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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ImpulseDE2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ImpulseDE2_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ImpulseDE2.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ImpulseDE2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ImpulseDE2’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ImpulseDE2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotGenes: no visible global function definition for ‘error’
plotGenes: no visible binding for global variable ‘normCounts’
plotGenes: no visible binding for global variable ‘Condition’
plotGenes: no visible binding for global variable ‘Batch’
plotGenes: no visible binding for global variable ‘value’
plotGenes: no visible binding for global variable ‘BatchFit’
Undefined global functions or variables:
  Batch BatchFit Condition error normCounts value
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ImpulseDE2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fitSigmoidModels
> ### Title: Fits sigmoidal models to all genes on all all samples of a
> ###   condition
> ### Aliases: fitSigmoidModels
> 
> ### ** Examples
> 
> lsSimulatedData <- simulateDataSetImpulseDE2(
+ vecTimePointsA   = rep(seq(1,8),3),
+ vecTimePointsB   = NULL,
+ vecBatchesA      = NULL,
+ vecBatchesB      = NULL,
+ scaNConst        = 0,
+ scaNImp          = 20,
+ scaNLin          = 10,
+ scaNSig          = 20)
[1] "Setting no batch structure."
> objectImpulseDE2 <- runImpulseDE2(
+ matCountData    = lsSimulatedData$matObservedCounts, 
+ dfAnnotation    = lsSimulatedData$dfAnnotation,
+ boolCaseCtrl    = FALSE,
+ vecConfounders  = NULL,
+ boolIdentifyTransients = FALSE,
+ scaNProc        = 1 )
ImpulseDE2 for count data, v1.12.0
# Process input
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
ImpulseDE2
 --- call from context --- 
system.time({
    strMessage <- "# Process input"
    if (boolVerbose) {
        message(strMessage)
    }
    strReport <- paste0(strReport, "\n", strMessage)
    if (class(matCountData) == "SummarizedExperiment") {
        matCountData <- assay(matCountData)
    }
    lsProcessedData <- processData(dfAnnotation = dfAnnotation, 
        matCountData = matCountData, boolCaseCtrl = boolCaseCtrl, 
        vecConfounders = vecConfounders, vecDispersionsExternal = vecDispersionsExternal, 
        vecSizeFactorsExternal = vecSizeFactorsExternal)
    matCountDataProc <- lsProcessedData$matCountDataProc
    dfAnnotationProc <- lsProcessedData$dfAnnotationProc
    vecSizeFactorsExternalProc <- lsProcessedData$vecSizeFactorsExternalProc
    vecDispersionsExternalProc <- lsProcessedData$vecDispersionsExternalProc
    if (boolVerbose) {
        write(lsProcessedData$strReportProcessing, file = "", 
            ncolumns = 1)
    }
    strReport <- paste0(strReport, lsProcessedData$strReportProcessing)
    if (scaNProc > 1) {
        register(MulticoreParam(workers = scaNProc))
    }
    else {
        register(SerialParam())
    }
    if (is.null(vecDispersionsExternal)) {
        strMessage <- paste0("# Run DESeq2: Using dispersion factors", 
            "computed by DESeq2.")
        if (boolVerbose) {
            message(strMessage)
        }
        strReport <- paste0(strReport, "\n", strMessage)
        tm_runDESeq2 <- system.time({
            vecDispersions <- runDESeq2(dfAnnotationProc = dfAnnotationProc, 
                matCountDataProc = matCountDataProc, boolCaseCtrl = boolCaseCtrl, 
                vecConfounders = vecConfounders)
        })
        strMessage <- paste0("Consumed time: ", round(tm_runDESeq2["elapsed"]/60, 
            2), " min.")
        if (boolVerbose) {
            message(strMessage)
        }
        strReport <- paste0(strReport, "\n", strMessage)
    }
    else {
        strMessage <- "# Using externally supplied dispersion factors."
        if (boolVerbose) {
            message(strMessage)
        }
        strReport <- paste0(strReport, "\n", strMessage)
        vecDispersions <- vecDispersionsExternalProc
    }
    strMessage <- "# Compute size factors"
    if (boolVerbose) {
        message(strMessage)
    }
    strReport <- paste0(strReport, "\n", strMessage)
    vecSizeFactors <- computeNormConst(matCountDataProc = matCountDataProc, 
        vecSizeFactorsExternal = vecSizeFactorsExternalProc)
    objectImpulseDE2 <- new("ImpulseDE2Object", dfImpulseDE2Results = NULL, 
        vecDEGenes = NULL, lsModelFits = NULL, matCountDataProc = matCountDataProc, 
        vecAllIDs = rownames(matCountData), dfAnnotationProc = dfAnnotationProc, 
        vecSizeFactors = vecSizeFactors, vecDispersions = vecDispersions, 
        boolCaseCtrl = boolCaseCtrl, vecConfounders = vecConfounders, 
        scaNProc = scaNProc, scaQThres = scaQThres, strReport = strReport)
    strMessage <- "# Fitting null and alternative model to the genes"
    if (boolVerbose) {
        message(strMessage)
    }
    objectImpulseDE2 <- append_strReport(obj = objectImpulseDE2, 
        s = strMessage)
    tm_fitImpulse <- system.time({
        objectImpulseDE2 <- fitModels(objectImpulseDE2 = objectImpulseDE2, 
            vecConfounders = vecConfounders, boolCaseCtrl = boolCaseCtrl)
    })
    strMessage <- paste0("Consumed time: ", round(tm_fitImpulse["elapsed"]/60, 
        2), " min.")
