Error(s) in re-building vignettes:
  ...
--- re-building 'iECAT.Rnw' using Sweave
Warning in if (class(Z) != "matrix") stop("Z is not a matrix") :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Z) != "matrix") stop("Z is not a matrix") :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Z) != "matrix") stop("Z is not a matrix") :
  the condition has length > 1 and only the first element will be used
Warning: 4 SNPs with either high missing rates or no-variation are excluded!
Warning in if (class(Z) != "matrix") stop("Z is not a matrix") :
  the condition has length > 1 and only the first element will be used
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
iECAT
 --- call from context --- 
iECAT.SSD.GetSNP_Weight(SSD.INFO, SetIndex, obj.EC, obj.SNPWeight = obj.SNPWeight)
 --- call from argument --- 
if (class(try1) != "try-error") {
    Z <- try1
    Is.Error <- FALSE
} else {
    err.msg <- geterrmessage()
    msg <- sprintf("Error to get genotypes of %s: %s", SetID, 
        err.msg)
    stop(msg)
}
 --- R stacktrace ---
where 1: iECAT.SSD.GetSNP_Weight(SSD.INFO, SetIndex, obj.EC, obj.SNPWeight = obj.SNPWeight)
where 2: iECAT.SSD.OneSet_SetIndex(EC.INFO = EC.INFO, SetIndex = i, obj = obj, 
    ..., obj.SNPWeight = obj.SNPWeight)
where 3: doTryCatch(return(expr), name, parentenv, handler)
where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 5: tryCatchList(expr, classes, parentenv, handlers)
where 6: 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 7: try(iECAT.SSD.OneSet_SetIndex(EC.INFO = EC.INFO, SetIndex = i, 
    obj = obj, ..., obj.SNPWeight = obj.SNPWeight))
where 8: iECAT.SSD.All(EC.INFO, obj = obj, method = "optimal")
where 9: eval(expr, .GlobalEnv)
where 10: eval(expr, .GlobalEnv)
where 11: withVisible(eval(expr, .GlobalEnv))
where 12: doTryCatch(return(expr), name, parentenv, handler)
where 13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 14: tryCatchList(expr, classes, parentenv, handlers)
where 15: 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 16: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 17: evalFunc(ce, options)
where 18: tryCatchList(expr, classes, parentenv, handlers)
where 19: tryCatch(evalFunc(ce, options), finally = {
    cat("\n")
    sink()
})
where 20: driver$runcode(drobj, chunk, chunkopts)
where 21: utils::Sweave(...)
where 22: engine$weave(file, quiet = quiet, encoding = enc)
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch({
    engine$weave(file, quiet = quiet, encoding = enc)
    setwd(startdir)
    output <- find_vignette_product(name, by = "weave", engine = engine)
    if (!have.makefile && vignette_is_tex(output)) {
        texi2pdf(file = output, clean = FALSE, quiet = quiet)
        output <- find_vignette_product(name, by = "texi2pdf", 
            engine = engine)
    }
    outputs <- c(outputs, output)
}, error = function(e) {
    thisOK <<- FALSE
    fails <<- c(fails, file)
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 27: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/iECAT.Rcheck/vign_test/iECAT", 
    ser_elibs = "/tmp/RtmpKUM0o9/file35a24b8eaf53.rds")

 --- value of length: 2 type: logical ---
[1] TRUE TRUE
 --- function from context --- 
function (SSD.INFO, SetIndex, obj.EC, obj.SNPWeight = NULL) 
{
    id1 <- which(SSD.INFO$SetInfo$SetIndex == SetIndex)
    if (length(id1) == 0) {
        MSG <- sprintf("Error: cannot find set index [%d] from SSD!", 
            SetIndex)
        stop(MSG)
    }
    SetID <- SSD.INFO$SetInfo$SetID[id1]
    try1 <- try(SKAT::Get_Genotypes_SSD(SSD.INFO, SetIndex, is_ID = TRUE), 
        silent = TRUE)
    if (class(try1) != "try-error") {
        Z <- try1
        Is.Error <- FALSE
    }
    else {
        err.msg <- geterrmessage()
        msg <- sprintf("Error to get genotypes of %s: %s", SetID, 
            err.msg)
        stop(msg)
    }
    Is.weights = FALSE
    if (!is.null(obj.SNPWeight)) {
        Is.weights = TRUE
    }
    SNP_ID <- colnames(Z)
    p <- ncol(Z)
    weights <- rep(0, p)
    EC_COUNT <- matrix(rep(-1, p * 2), ncol = 2)
    for (i in 1:p) {
        val1 <- SNP_ID[i]
        if (Is.weights) {
            val2 <- obj.SNPWeight$hashset[[val1]]
            if (is.null(val2)) {
                msg <- sprintf("SNP %s is not found in obj.SNPWeight!", 
                  val1)
                stop(msg)
            }
            weights[i] <- val2
        }
        idx <- obj.EC$EC_hash[[val1]]
        if (is.null(idx)) {
            msg <- sprintf("SNP %s is not found in obj.SNPWeight!", 
                val1)
            warnings(msg)
        }
        else {
            EC_COUNT[i, 1] <- obj.EC$EC_INFO$EC_C1[idx]
            EC_COUNT[i, 2] <- obj.EC$EC_INFO$EC_C2[idx]
        }
    }
    re = list(Z = Z, Is.weights = Is.weights, weights = weights, 
        EC_COUNT = EC_COUNT)
    return(re)
}
<bytecode: 0x2dfe8b8>
<environment: namespace:iECAT>
 --- function search by body ---
Function iECAT.SSD.GetSNP_Weight in namespace iECAT has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1