Running examples in 'vcfR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create.chromR
> ### Title: Create chromR object
> ### Aliases: create.chromR vcfR2chromR vcf2chromR seq2chromR ann2chromR
> 
> ### ** Examples
> 
> library(vcfR)
> data(vcfR_example)
> chrom <- create.chromR('sc50', seq=dna, vcf=vcf, ann=gff)
Names in vcf:
  Supercontig_1.50
Names of sequences:
  Supercontig_1.50 of Phytophthora infestans T30-4
Warning in create.chromR("sc50", seq = dna, vcf = vcf, ann = gff) :
  
        Names in variant data and sequence data do not match perfectly.
        If you choose to proceed, we'll do our best to match the data.
        But prepare yourself for unexpected results.
Names in annotation:
  Supercontig_1.50
Initializing var.info slot.
var.info slot initialized.
> head(chrom)
*****   Class chromR, method head   *****
Name:  sc50
Length:  100,001

*****     Sample names (chromR)     *****
[1] "BL2009P4_us23" "DDR7602"       "IN2009T1_us22" "LBUS5"        
[5] "NL07434"       "P10127"       
[1] "..."
[1] "P17777us22"   "P6096"        "P7722"        "RS2009P1_us8" "blue13"      
[6] "t30-4"       

*****    VCF fixed data (chromR)    *****
     CHROM              POS   ID REF ALT QUAL     FILTER
[1,] "Supercontig_1.50" "2"   NA "T" "A" "44.44"  NA    
[2,] "Supercontig_1.50" "246" NA "C" "G" "144.21" NA    
[3,] "Supercontig_1.50" "549" NA "A" "C" "68.49"  NA    
[4,] "Supercontig_1.50" "668" NA "G" "C" "108.07" NA    
[5,] "Supercontig_1.50" "765" NA "A" "C" "92.78"  NA    
[6,] "Supercontig_1.50" "780" NA "G" "T" "58.38"  NA    
[1] "..."
        CHROM              POS     ID REF ALT QUAL      FILTER
[2528,] "Supercontig_1.50" "99946" NA "T" "A" "133.41"  NA    
[2529,] "Supercontig_1.50" "99961" NA "T" "C" "90.77"   NA    
[2530,] "Supercontig_1.50" "99969" NA "G" "T" "6547.20" NA    
[2531,] "Supercontig_1.50" "99975" NA "T" "A" "48.24"   NA    
[2532,] "Supercontig_1.50" "99983" NA "T" "G" "7172.77" NA    
[2533,] "Supercontig_1.50" "99989" NA "C" "T" "7314.05" NA    

INFO column has been suppressed, first INFO record:
 [1] "AC=1"                    "AF=0.042"               
 [3] "AN=24"                   "BaseQRankSum=1.332"     
 [5] "ClippingRankSum=-0.097"  "DP=197"                 
 [7] "FS=2.536"                "InbreedingCoeff=-0.0879"
 [9] "MLEAC=1"                 "MLEAF=0.042"            
[11] "MQ=21.70"                "MQ0=0"                  
[13] "MQRankSum=0.148"         "QD=2.34"                
[15] "ReadPosRankSum=0.832"    "SOR=1.414"              

*****  VCF genotype data (chromR)  *****
*****     First 6 columns      *********
     FORMAT           BL2009P4_us23               DDR7602                  
[1,] "GT:AD:DP:GQ:PL" "0|0:62,0:62:99:0,190,2835" "0|0:12,0:12:39:0,39,585"
[2,] "GT:AD:DP:GQ:PL" "1|0:5,5:10:99:111,0,114"   NA                       
[3,] "GT:AD:DP:GQ:PL" NA                          NA                       
[4,] "GT:AD:DP:GQ:PL" "0|0:1,0:1:3:0,3,44"        NA                       
[5,] "GT:AD:DP:GQ:PL" "0|0:2,0:2:6:0,6,49"        "0|0:1,0:1:3:0,3,34"     
[6,] "GT:AD:DP:GQ:PL" "0|0:2,0:2:6:0,6,49"        "0|0:1,0:1:3:0,3,34"     
     IN2009T1_us22               LBUS5                     NL07434             
[1,] "0|0:37,0:37:99:0,114,1709" "0|0:12,0:12:39:0,39,585" NA                  
[2,] "0|1:2,1:3:16:16,0,48"      NA                        NA                  
[3,] "0|0:2,0:2:6:0,6,51"        NA                        NA                  
[4,] "1|1:0,1:1:3:25,3,0"        NA                        "0|0:1,0:1:3:0,3,28"
[5,] "0|0:1,0:1:3:0,3,31"        "0|0:1,0:1:3:0,3,34"      "0|0:1,0:1:3:0,3,26"
[6,] "0|0:3,0:3:9:0,9,85"        "0|0:1,0:1:3:0,3,34"      NA                  

