############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:TEQC.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings TEQC_4.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/TEQC.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘TEQC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TEQC’ version ‘4.24.0’ * 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 ‘TEQC’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: fixed problem with IRanges version >=2.13.28 in coverage.target() * 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 loading without being on the library search path ... OK * checking startup messages can be suppressed ... 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 .coverage.hist: no visible global function definition for ‘par’ .coverage.hist: no visible global function definition for ‘boxplot.stats’ .coverage.hist: no visible global function definition for ‘hist’ .coverage.hist: no visible global function definition for ‘lines’ .coverage.hist: no visible global function definition for ‘axis’ .coverage.hist: no visible global function definition for ‘mtext’ .coverage.hist: no visible global function definition for ‘legend’ Rlepairs : localAxis: no visible global function definition for ‘Axis’ Rlepairs : localUpperPanel: no visible global function definition for ‘text’ Rlepairs : localLowerPanel: no visible global function definition for ‘points’ Rlepairs : localLowerPanel: no visible global function definition for ‘abline’ Rlepairs: no visible global function definition for ‘par’ Rlepairs: no visible global function definition for ‘box’ Rlepairs: no visible global function definition for ‘strwidth’ Rlepairs: no visible global function definition for ‘text’ Rlepairs: no visible global function definition for ‘mtext’ TEQCreport: no visible global function definition for ‘write.table’ chrom.barplot: no visible global function definition for ‘seqnames’ chrom.barplot: no visible global function definition for ‘barplot’ chrom.barplot: no visible global function definition for ‘text’ chrom.barplot: no visible global function definition for ‘par’ chrom.barplot: no visible global function definition for ‘legend’ cortext: no visible global function definition for ‘text’ covBoxplot: no visible global function definition for ‘par’ covBoxplot: no visible global function definition for ‘points’ covBoxplot: no visible global function definition for ‘legend’ covcorplot: no visible global function definition for ‘pairs’ coverage.GC: no visible global function definition for ‘values’ coverage.GC: no visible global function definition for ‘seqnames’ coverage.GC: no visible global function definition for ‘lines’ coverage.GC: no visible global function definition for ‘smooth.spline’ coverage.density: no visible global function definition for ‘lines’ coverage.hist: no visible global function definition for ‘par’ coverage.hist: no visible global function definition for ‘boxplot.stats’ coverage.hist: no visible global function definition for ‘hist’ coverage.hist: no visible global function definition for ‘lines’ coverage.hist: no visible global function definition for ‘axis’ coverage.hist: no visible global function definition for ‘mtext’ coverage.hist: no visible global function definition for ‘legend’ coverage.plot: no visible global function definition for ‘Rle’ coverage.plot: no visible global function definition for ‘abline’ coverage.plot: no visible global function definition for ‘lines’ coverage.plot: no visible global function definition for ‘seqnames’ coverage.plot: no visible global function definition for ‘par’ coverage.plot: no visible global function definition for ‘rect’ coverage.target: no visible global function definition for ‘seqnames’ coverage.target: no visible global function definition for ‘Rle’ coverage.targetlength.plot: no visible global function definition for ‘mcols’ coverage.targetlength.plot: no visible global function definition for ‘lines’ coverage.targetlength.plot: no visible global function definition for ‘smooth.spline’ coverage.uniformity: no visible global function definition for ‘lines’ covplot: no visible global function definition for ‘par’ covplot: no visible global function definition for ‘points’ covplot: no visible global function definition for ‘axis’ covplot: no visible global function definition for ‘legend’ duplicates.barplot: no visible global function definition for ‘barplot’ duplicates.barplot: no visible global function definition for ‘legend’ duplicates.barplot: no visible global function definition for ‘text’ get.baits: no visible global function definition for ‘read.delim’ get.baits: no visible global function