T                            
  2     Trt2  T/T  1.45578508 52 142/140 T/A                            
  3     Trt2 <NA> -0.64432843  1 146/134 T/A                            
  4     Trt2  T/A -1.55313741  2 142/142 T/T                            
  5     Trt1  T/A -1.59770952 15 142/140 T/A Possible Bad Data/Lab Error
  6  Control  T/T  1.80509752 31 146/146 T/A Possible Bad Data/Lab Error
  7  Control  T/A -0.48164736 83 142/146 T/A                            
  8     Trt1  T/A  0.62037980 51 146/134 T/T Possible Bad Data/Lab Error
  9     Trt2  T/A  0.61212349 81 138/138 T/A                            
  10    Trt2  T/T -0.16231098  7 142/138 T/T Possible Bad Data/Lab Error
  11 Control <NA>  0.81187318 93 142/134 T/A                            
  12 Control  T/A  2.19683355 81 142/138 T/T Possible Bad Data/Lab Error
  13    Trt2  T/A  2.04919034  8 142/146 T/A                            
  14 Control  T/A  1.63244564 61 142/138 T/T Possible Bad Data/Lab Error
  15    Trt1  T/T  0.25427119 72 142/146 T/A Possible Bad Data/Lab Error
  16    Trt1  T/T  0.49118828 52 146/146 T/A                            
  17    Trt1 <NA> -0.32408658 73 142/146 T/A                            
  18    Trt1 <NA> -1.66205024 75 134/140 T/T                            
  19 Control  T/A  1.76773385 10 134/134 T/A                            
  20    Trt2  T/A  0.02580105 40 146/138 T/T                            
  > 
  > 
  > 
  > 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))
  > 
  > 
  > proc.time()
     user  system elapsed 
     0.28    0.09    0.36