    if (boolVerbose) {
        message(strMessage)
    }
    objectImpulseDE2 <- append_strReport(obj = objectImpulseDE2, 
        s = strMessage)
    if (boolIdentifyTransients) {
        strMessage <- "# Fitting sigmoid model to case condition"
        if (boolVerbose) {
            message(strMessage)
        }
        objectImpulseDE2 <- append_strReport(obj = objectImpulseDE2, 
            s = strMessage)
        tm_fitSigmoid <- system.time({
            objectImpulseDE2 <- fitSigmoidModels(objectImpulseDE2 = objectImpulseDE2, 
                vecConfounders = vecConfounders, strCondition = "case")
        })
        strMessage <- paste0("Consumed time: ", round(tm_fitSigmoid["elapsed"]/60, 
            2), " min.")
        if (boolVerbose) {
            message(strMessage)
        }
        objectImpulseDE2 <- append_strReport(obj = objectImpulseDE2, 
            s = strMessage)
    }
    strMessage <- "# Differentially expression analysis based on model fits"
    if (boolVerbose) {
        message(strMessage)
    }
    objectImpulseDE2 <- append_strReport(obj = objectImpulseDE2, 
        s = strMessage)
    objectImpulseDE2 <- runDEAnalysis(objectImpulseDE2 = objectImpulseDE2, 
        boolCaseCtrl = get_boolCaseCtrl(obj = objectImpulseDE2), 
        boolIdentifyTransients = boolIdentifyTransients)
    if (!is.null(scaQThres)) {
        vecDEGenes <- as.vector(objectImpulseDE2$dfImpulseDE2Results[as.numeric(objectImpulseDE2$dfImpulseDE2Results$padj) <= 
            scaQThres, "Gene"])
        strMessage <- paste0("Found ", length(vecDEGenes), " DE genes", 
            " at a FDR corrected p-value cut off of ", scaQThres, 
            ".")
        if (boolVerbose) {
            message(strMessage)
        }
        objectImpulseDE2 <- append_strReport(obj = objectImpulseDE2, 
            s = strMessage)
    }
    else {
        vecDEGenes <- NULL
    }
    objectImpulseDE2 <- set_vecDEGenes(obj = objectImpulseDE2, 
        element = vecDEGenes)
})
 --- call from argument --- 
if (class(matCountData) == "SummarizedExperiment") {
    matCountData <- assay(matCountData)
}
 --- R stacktrace ---
where 1: system.time({
    strMessage <- "# Process input"
    if (boolVerbose) {
        message(strMessage)
    }
    strReport <- paste0(strReport, "\n", strMessage)
    if (class(matCountData) == "SummarizedExperiment") {
        matCountData <- assay(matCountData)
    }
    lsProcessedData <- processData(dfAnnotation = dfAnnotation, 
        matCountData = matCountData, boolCaseCtrl = boolCaseCtrl, 
        vecConfounders = vecConfounders, vecDispersionsExternal = vecDispersionsExternal, 
        vecSizeFactorsExternal = vecSizeFactorsExternal)
    matCountDataProc <- lsProcessedData$matCountDataProc
    dfAnnotationProc <- lsProcessedData$dfAnnotationProc
    vecSizeFactorsExternalProc <- lsProcessedData$vecSizeFactorsExternalProc
    vecDispersionsExternalProc <- lsProcessedData$vecDispersionsExternalProc
    if (boolVerbose) {
        write(lsProcessedData$strReportProcessing, file = "", 
            ncolumns = 1)
    }
    strReport <- paste0(strReport, lsProcessedData$strReportProcessing)
    if (scaNProc > 1) {
        register(MulticoreParam(workers = scaNProc))
    }
    else {
        register(SerialParam())
    }
    if (is.null(vecDispersionsExternal)) {
        strMessage <- paste0("# Run DESeq2: Using dispersion factors", 
            "computed by DESeq2.")
        if (boolVerbose) {
            message(strMessage)
        }
        strReport <- paste0(strReport, "\n", strMessage)
        tm_runDESeq2 <- system.time({
            vecDispersions <- runDESeq2(dfAnnotationProc = dfAnnotationProc, 
                matCountDataProc = matCountDataProc, boolCaseCtrl = boolCaseCtrl, 
                vecConfounders = vecConfounders)
        })
        strMessage <- paste0("Consumed time: ", round(tm_runDESeq2["elapsed"]/60, 
            2), " min.")
        if (boolVerbose) {
            message(strMessage)
        }
        strReport <- paste0(strReport, "\n", strMessage)
    }
    else {
        strMessage <- "# Using externally supplied dispersion factors."