definition for ‘GRanges’ get.baits: no visible global function definition for ‘sortSeqlevels’ get.reads: no visible global function definition for ‘count.fields’ get.reads: no visible global function definition for ‘read.delim’ get.reads: no visible global function definition for ‘GRanges’ get.reads: no visible global function definition for ‘keepSeqlevels’ get.reads: no visible global function definition for ‘seqlevelsInUse’ get.reads: no visible global function definition for ‘sortSeqlevels’ get.targets: no visible global function definition for ‘count.fields’ get.targets: no visible global function definition for ‘read.delim’ get.targets: no visible global function definition for ‘GRanges’ get.targets: no visible global function definition for ‘sortSeqlevels’ htmlChromBarplot: no visible global function definition for ‘jpeg’ htmlChromBarplot: no visible global function definition for ‘png’ htmlChromBarplot: no visible global function definition for ‘tiff’ htmlChromBarplot: no visible global function definition for ‘dev.off’ htmlChromBarplot: no visible global function definition for ‘pdf’ htmlCovBoxplot: no visible global function definition for ‘jpeg’ htmlCovBoxplot: no visible global function definition for ‘png’ htmlCovBoxplot: no visible global function definition for ‘tiff’ htmlCovBoxplot: no visible global function definition for ‘dev.off’ htmlCovBoxplot: no visible global function definition for ‘pdf’ htmlCovCorrelationPlot: no visible global function definition for ‘jpeg’ htmlCovCorrelationPlot: no visible global function definition for ‘png’ htmlCovCorrelationPlot: no visible global function definition for ‘tiff’ htmlCovCorrelationPlot: no visible global function definition for ‘dev.off’ htmlCovCorrelationPlot: no visible global function definition for ‘pdf’ htmlCovGC: no visible global function definition for ‘jpeg’ htmlCovGC: no visible global function definition for ‘png’ htmlCovGC: no visible global function definition for ‘tiff’ htmlCovGC: no visible global function definition for ‘dev.off’ htmlCovGC: no visible global function definition for ‘pdf’ htmlCovTargetLength: no visible global function definition for ‘jpeg’ htmlCovTargetLength: no visible global function definition for ‘png’ htmlCovTargetLength: no visible global function definition for ‘tiff’ htmlCovTargetLength: no visible global function definition for ‘par’ htmlCovTargetLength: no visible global function definition for ‘dev.off’ htmlCovTargetLength: no visible global function definition for ‘pdf’ htmlCovUniformity: no visible global function definition for ‘jpeg’ htmlCovUniformity: no visible global function definition for ‘png’ htmlCovUniformity: no visible global function definition for ‘tiff’ htmlCovUniformity: no visible global function definition for ‘dev.off’ htmlCovUniformity: no visible global function definition for ‘pdf’ htmlCoverageHist: no visible global function definition for ‘jpeg’ htmlCoverageHist: no visible global function definition for ‘png’ htmlCoverageHist: no visible global function definition for ‘tiff’ htmlCoverageHist: no visible global function definition for ‘dev.off’ htmlCoverageHist: no visible global function definition for ‘write.table’ htmlCoverageHist: no visible global function definition for ‘pdf’ htmlDuplicatesBarplot: no visible global function definition for ‘jpeg’ htmlDuplicatesBarplot: no visible global function definition for ‘png’ htmlDuplicatesBarplot: no visible global function definition for ‘tiff’ htmlDuplicatesBarplot: no visible global function definition for ‘dev.off’ htmlDuplicatesBarplot: no visible global function definition for ‘pdf’ htmlInsertSizeHist: no visible global function definition for ‘jpeg’ htmlInsertSizeHist: no visible global function definition for ‘png’ htmlInsertSizeHist: no visible global function definition for ‘tiff’ htmlInsertSizeHist: no visible global function definition for ‘dev.off’ htmlInsertSizeHist: no visible global function definition for ‘pdf’ htmlSensiBarplot: no visible global function definition for ‘jpeg’ htmlSensiBarplot: no visible global function definition for ‘png’ htmlSensiBarplot: no visible global function definition for ‘tiff’ htmlSensiBarplot: no visible global function definition for ‘dev.off’ htmlSensiBarplot: no visible global function definition for ‘pdf’ htmlSpeciBarplot: no visible global function definition for ‘jpeg’ htmlSpeciBarplot: no visible global function definition for ‘png’ htmlSpeciBarplot: no visible global function definition for ‘tiff’ htmlSpeciBarplot: no visible global function definition for ‘dev.off’ htmlSpeciBarplot: no visible global function definition for ‘pdf’ htmlUniformityPlot: no visible