CRAN Package Check Results for Package COMBIA

Last updated on 2020-01-20 01:50:17 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.6 7.52 50.55 58.07 ERROR
r-devel-linux-x86_64-debian-gcc 1.0.6 5.33 41.70 47.03 OK
r-devel-linux-x86_64-fedora-clang 1.0.6 72.08 OK
r-devel-linux-x86_64-fedora-gcc 1.0.6 75.14 OK
r-devel-windows-ix86+x86_64 1.0.6 12.00 67.00 79.00 OK
r-devel-windows-ix86+x86_64-gcc8 1.0.6 13.00 66.00 79.00 OK
r-patched-linux-x86_64 1.0.6 6.55 49.62 56.17 OK
r-patched-solaris-x86 1.0.6 99.30 OK
r-release-linux-x86_64 1.0.6 5.21 50.21 55.42 OK
r-release-windows-ix86+x86_64 1.0.6 17.00 54.00 71.00 OK
r-release-osx-x86_64 1.0.6 OK
r-oldrel-windows-ix86+x86_64 1.0.6 8.00 70.00 78.00 OK
r-oldrel-osx-x86_64 1.0.6 OK

Check Details

Version: 1.0.6
Check: examples
Result: ERROR
    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: 0x3f8cd50>
    <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
Flavor: r-devel-linux-x86_64-debian-clang