        if (boolVerbose) {
            message(strMessage)
        }
        strReport <- paste0(strReport, "\n", strMessage)
        vecDispersions <- vecDispersionsExternalProc
    }
    strMessage <- "# Compute size factors"
    if (boolVerbose) {
        message(strMessage)
    }
    strReport <- paste0(strReport, "\n", strMessage)
    vecSizeFactors <- computeNormConst(matCountDataProc = matCountDataProc, 
        vecSizeFactorsExternal = vecSizeFactorsExternalProc)
    objectImpulseDE2 <- new("ImpulseDE2Object", dfImpulseDE2Results = NULL, 
        vecDEGenes = NULL, lsModelFits = NULL, matCountDataProc = matCountDataProc, 
        vecAllIDs = rownames(matCountData), dfAnnotationProc = dfAnnotationProc, 
        vecSizeFactors = vecSizeFactors, vecDispersions = vecDispersions, 
        boolCaseCtrl = boolCaseCtrl, vecConfounders = vecConfounders, 
        scaNProc = scaNProc, scaQThres = scaQThres, strReport = strReport)
    strMessage <- "# Fitting null and alternative model to the genes"
    if (boolVerbose) {
        message(strMessage)
    }
    objectImpulseDE2 <- append_strReport(obj = objectImpulseDE2, 
        s = strMessage)
    tm_fitImpulse <- system.time({
        objectImpulseDE2 <- fitModels(objectImpulseDE2 = objectImpulseDE2, 
            vecConfounders = vecConfounders, boolCaseCtrl = boolCaseCtrl)
    })
    strMessage <- paste0("Consumed time: ", round(tm_fitImpulse["elapsed"]/60, 
        2), " min.")
    if (boolVerbose) {
        message(strMessage)
    }
    objectImpulseDE2 <- append_strReport(obj = objectImpulseDE2, 
        s = strMessage)
    if (boolIdentifyTransients) {
        strMessage <- "# Fitting sigmoid model to case condition"
        if (boolVerbose) {
            message(strMessage)
        }
        objectImpulseDE2 <- append_strReport(obj = objectImpulseDE2, 
            s = strMessage)
        tm_fitSigmoid <- system.time({
            objectImpulseDE2 <- fitSigmoidModels(objectImpulseDE2 = objectImpulseDE2, 
                vecConfounders = vecConfounders, strCondition = "case")
        })
        strMessage <- paste0("Consumed time: ", round(tm_fitSigmoid["elapsed"]/60, 
            2), " min.")
        if (boolVerbose) {
            message(strMessage)
        }
        objectImpulseDE2 <- append_strReport(obj = objectImpulseDE2, 
            s = strMessage)
    }
    strMessage <- "# Differentially expression analysis based on model fits"
    if (boolVerbose) {
        message(strMessage)
    }
    objectImpulseDE2 <- append_strReport(obj = objectImpulseDE2, 
        s = strMessage)
    objectImpulseDE2 <- runDEAnalysis(objectImpulseDE2 = objectImpulseDE2, 
        boolCaseCtrl = get_boolCaseCtrl(obj = objectImpulseDE2), 
        boolIdentifyTransients = boolIdentifyTransients)
    if (!is.null(scaQThres)) {
        vecDEGenes <- as.vector(objectImpulseDE2$dfImpulseDE2Results[as.numeric(objectImpulseDE2$dfImpulseDE2Results$padj) <= 
            scaQThres, "Gene"])
        strMessage <- paste0("Found ", length(vecDEGenes), " DE genes", 
            " at a FDR corrected p-value cut off of ", scaQThres, 
            ".")
        if (boolVerbose) {
            message(strMessage)
        }
        objectImpulseDE2 <- append_strReport(obj = objectImpulseDE2, 
            s = strMessage)
    }
    else {
        vecDEGenes <- NULL
    }
    objectImpulseDE2 <- set_vecDEGenes(obj = objectImpulseDE2, 
        element = vecDEGenes)
})
where 2: runImpulseDE2(matCountData = lsSimulatedData$matObservedCounts, 
    dfAnnotation = lsSimulatedData$dfAnnotation, boolCaseCtrl = FALSE, 
    vecConfounders = NULL, boolIdentifyTransients = FALSE, scaNProc = 1)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (expr, gcFirst = TRUE) 
{
    ppt <- function(y) {
        if (!is.na(y[4L])) 
            y[1L] <- y[1L] + y[4L]
        if (!is.na(y[5L])) 
            y[2L] <- y[2L] + y[5L]
        paste(formatC(y[1L:3L]), collapse = " ")
    }
    if (gcFirst) 
        gc(FALSE)
    time <- proc.time()
    on.exit(message("Timing stopped at: ", ppt(proc.time() - 
        time)))
    expr
    new.time <- proc.time()
    on.exit()
    structure(new.time - time, class = "proc_time")
}
<bytecode: 0x7fb85aa381a8>
<environment: namespace:base>
 --- function search by body ---
Function system.time in namespace base has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/ImpulseDE2.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ImpulseDE2
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ImpulseDE2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ImpulseDE2)