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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OGSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings OGSA_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/OGSA.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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: 0x0486c7b0>
<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

** running examples for arch 'x64' ... 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: 0x000000000905f900>
<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: 2 ERRORs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/OGSA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/OGSA_1.18.0.tar.gz && rm -rf OGSA.buildbin-libdir && mkdir OGSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OGSA.buildbin-libdir OGSA_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL OGSA_1.18.0.zip && rm OGSA_1.18.0.tar.gz OGSA_1.18.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3176k  100 3176k    0     0  32.4M      0 --:--:-- --:--:-- --:--:-- 35.2M

install for i386

* 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
  converting help for package 'OGSA'
    finding HTML links ... done
    OGSA-package                            html  
    cnv                                     html  
    copaInt                                 html  
    copaIntE                                html  
    copaStat                                html  
    expr                                    html  
    expressionSetDataSet                    html  
    expressionSetPheno                      html  
    meth                                    html  
    outCallRank                             html  
    outCallRankE                            html  
    outCallTib                              html  
    outCallTibE                             html  
    outCount                                html  
    outMap                                  html  
    outRank                                 html  
    pathGS                                  html  
    pheno                                   html  
    testGScogps                             html  
** 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

install for x64

* installing *source* package 'OGSA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OGSA' as OGSA_1.18.0.zip
* DONE (OGSA)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'OGSA' successfully unpacked and MD5 sums checked