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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OGSA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OGSA_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/OGSA.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 ‘OGSA/DESCRIPTION’ ... OK
* this is package ‘OGSA’ version ‘1.18.0’
* 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 ‘OGSA’ 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
copaStat: no visible binding for global variable ‘median’
copaStat: no visible binding for global variable ‘mad’
copaStat: no visible binding for global variable ‘IQR’
copaStat: no visible binding for global variable ‘quantile’
expressionSetPheno: no visible global function definition for ‘relevel’
outCallTib: no visible binding for global variable ‘median’
outCallTib: no visible binding for global variable ‘mad’
outCallTib: no visible binding for global variable ‘IQR’
outCallTib: no visible binding for global variable ‘quantile’
outCallTibE: no visible binding for global variable ‘median’
outCallTibE: no visible binding for global variable ‘mad’
outCallTibE: no visible binding for global variable ‘IQR’
outCallTibE: no visible binding for global variable ‘quantile’
outCount: no visible binding for global variable ‘median’
outCount: no visible binding for global variable ‘mad’
outCount: no visible binding for global variable ‘IQR’
outCount: no visible binding for global variable ‘quantile’
outMap: no visible global function definition for ‘pdf’
outMap: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  IQR dev.off mad median pdf quantile relevel
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "IQR", "mad", "median", "quantile", "relevel")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OGSA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: outCallRank
> ### Title: outCallRank
> ### Aliases: outCallRank
> 
> ### ** Examples
> 
> data(ExampleData)
> 
> #set up dataSet
> dataSet <- list(expr, meth,cnv)
> 
> # Set up Phenotype
> phenotype <- pheno
> names(phenotype) <- colnames(cnv)
> 
> # set up values for expr-meth-cnv in that order
> tailLRL <- c('left', 'right', 'left')
> 
> outRankLRL <- outCallRank(dataSet, phenotype, names=c('Expr',
+                              'Meth', 'CNV'), tail=tailLRL)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
OGSA
 --- call from context --- 
outCallRank(dataSet, phenotype, names = c("Expr", "Meth", "CNV"), 
    tail = tailLRL)
 --- call from argument --- 
tail == "right" || tail == "left"
 --- R stacktrace ---
where 1: outCallRank(dataSet, phenotype, names = c("Expr", "Meth", "CNV"), 
    tail = tailLRL)

 --- value of length: 3 type: logical ---
[1] FALSE  TRUE FALSE
 --- function from context --- 
function (dataSet, phenotype, thres = 0.05, tail = "right", corr = FALSE, 
    offsets = NULL, names = NULL) 
{
    if (all(thres <= 0 & thres > 1)) {
        stop("the thres alpha value must be between 0 and 1")
    }
    if (all(tail == "right" || tail == "left")) {
    }
    else {
        stop("values in 'tail' must be 'right' or 'left'")
    }
    if (length(dataSet) != length(tail)) {
        stop("length of 'tail' must equal length of 'dataSet'")
    }
    if (is.null(names)) {
        names <- vector(length = length(dataSet), mode = "character")
        for (d in 1:length(dataSet)) {
            names[d] <- paste("Data", d)
        }
    }
    temp <- dataSet[[1]]
    nG <- dim(temp)[1]
    outList <- list()
    if (!corr) {
        offsets <- rep(0, dim(temp)[2])
    }
    else if (is.null(offsets)) {
        print("No Offsets Set with Correction Requested")
        return()
    }
    outP <- matrix(nrow = nG, ncol = 2)
    outCount <- rep(0, nG)
    for (d in 1:length(dataSet)) {
        data <- dataSet[[d]]
        nS <- length(phenotype)
        thisTail <- tail[d]
        adjust <- offsets[d]
        nData <- data[, phenotype == 0]
        tData <- data[, phenotype == 1]
        nT <- dim(tData)[2]
        empirP <- matrix(nrow = nG, ncol = nT)
        if (thisTail == "right") {
            for (i in 1:nG) {
                tumor <- tData[i, ]
                baseline <- nData[i, ]
                result <- sapply(1:length(tumor), function(j) sum((baseline + 
                  adjust) > tumor[j]))
                empirP[i, ] <- result/length(baseline)
            }
        }
        else if (thisTail == "left") {
            for (i in 1:nG) {
                tumor <- tData[i, ]
                baseline <- nData[i, ]
                result <- sapply(1:length(tumor), function(j) sum((baseline - 
                  adjust) < tumor[j]))
                empirP[i, ] <- result/length(baseline)
            }
        }
        empirP <- empirP < thres
        rownames(empirP) <- rownames(data)
        colnames(empirP) <- colnames(tData)
        outList[[d]] <- empirP
    }
    names(outList) <- names
    return(outList)
}
<bytecode: 0x7fa304d3a158>
<environment: namespace:OGSA>
 --- function search by body ---
Function outCallRank in namespace OGSA has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical
* 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/OGSA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL OGSA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘OGSA’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (OGSA)