*****      Var info (chromR)       *****
             CHROM POS    MQ  DP mask
1 Supercontig_1.50   2 21.70 197 TRUE
2 Supercontig_1.50 246 26.05  28 TRUE
3 Supercontig_1.50 549 35.16   7 TRUE
4 Supercontig_1.50 668 27.95  10 TRUE
5 Supercontig_1.50 765 37.80  78 TRUE
6 Supercontig_1.50 780 36.07  62 TRUE

*****      VCF mask (chromR)        *****
Percent unmasked: 100

*****      End head (chromR)        *****
> chrom
*****   Class chromR, method Show   *****
Name: sc50 
Chromosome length: 100,001 bp
  Chromosome labels: Supercontig_1.50 of Phytophthora infestans T30-4
Annotation (@ann) count: 23 
  Annotation chromosome names: Supercontig_1.50
Variant (@vcf) count: 2,533 
  Variant (@vcf) chromosome names: Supercontig_1.50
Object size: 3.4 Mb
Use head(object) for more details.
*****      End Show (chromR)        *****
> plot(chrom)
> 
> chrom <- masker(chrom, min_QUAL = 1, min_DP = 300, max_DP = 700, min_MQ = 59, max_MQ = 61)
> chrom <- proc.chromR(chrom, win.size=1000)
Nucleotide regions complete.
  elapsed time:  0.033
N regions complete.
  elapsed time:  0.031
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
vcfR
 --- call from context --- 
extract.gt(x, element = "GT")
 --- call from argument --- 
if (class(x@gt) != "matrix") {
    stop(paste("gt slot expected to be of class matrix. Instead found class", 
        class(x@gt)))
}
 --- R stacktrace ---
where 1: extract.gt(x, element = "GT")
where 2: gt.to.popsum(x)
where 3: system.time(x <- gt.to.popsum(x))
where 4: proc.chromR(chrom, win.size = 1000)

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (x, element = "GT", mask = FALSE, as.numeric = FALSE, 
    return.alleles = FALSE, IDtoRowNames = TRUE, extract = TRUE, 
    convertNA = TRUE) 
{
    if (class(x) != "chromR" & class(x) != "vcfR") {
        stop("Expected an object of class chromR or vcfR")
    }
    if (class(x) == "vcfR") {
        if (length(mask) == 1 && mask == TRUE) {
            mask <- FALSE
        }
    }
    if (class(x) == "chromR") {
        tmpMask <- x@var.info$mask
        x <- x@vcf
    }
    if (length(mask) > 1) {
        tmpMask <- mask
        mask <- TRUE
    }
    if (class(x@gt) != "matrix") {
        stop(paste("gt slot expected to be of class matrix. Instead found class", 
            class(x@gt)))
    }
    if (as.numeric == TRUE & return.alleles == TRUE) {
        stop("Invalid parameter choice, as.numeric and return.alleles can't both be true, alleles are characters!")
    }
    if (class(x) == "vcfR") {
        if (colnames(x@gt)[1] != "FORMAT") {
            stop("First column is not named 'FORMAT', this is essential information.")
        }
        outM <- .extract_GT_to_CM(x@fix, x@gt, element, return.alleles, 
            as.integer(extract), convertNA = as.numeric(convertNA))
    }
    if (as.numeric == TRUE) {
        outM <- .CM_to_NM(outM)
    }
    if (IDtoRowNames == TRUE) {
        if (sum(is.na(x@fix[, "ID"])) > 0) {
            x <- addID(x)
        }
        if (length(unique(x@fix[, "ID"])) != nrow(x@fix)) {
            stop("ID column contains non-unique names")
        }
        rownames(outM) <- x@fix[, "ID"]
    }
    if (mask == TRUE) {
        outM <- outM[tmpMask, ]
    }
    return(outM)
}
<bytecode: 0xf176028>
<environment: namespace:vcfR>
 --- function search by body ---
Function extract.gt in namespace vcfR has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(x@gt) != "matrix") { : the condition has length > 1
Calls: proc.chromR -> system.time -> gt.to.popsum -> extract.gt
Timing stopped at: 2.167 0.223 2.492
Execution halted