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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:qPLEXanalyzer.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings qPLEXanalyzer_1.17.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/qPLEXanalyzer.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'qPLEXanalyzer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'qPLEXanalyzer' version '1.17.0'
* 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 whether package 'qPLEXanalyzer' 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
convertToMSnset: no visible binding for global variable 'SampleName'
corrPlot: no visible binding for global variable 'X'
corrPlot: no visible binding for global variable 'AddValues'
corrPlot: no visible binding for global variable 'Cor'
corrPlot: no visible binding for global variable 'Y'
corrPlot: no visible binding for global variable 'CorTxt'
coveragePlot: no visible binding for global variable 'Accessions'
coveragePlot: no visible binding for global variable 'Sequences'
getContrastResults: no visible binding for global variable 'B'
getContrastResults: no visible binding for global variable 'AveExpr'
getContrastResults: no visible binding for global variable 'logFC'
groupScaling: no visible binding for global variable 'sInt'
groupScaling: no visible binding for global variable
  'meanscaledIntensity'
hierarchicalPlot: no visible binding for global variable 'x'
hierarchicalPlot: no visible binding for global variable 'y'
hierarchicalPlot: no visible binding for global variable 'xend'
hierarchicalPlot: no visible binding for global variable 'yend'
hierarchicalPlot: no visible binding for global variable 'SampleName'
intensityBoxplot: no visible binding for global variable 'Intensity'
intensityBoxplot: no visible binding for global variable 'logInt'
intensityBoxplot: no visible binding for global variable 'SampleName'
intensityPlot: no visible binding for global variable 'Intensity'
intensityPlot: no visible binding for global variable 'SampleName'
maVolPlot: no visible binding for global variable 'group'
maVolPlot: no visible binding for global variable 'adj.P.Val'
maVolPlot: no visible binding for global variable 'GeneSymbol'
maVolPlot: no visible binding for global variable 'SymbolLab'
mergePeptides: no visible binding for global variable 'Accessions'
mergePeptides: no visible binding for global variable 'Sequences'
mergePeptides: no visible binding for global variable 'Seq_Acc'
mergePeptides: no visible global function definition for 'where'
mergePeptides: no visible binding for global variable 'Count'
mergeSites: no visible binding for global variable 'Accessions'
mergeSites: no visible binding for global variable 'Sites'
mergeSites: no visible binding for global variable 'Type'
mergeSites: no visible binding for global variable 'Sites_Acc'
mergeSites: no visible global function definition for 'where'
mergeSites: no visible binding for global variable 'Count'
peptideIntensityPlot: no visible binding for global variable
  'PeptideID'
peptideIntensityPlot: no visible binding for global variable
  'Intensity'
peptideIntensityPlot: no visible binding for global variable
  'Accessions'
peptideIntensityPlot: no visible binding for global variable
  'SampleName'
peptideIntensityPlot: no visible binding for global variable
  'logIntensity'
peptideIntensityPlot: no visible binding for global variable
  'Sequences'
peptideIntensityPlot: no visible binding for global variable
  'Modifications'
plotMeanVar: no visible binding for global variable 'x'
plotMeanVar: no visible binding for global variable 'y'
plotMeanVar: no visible binding for global variable 'Mean'
plotMeanVar: no visible binding for global variable 'Variance'
rliPlot: no visible binding for global variable 'RowID'
rliPlot: no visible binding for global variable 'Intensity'
rliPlot: no visible binding for global variable 'logInt'
rliPlot: no visible binding for global variable 'medianLogInt'
rliPlot: no visible binding for global variable 'SampleName'
rliPlot: no visible binding for global variable 'RLI'
summarizeIntensities: no visible binding for global variable
  'Accessions'
summarizeIntensities: no visible binding for global variable
  'Sequences'
summarizeIntensities: no visible global function definition for 'where'
summarizeIntensities: no visible binding for global variable 'Count'
Undefined global functions or variables:
  Accessions AddValues AveExpr B Cor CorTxt Count GeneSymbol Intensity
  Mean Modifications PeptideID RLI RowID SampleName Seq_Acc Sequences
  Sites Sites_Acc SymbolLab Type Variance X Y adj.P.Val group logFC
  logInt logIntensity meanscaledIntensity medianLogInt sInt where x
  xend y yend
* 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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  • hierarchicalPlot/hierarchical-plot-custom-colour.svg
  • hierarchicalPlot/hierarchical-plot-veritcal.svg
  • intensityBoxplot/intensity-boxplot-colour-by-rep.svg
  • intensityBoxplot/intensity-boxplot-custom-colour.svg
  • intensityPlot/intensity-density-plot-colour-by-rep.svg
  • intensityPlot/intensity-density-plot-custom-colour.svg
  • pcaPlot/pca-plot-colour-by-biorep-omit-igg.svg
  • pcaPlot/pca-plot-custom-colours-and-pc2-v-pc3.svg
  • peptideIntensityPlot/no-combined-intensity.svg
  • peptideIntensityPlot/with-selected-modification.svg
  • peptideIntensityPlot/with-selected-sequence.svg
  • rliPlot/rli-plot-colour-by-biorep-include-igg.svg
  • rliPlot/rli-plot-custom-colours.svg
  Error: Test failures
  Execution halted
* 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/qPLEXanalyzer.Rcheck/00check.log'
for details.