Multiple platform build/check report for BioC 3.11 - CHECK report for pcaGoPromoter on tokay2

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### Running command:
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###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pcaGoPromoter.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pcaGoPromoter_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/pcaGoPromoter.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 '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 whether package 'pcaGoPromoter' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'pcaGoPromoter' is deprecated and will be removed from
See 'C:/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
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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: 0x1225de90>
<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

** running examples for arch 'x64' ... 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: 0x000000001ca4c9e0>
<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: 2 ERRORs, 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/pcaGoPromoter.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/pcaGoPromoter_1.32.0.tar.gz && rm -rf pcaGoPromoter.buildbin-libdir && mkdir pcaGoPromoter.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pcaGoPromoter.buildbin-libdir pcaGoPromoter_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL pcaGoPromoter_1.32.0.zip && rm pcaGoPromoter_1.32.0.tar.gz pcaGoPromoter_1.32.0.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  135k  100  135k    0     0  2108k      0 --:--:-- --:--:-- --:--:-- 2370k

install for i386

* installing *source* package 'pcaGoPromoter' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pcaGoPromoter'
    finding HTML links ... done
    GOtree                                  html  
    pca                                     html  
    pcaGoPromoter-package                   html  
    primo                                   html  
    primoData                               html  
** 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

install for x64

* installing *source* package 'pcaGoPromoter' ...
** testing if installed package can be loaded
Warning: Package 'pcaGoPromoter' is deprecated and will be removed from
  Bioconductor version 3.12
* MD5 sums
packaged installation of 'pcaGoPromoter' as pcaGoPromoter_1.32.0.zip
* DONE (pcaGoPromoter)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'pcaGoPromoter' successfully unpacked and MD5 sums checked

CHECK report for pcaGoPromoter on tokay2

Summary

Command output

Installation output

Tests output

Example timings