CRAN Package Check Results for Package genetics

Last updated on 2019-04-22 01:47:39 CEST.

Check Details

Version: 1.3.8.1.1
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: 'GeneticsDesign'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.3.8.1.1
Check: tests
Result: ERROR
     Running 'ci.balance.R' [1s/1s]
     Running 'makeGenotype_with_sep.R' [1s/1s]
     Running 'test.NA.R' [1s/1s]
    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: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
    
     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
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64

Version: 1.3.8.1.1
Check: tests
Result: ERROR
     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: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
    
     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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.3.8.1.1
Check: tests
Result: ERROR
     Running 'ci.balance.R' [1s]
     Running 'makeGenotype_with_sep.R' [1s]
     Running 'test.NA.R' [1s]
    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
Flavor: r-devel-windows-ix86+x86_64

Version: 1.3.8.1.1
Check: tests
Result: ERROR
     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
Flavor: r-patched-solaris-x86

Version: 1.3.8.1.1
Check: Rd \usage sections
Result: NOTE
    S3 methods shown with full name in documentation object 'diseq':
     ‘diseq.ci’
    
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64