Running examples in ‘RAINBOWR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RGWAS.multisnp
> ### Title: Testing multiple SNPs simultaneously for GWAS
> ### Aliases: RGWAS.multisnp
> 
> ### ** Examples
> 
> ## Don't show: 
>   ### Import RAINBOWR
>   require(RAINBOWR)
>   
>   ### Load example datasets
>   data("Rice_Zhao_etal")
>   Rice_geno_score <- Rice_Zhao_etal$genoScore
>   Rice_geno_map <- Rice_Zhao_etal$genoMap
>   Rice_pheno <- Rice_Zhao_etal$pheno
>   
>   
>   ### Select one trait for example
>   trait.name <- "Flowering.time.at.Arkansas"
>   y <- as.matrix(Rice_pheno[1:30, trait.name, drop = FALSE])
>   # use first 30 accessions
>   
>   
>   ### Remove SNPs whose MAF <= 0.05
>   x.0 <- t(Rice_geno_score)
>   MAF.cut.res <- MAF.cut(x.0 = x.0, map.0 = Rice_geno_map)
>   x <- MAF.cut.res$x
>   map <- MAF.cut.res$map
>   
>   
>   ### Estimate genomic relationship matrix (GRM)
>   K.A <- calcGRM(genoMat = x)
>   
>   
>   ### Modify data
>   modify.data.res <- modify.data(pheno.mat = y, geno.mat = x, map = map,
+                                  return.ZETA = TRUE, return.GWAS.format = TRUE)
Warning in modify.data(pheno.mat = y, geno.mat = x, map = map, return.ZETA = TRUE,  :
  The following lines have phenotypes but no genotypes:  L14, L31, L33
>   pheno.GWAS <- modify.data.res$pheno.GWAS
>   geno.GWAS <- modify.data.res$geno.GWAS[1:300, ]  ### first 300 SNPs
>   ZETA <- modify.data.res$ZETA
>   
>   
>   
>   ### Perform SNP-set GWAS (by regarding 41 SNPs as one SNP-set)
>   SNP_set.res <- RGWAS.multisnp(pheno = pheno.GWAS, geno = geno.GWAS,
+                                 ZETA = ZETA, n.PC = 4, test.method = "LR",
+                                 kernel.method = "linear", gene.set = NULL,
+                                 test.effect = "additive", window.size.half = 10,
+                                 window.slide = 21, plot.Manhattan = FALSE,
+                                 plot.qq = FALSE, verbose = FALSE,
+                                 count = FALSE, time = FALSE)
> ## End(Don't show)
> 
> 
> ## No test: 
>   ### Import RAINBOWR
>   require(RAINBOWR)
>   
>   ### Load example datasets
>   data("Rice_Zhao_etal")
>   Rice_geno_score <- Rice_Zhao_etal$genoScore
>   Rice_geno_map <- Rice_Zhao_etal$genoMap
>   Rice_pheno <- Rice_Zhao_etal$pheno
>   
>   ### View each dataset
>   See(Rice_geno_score)
                 L1        L2        L3        L4        L5        L6
class     <integer> <integer> <integer> <integer> <integer> <integer>
id1000223         1         1        -1        -1        -1        -1
id1000556        -1        -1         1         1        -1         1
id1000673        -1         1        -1         1        -1         1
id1000830        -1         1         1         1         1         1
id1000955        -1         1         1         1        -1         1
id1001073        -1        -1        -1         1         1        -1
[1] "class: data.frame"
[1] "dimension: 1311 x 395"
>   See(Rice_geno_map)
             marker       chr       pos
class      <factor> <integer> <integer>
id1000223 id1000223         1    420422
id1000556 id1000556         1    655693
id1000673 id1000673         1    740153
id1000830 id1000830         1    913806
id1000955 id1000955         1   1041748
id1001073 id1001073         1   1172387
[1] "class: data.frame"
[1] "dimension: 1311 x 3"
>   See(Rice_pheno)
      Flowering.time.at.Arkansas Flowering.time.at.Faridpur
class                  <numeric>                  <integer>
L1                   75.08333333                         64
L3                          89.5                         66
L4                          94.5                         67
L5                          87.5                         70
L6                   89.08333333                         73
L7                           105                       <NA>
      Flowering.time.at.Aberdeen FT.ratio.of.Arkansas.Aberdeen
class                  <integer>                     <numeric>
L1                            81                   0.926954733
L3                            83                   1.078313253
L4                            93                   1.016129032
L5                           108                   0.810185185
L6                           101                   0.882013201
L7                           158                   0.664556962
      FT.ratio.of.Faridpur.Aberdeen Culm.habit
class                     <numeric>  <numeric>
L1                      0.790123457          4
L3                      0.795180723        7.5
L4                      0.720430108          6
L5                      0.648148148        3.5
L6                      0.722772277          6
L7                             <NA>          3
[1] "class: data.frame"
[1] "dimension: 413 x 36"
>   
>   ### Select one trait for example
>   trait.name <- "Flowering.time.at.Arkansas"
>   y <- as.matrix(Rice_pheno[, trait.name, drop = FALSE])
>   
>   ### Remove SNPs whose MAF <= 0.05
>   x.0 <- t(Rice_geno_score)
>   MAF.cut.res <- MAF.cut(x.0 = x.0, map.0 = Rice_geno_map)

Execution halted