global function definition for ‘jpeg’ htmlUniformityPlot: no visible global function definition for ‘png’ htmlUniformityPlot: no visible global function definition for ‘tiff’ htmlUniformityPlot: no visible global function definition for ‘dev.off’ htmlUniformityPlot: no visible global function definition for ‘pdf’ html_img: no visible global function definition for ‘jpeg’ html_img: no visible global function definition for ‘png’ html_img: no visible global function definition for ‘tiff’ html_img: no visible global function definition for ‘dev.off’ html_img: no visible global function definition for ‘pdf’ insert.size.hist: no visible global function definition for ‘boxplot.stats’ insert.size.hist: no visible global function definition for ‘hist’ insert.size.hist: no visible global function definition for ‘abline’ insert.size.hist: no visible global function definition for ‘legend’ insert.size.hist: no visible global function definition for ‘values’ make.multi.report: no visible global function definition for ‘packageDescription’ make.report: no visible global function definition for ‘packageDescription’ make.wigfiles: no visible global function definition for ‘write.table’ multiTEQCreport: no visible global function definition for ‘read.table’ multiTEQCreport: no visible global function definition for ‘write.table’ myreduce: no visible global function definition for ‘isTRUEorFALSE’ myreduce: no visible global function definition for ‘isSingleNumber’ myreduce : FUN: no visible global function definition for ‘new2’ myreduce: no visible global function definition for ‘new2’ myreduce: no visible global function definition for ‘endoapply’ plot.i: no visible global function definition for ‘points’ plot.i: no visible global function definition for ‘abline’ reads2pairs: no visible global function definition for ‘seqnames’ reads2pairs: no visible global function definition for ‘Rle’ reads2pairs: no visible global function definition for ‘GRanges’ readsPerTarget: no visible global function definition for ‘queryHits’ sensiBarplot: no visible global function definition for ‘colorRampPalette’ sensiBarplot: no visible global function definition for ‘par’ sensiBarplot: no visible global function definition for ‘barplot’ sensiBarplot: no visible global function definition for ‘legend’ speciBarplot: no visible global function definition for ‘par’ speciBarplot: no visible global function definition for ‘barplot’ unifplot: no visible global function definition for ‘par’ unifplot: no visible global function definition for ‘lines’ unifplot: no visible global function definition for ‘legend’ Undefined global functions or variables: Axis GRanges Rle abline axis barplot box boxplot.stats colorRampPalette count.fields dev.off endoapply hist isSingleNumber isTRUEorFALSE jpeg keepSeqlevels legend lines mcols mtext new2 packageDescription pairs par pdf png points queryHits read.delim read.table rect seqlevelsInUse seqnames smooth.spline sortSeqlevels strwidth text tiff values write.table Consider adding importFrom("grDevices", "boxplot.stats", "colorRampPalette", "dev.off", "jpeg", "pdf", "png", "tiff") importFrom("graphics", "Axis", "abline", "axis", "barplot", "box", "hist", "legend", "lines", "mtext", "pairs", "par", "points", "rect", "strwidth", "text") importFrom("stats", "smooth.spline") importFrom("utils", "count.fields", "packageDescription", "read.delim", "read.table", "write.table") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in documentation object 'TEQCreport.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'chrom.barplot.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'coverage.GC.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'coverage.plot.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'coverage.target.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'coverage.targetlength.plot.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'duplicates.barplot.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'fraction.reads.target.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'fraction.target.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'get.baits.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'get.reads.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'get.targets.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'insert.size.hist.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'reads2pairs.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'readsPerTarget.Rd': ‘[IRanges:RangedData-class]{RangedData}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘TEQC.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/TEQC.Rcheck/00check.log’ for details.