############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:qPLEXanalyzer.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings qPLEXanalyzer_1.14.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/qPLEXanalyzer.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘qPLEXanalyzer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘qPLEXanalyzer’ version ‘1.14.1’ * 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 for sufficient/correct file permissions ... 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 ‘/home/biocbuild/bbs-3.15-bioc/meat/qPLEXanalyzer.Rcheck/00check.log’ for details.