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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: QTL.gCIMapping
> ### Title: QTL Genome-Wide Composite Interval Mapping
> ### Aliases: QTL.gCIMapping QTL.gCIMapping
> ### Keywords: R QTL.gCIMapping package
> 
> ### ** Examples
> 
> G=data(f2data)
> QTL.gCIMapping(file=f2data,fileFormat="GCIM",fileICIMcov=NULL,Population="F2",
+ Model="Random",WalkSpeed=1,CriLOD=2.5,Likelihood="REML",flagrqtl="FALSE",
+ DrawPlot="FALSE",PlotFormat="png",Resolution="Low",Trait=1:1,dir=tempdir()) 
[1] "Running in progress, please be patient..."
 --Read the following data:
	 76  individuals
	 462  markers
	 1  phenotypes
 --Cross type: f2 
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
QTL.gCIMapping
 --- call from context --- 
cal.xx(x = x, y = x, H = v.inv)
 --- call from argument --- 
if (is.na(H)) H <- diag(n0)
 --- R stacktrace ---
where 1: cal.xx(x = x, y = x, H = v.inv)
where 2: fn(par, ...)
where 3: (function (par) 
fn(par, ...))(c(1, 1, 1))
where 4: optim(par = theta, fn = loglike, hessian = TRUE, method = "L-BFGS-B", 
    lower = 1e-10, upper = 1e+10)
where 5: mixed.vars(data.wy, kinship, optim.speed = TRUE)
where 6: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
where 7: suppressWarnings(mixed.vars(data.wy, kinship, optim.speed = TRUE))
where 8: WenS(flag, CriLOD, NUM, pheRaw, Likelihood, flagrqtl, WEN1re$yygg, 
    WEN1re$mx, WEN1re$phe, WEN1re$chr_name, WEN1re$v.map, WEN1re$gen.raw, 
    WEN1re$a.gen.orig, WEN1re$d.gen.orig, WEN1re$n, WEN1re$names.insert2, 
    WEN1re$X.ad.tran.data, WEN1re$X.ad.t4, dir)
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(expr, error = function(e) {
    call <- conditionCall(e)
    if (!is.null(call)) {
        if (identical(call[[1L]], quote(doTryCatch))) 
            call <- sys.call(-4L)
        dcall <- deparse(call)[1L]
        prefix <- paste("Error in", dcall, ": ")
        LONG <- 75L
        sm <- strsplit(conditionMessage(e), "\n")[[1L]]
        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
        if (is.na(w)) 
            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 
                type = "b")
        if (w > LONG) 
            prefix <- paste0(prefix, "\n  ")
    }
    else prefix <- "Error : "
    msg <- paste0(prefix, conditionMessage(e), "\n")
    .Internal(seterrmessage(msg[1L]))
    if (!silent && isTRUE(getOption("show.error.messages"))) {
        cat(msg, file = outFile)
        .Internal(printDeferredWarnings())
    }
    invisible(structure(msg, class = "try-error", condition = e))
})
where 13: try({
    outWEN <- WenS(flag, CriLOD, NUM, pheRaw, Likelihood, flagrqtl, 
        WEN1re$yygg, WEN1re$mx, WEN1re$phe, WEN1re$chr_name, 
        WEN1re$v.map, WEN1re$gen.raw, WEN1re$a.gen.orig, WEN1re$d.gen.orig, 
        WEN1re$n, WEN1re$names.insert2, WEN1re$X.ad.tran.data, 
        WEN1re$X.ad.t4, dir)
    rewen <- outWEN$result
    mxmp <- outWEN$mxmp
    galaxyy1 <- outWEN$galaxyy1
    res1a <- outWEN$res1a
    res1d <- outWEN$res1d
    chr_name <- outWEN$chr_name
}, silent = FALSE)
where 14: QTL.gCIMapping(file = f2data, fileFormat = "GCIM", fileICIMcov = NULL, 
    Population = "F2", Model = "Random", WalkSpeed = 1, CriLOD = 2.5, 
    Likelihood = "REML", flagrqtl = "FALSE", DrawPlot = "FALSE", 
    PlotFormat = "png", Resolution = "Low", Trait = 1:1, dir = tempdir())

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 [7,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
 [8,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
 [9,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[10,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[11,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[12,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[13,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[14,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[15,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[16,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[17,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[18,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[19,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[20,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[21,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[22,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[23,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[24,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[25,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[26,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[27,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[28,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[29,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[30,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[31,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[32,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[33,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[34,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[35,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[36,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[37,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[38,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[39,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[40,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[41,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[42,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[43,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[44,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[45,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[46,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[47,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[48,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[49,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[50,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[51,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[52,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[53,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[54,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[55,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[56,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[57,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[58,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[59,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[60,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[61,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[62,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[63,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[64,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[65,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[66,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[67,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[68,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[69,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[70,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
 --- function from context --- 
function (x, y, H = NA) 
{
    x <- as.matrix(x)
    y <- as.matrix(y)
    nr <- ncol(x)
    nc <- ncol(y)
    n0 <- nrow(x)
    if (is.na(H)) 
        H <- diag(n0)
    xx <- t(x) %*% H %*% y
    xx <- as.matrix(xx)
    return(xx)
}
<bytecode: 0x55a1ef1eff70>
<environment: 0x55a1ef36a130>
 --- function search by body ---
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1