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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: analyzeCOMBO
> ### Title: This function calculates significant synergy/antagonism
> ###   according to Bliss or Loewe model and creates scientific publication
> ###   ready graphs.
> ### Aliases: analyzeCOMBO
> 
> ### ** Examples
> 
> fl <- system.file("extdata", "testData.csv", package="COMBIA")
> wellR <- list(c("l3:l10","m3:m10","b3:k10", "l13:l20","m13:m20","b13:k20", 
+            "l23:l30","m23:m30","b23:k30", "l33:l40","m33:m40","b33:k40") )
> mdl <- "bliss"
> xConc <- c(0.00,  0.20,  0.39,  0.78,  1.56,  3.12,  6.25, 12.50, 25.00, 50) 
> yConc <- c(128,  64,  32,  16,   8,   4,   2,   0)
> xDrug <- "A"
> yDrug <- "B"
> cellLine <-"Cell"
> analyzeCOMBO(filename = c(fl), model = "bliss", inputFormates = "macsynergy", 
+                  wells = wellR, yConcentration = yConc, xConcentration = xConc,
+                  xDrug = xDrug, yDrug=yDrug, cellLine = cellLine, nBoot=500)
[1] "Ratio between empty and control 215.34756097561"
[1] "CV for control: 1 : 2.30698484671909"
[1] "Ratio between empty and control 216.431571815718"
[1] "CV for control: 2 : 3.97477131010254"
[1] "Ratio between empty and control 212.255570117955"
[1] "CV for control: 3 : 6.4008999376604"
[1] "Ratio between empty and control 191.453473132372"
[1] "CV for control: 4 : 5.87005801002331"
[1] "Number of the variable datapoints before data removal= 22"
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
COMBIA
 --- call from context --- 
removeOutliers(arrangeReplicates, minThersholdForCVCal, minThersholdForCV)
 --- call from argument --- 
if (class(apply(arrangeReplicates_NA, 2, function(x) which(!is.na(x)))) == 
    "matrix") {
    replicateCount_indices <- as.list(data.frame(apply(arrangeReplicates_NA, 
        2, function(x) which(!is.na(x)))))
} else {
    replicateCount_indices <- apply(arrangeReplicates_NA, 2, 
        function(x) which(!is.na(x)))
}
 --- R stacktrace ---
where 1: removeOutliers(arrangeReplicates, minThersholdForCVCal, minThersholdForCV)
where 2: readMacSynergyValues(filename, sheet, nrow = 41, wellRangesExcel, 
    minThersholdForCVCal, minThersholdForCV, survivalFunc)
where 3: analyzeCOMBO(filename = c(fl), model = "bliss", inputFormates = "macsynergy", 
    wells = wellR, yConcentration = yConc, xConcentration = xConc, 
    xDrug = xDrug, yDrug = yDrug, cellLine = cellLine, nBoot = 500)

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (arrangeReplicates, minThersholdForCVCal, minThersholdForCV) 
{
    arrangeReplicates_NA <- arrangeReplicates
    arrangeReplicates_NA[which(arrangeReplicates == 0)] <- NA
    replicateCount_individual <- apply(arrangeReplicates_NA, 
        2, function(x) length(which(!is.na(x))))
    if (class(apply(arrangeReplicates_NA, 2, function(x) which(!is.na(x)))) == 
        "matrix") {
        replicateCount_indices <- as.list(data.frame(apply(arrangeReplicates_NA, 
            2, function(x) which(!is.na(x)))))
    }
    else {
        replicateCount_indices <- apply(arrangeReplicates_NA, 
            2, function(x) which(!is.na(x)))
    }
    totalCombinationsnSingle <- (ncol(arrangeReplicates_NA))
    for (i in 1:totalCombinationsnSingle) {
        if (length(which(arrangeReplicates_NA[, i] > minThersholdForCVCal)) > 
            0) {
            currCV <- cVCal(c(arrangeReplicates_NA[, i]))
            if ((currCV > minThersholdForCV) == TRUE) {
                cvfound <- 0
                currentNoOfPerts <- 0
                currentPertList <- 0
                if (replicateCount_individual[i] > 2) {
                  perturblist <- createUniquePertbs(replicateCount_individual[i])
                  rangeOfPerturbation <- 2:(length(perturblist) - 
                    1)
                  cntPertb <- length(rangeOfPerturbation)
                  indecesOfReplicatesIn_arrangeReplicates <- replicateCount_indices[[i]]
                  while (cntPertb > 0) {
                    currentPertList <- perturblist[[rangeOfPerturbation[cntPertb]]]
                    pertSIval <- matrix(arrangeReplicates_NA[indecesOfReplicatesIn_arrangeReplicates[currentPertList], 
                      i], nrow = nrow(currentPertList), ncol = ncol(currentPertList))
                    if (cntPertb > 1) {
                      if (min(apply(pertSIval, 2, cVCal)) < minThersholdForCV) {
                        indPert <- which(min(apply(pertSIval, 
                          2, cVCal)) == apply(pertSIval, 2, cVCal))
                        indicesToBeZerod <- setdiff(c(replicateCount_indices[[i]]), 
                          c(indecesOfReplicatesIn_arrangeReplicates[currentPertList[, 
                            indPert]]))
                        arrangeReplicates[indicesToBeZerod, i] <- 0
                        cvfound <- 1
                        break
                      }
                    }
                    else {
                      indPert <- which(min(apply(pertSIval, 2, 
                        cVCal)) == apply(pertSIval, 2, cVCal))
                      indicesToBeZerod <- setdiff(c(replicateCount_indices[[i]]), 
                        c(indecesOfReplicatesIn_arrangeReplicates[currentPertList[, 
                          indPert]]))
                      arrangeReplicates[indicesToBeZerod, i] <- 0
                    }
                    cntPertb <- cntPertb - 1
                  }
                }
            }
        }
    }
    return(arrangeReplicates)
}
<bytecode: 0x4a33670>
<environment: namespace:COMBIA>
 --- function search by body ---
Function removeOutliers in namespace COMBIA has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(apply(arrangeReplicates_NA, 2, function(x) which(!is.na(x)))) ==  : 
  the condition has length > 1
Calls: analyzeCOMBO -> readMacSynergyValues -> removeOutliers
Execution halted