Last updated on 2020-02-19 10:48:49 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.6 | 6.62 | 52.19 | 58.81 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.6 | 6.24 | 40.40 | 46.64 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.6 | 71.08 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.6 | 69.18 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.0.6 | 13.00 | 70.00 | 83.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.0.6 | 17.00 | 92.00 | 109.00 | OK | |
| r-patched-linux-x86_64 | 1.0.6 | 6.52 | 48.86 | 55.38 | OK | |
| r-patched-solaris-x86 | 1.0.6 | 103.30 | OK | |||
| r-release-linux-x86_64 | 1.0.6 | 6.76 | 50.07 | 56.83 | OK | |
| r-release-windows-ix86+x86_64 | 1.0.6 | 12.00 | 61.00 | 73.00 | OK | |
| r-release-osx-x86_64 | 1.0.6 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.6 | 8.00 | 60.00 | 68.00 | OK | |
| r-oldrel-osx-x86_64 | 1.0.6 | OK |
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: 0x108bf88>
<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
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: 0x560f54a66af0>
<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-gcc
Version: 1.0.6
Check: examples
Result: ERROR
Running examples in ‘COMBIA-Ex.R’ failed
The error most likely occurred in:
> ### 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: 0x1602a78>
<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-fedora-clang
Version: 1.0.6
Check: examples
Result: ERROR
Running examples in ‘COMBIA-Ex.R’ failed
The error most likely occurred in:
> ### 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: 0x14cef08>
<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-fedora-gcc