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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pcaGoPromoter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pcaGoPromoter_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/pcaGoPromoter.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 ‘pcaGoPromoter/DESCRIPTION’ ... OK
* this is package ‘pcaGoPromoter’ version ‘1.32.0’
* 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 ‘pcaGoPromoter’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'pcaGoPromoter' is deprecated and will be removed from
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/pcaGoPromoter.Rcheck/00install.out’ for details.
* 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 ... NOTE
'library' or 'require' calls in package code:
  ‘GO.db’ ‘Rgraphviz’ ‘parallel’ ‘pcaGoPromoter.Hs.hg19’
  ‘pcaGoPromoter.Mm.mm9’ ‘pcaGoPromoter.Rn.rn4’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  getRankedProbeIds.pca plot.GOtree plot.pca print.GOtree print.pca
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
dropVarNull: no visible global function definition for ‘var’
dropVarNull: no visible global function definition for ‘na.omit’
getMatricesWithHits: no visible global function definition for
  ‘fisher.test’
getMatricesWithHits: no visible global function definition for
  ‘p.adjust’
getSigGOTermsOnce: no visible global function definition for
  ‘fisher.test’
getSigGOTermsOnce : <anonymous>: no visible global function definition
  for ‘binom.test’
getSigGOTermsOnce: no visible global function definition for ‘p.adjust’
leaveOutFindPvalues : <anonymous>: no visible global function
  definition for ‘median’
makeGOtreeRgraphviz: no visible global function definition for ‘new’
makeGOtreeRgraphviz: no visible global function definition for ‘rgb’
makeGOtreeRgraphviz: no visible global function definition for
  ‘addNode’
makeGOtreeRgraphviz: no visible global function definition for
  ‘addEdge’
makeGOtreeRgraphviz: no visible global function definition for ‘nodes’
makeGOtreeRgraphviz: no visible global function definition for
  ‘nodeRenderInfo<-’
makeGOtreeRgraphviz: no visible global function definition for
  ‘edgeRenderInfo<-’
makeGOtreeRgraphviz: no visible global function definition for
  ‘parRenderInfo<-’
makeGOtreeRgraphviz: no visible global function definition for ‘par’
makeGOtreeRgraphviz: no visible global function definition for
  ‘renderGraph’
makeGOtreeRgraphviz: no visible global function definition for
  ‘layoutGraph’
makeGOtreeRgraphviz: no visible global function definition for ‘legend’
newSearchGOtreeForTerms: no visible binding for global variable
  ‘GOBPANCESTOR’
pca: no visible global function definition for ‘annotation’
pca: no visible global function definition for ‘exprs’
pca: no visible global function definition for ‘var’
pca: no visible global function definition for ‘na.omit’
pca: no visible global function definition for ‘prcomp’
plot.pca: no visible global function definition for ‘par’
plot.pca: no visible global function definition for ‘layout’
plot.pca: no visible global function definition for ‘var’
plot.pca: no visible global function definition for ‘polygon’
plot.pca: no visible global function definition for ‘lines’
plot.pca: no visible global function definition for ‘points’
plot.pca: no visible global function definition for ‘abline’
plot.pca: no visible global function definition for ‘box’
plot.pca: no visible global function definition for ‘text’
plot.pca: no visible global function definition for ‘plot.new’
plot.pca: no visible global function definition for ‘legend’
primo: no visible global function definition for ‘data’
primoData.getPromoters: no visible global function definition for
  ‘readFASTA’
primoHits: no visible global function definition for ‘data’
printAnnText: no visible global function definition for ‘mtext’
printAnnotation: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  GOBPANCESTOR abline addEdge addNode annotation binom.test box data
  edgeRenderInfo<- exprs fisher.test layout layoutGraph legend lines
  median mtext na.omit new nodeRenderInfo<- nodes p.adjust par
  parRenderInfo<- plot.new points polygon prcomp readFASTA renderGraph
  rgb text var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "box", "layout", "legend", "lines",
             "mtext", "par", "plot.new", "points", "polygon", "text")
  importFrom("methods", "new")
  importFrom("stats", "binom.test", "fisher.test", "median", "na.omit",
             "p.adjust", "prcomp", "var")
  importFrom("utils", "data")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘pcaGoPromoter-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GOtree
> ### Title: GOtree, plot.GOtree and GOtreeWithLeaveOneOut
> ### Aliases: GOtree print.GOtree plot.GOtree GOtreeHits GOtreeWithLeaveOut
> ### Keywords: methods
> 
> ### ** Examples
> 
> library(serumStimulation)
> data(serumStimulation)
> pcaOutput <- pca( serumStimulation )
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
pcaGoPromoter
 --- call from context --- 
pca(serumStimulation)
 --- call from argument --- 
if (class(eData) == "ExpressionSet") {
    annotationData <- annotation(eData)
    phenoData <- phenoData(eData)
    exprsData <- exprs(eData)
    expressionData <- list(annotationData, phenoData)
} else {
    exprsData <- as.matrix(eData)
    expressionData <- NA
}
 --- R stacktrace ---
where 1: pca(serumStimulation)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (eData, printDropped = TRUE, scale = TRUE, center = TRUE) 
{
    if (class(eData) == "ExpressionSet") {
        annotationData <- annotation(eData)
        phenoData <- phenoData(eData)
        exprsData <- exprs(eData)
        expressionData <- list(annotationData, phenoData)
    }
    else {
        exprsData <- as.matrix(eData)
        expressionData <- NA
    }
    for (i in 1:length(exprsData[, 1])) {
        if (var(exprsData[i, ]) == 0) {
            exprsData[i, ] <- NA
            if (printDropped) {
                print(paste("Dropped variable", rownames(exprsData)[i], 
                  "because scaling is not possible (all values are equal)"))
            }
        }
    }
    exprsData <- na.omit(exprsData)
    p <- prcomp(t(exprsData), scale = scale, center = center)
    res <- list(scores = p$x, loadings = p$rotation, pov = p$sdev^2/sum(p$sdev^2), 
        expressionData = expressionData)
    class(res) <- "pca"
    res
}
<bytecode: 0x7fb40ebcac90>
<environment: namespace:pcaGoPromoter>
 --- function search by body ---
Function pca in namespace pcaGoPromoter 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 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/pcaGoPromoter.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pcaGoPromoter
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘pcaGoPromoter’ ...
** 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
Warning: Package 'pcaGoPromoter' is deprecated and will be removed from
  Bioconductor version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'pcaGoPromoter' is deprecated and will be removed from
  Bioconductor version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (pcaGoPromoter)