* using log directory 'C:/msys64/home/tomas/utf/ucrt64/inst_all/copynumber.Rcheck' * using R Under development (unstable) (2020-06-23 r78739) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'copynumber/DESCRIPTION' ... OK * this is package 'copynumber' version '1.24.0' * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'copynumber' can be installed ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Package in Depends field not imported from: 'BiocGenerics' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE addArmlines: no visible global function definition for 'modifyList' addArmlines: no visible global function definition for 'abline' addChromlines: no visible global function definition for 'modifyList' addChromlines: no visible global function definition for 'abline' addChromlines: no visible global function definition for 'mtext' addToFreqPlot: no visible global function definition for 'abline' addToFreqPlot: no visible global function definition for 'axis' addToFreqPlot: no visible global function definition for 'title' addToPlot: no visible global function definition for 'axis' addToPlot: no visible global function definition for 'mtext' addToPlot: no visible global function definition for 'title' addToPlot: no visible global function definition for 'abline' aspcf: no visible global function definition for 'read.table' aspcf: no visible global function definition for 'write.table' c.lines: no visible global function definition for 'lines' chromPattern: no visible global function definition for 'rect' chromPattern: no visible global function definition for 'par' chromosomeAberration: no visible global function definition for 'dev.cur' chromosomeAberration: no visible global function definition for 'dev.new' chromosomeAberration: no visible global function definition for 'par' chromosomeAberration: no visible global function definition for 'rect' chromosomeAberration: no visible global function definition for 'title' chromosomeAberration: no visible global function definition for 'axis' chromosomeAberration: no visible global function definition for 'abline' chromosomeAberration: no visible global function definition for 'devAskNewPage' chromosomeFreq: no visible global function definition for 'dev.cur' chromosomeFreq: no visible global function definition for 'dev.new' chromosomeFreq: no visible global function definition for 'par' chromosomeFreq: no visible global function definition for 'rect' chromosomeFreq: no visible global function definition for 'abline' chromosomeFreq: no visible global function definition for 'title' chromosomeFreq: no visible global function definition for 'devAskNewPage' chromosomeHeat: no visible global function definition for 'dev.cur' chromosomeHeat: no visible global function definition for 'dev.new' chromosomeHeat: no visible global function definition for 'par' chromosomeHeat: no visible global function definition for 'rect' chromosomeHeat: no visible global function definition for 'title' chromosomeHeat: no visible global function definition for 'axis' chromosomeHeat: no visible global function definition for 'abline' chromosomeHeat: no visible global function definition for 'devAskNewPage' colorSetup: no visible global function definition for 'colorRampPalette' connectSeg: no visible global function definition for 'segments' draw.roundEdge: no visible global function definition for 'polygon' drawStalk: no visible global function definition for 'polygon' filterMarkS4: no visible global function definition for 'quantile' genomeAberration: no visible global function definition for 'dev.cur' genomeAberration: no visible global function definition for 'dev.new' genomeAberration: no visible global function definition for 'par' genomeAberration: no visible global function definition for 'rect' genomeAberration: no visible global function definition for 'title' genomeAberration: no visible global function definition for 'axis' genomeAberration: no visible global function definition for 'abline' genomeAberration: no visible global function definition for 'devAskNewPage' genomeFreq: no visible global function definition for 'dev.cur' genomeFreq: no visible global function definition for 'dev.new' genomeFreq: no visible global function definition for 'par' genomeFreq: no visible global function definition for 'title' genomeFreq: no visible global function definition for 'rect' genomeFreq: no visible global function definition for 'abline' genomeFreq: no visible global function definition for 'devAskNewPage' genomeHeat: no visible global function definition for 'dev.cur' genomeHeat: no visible global function definition for 'dev.new' genomeHeat: no visible global function definition for 'par' genomeHeat: no visible global function definition for 'rect' genomeHeat: no visible global function definition for 'title' genomeHeat: no visible global function definition for 'axis' genomeHeat: no visible global function definition for 'abline' genomeHeat: no visible global function definition for 'devAskNewPage' getFreqPlotParameters: no visible global function definition for 'modifyList' getHeatParameters: no visible global function definition for 'modifyList' getMad: no visible global function definition for 'mad' getPlotParameters: no visible global function definition for 'rainbow' getPlotParameters: no visible global function definition for 'modifyList' madWins: no visible global function definition for 'mad' medianFilter: no visible global function definition for 'runmed' multipcf: no visible global function definition for 'read.table' multipcf: no visible global function definition for 'write.table' pcf: no visible global function definition for 'read.table' pcf: no visible global function definition for 'write.table' pcfWins: no visible global function definition for 'mad' plotAllele: no visible global function definition for 'modifyList' plotAllele: no visible global function definition for 'pdf' plotAllele: no visible global function definition for 'dev.cur' plotAllele: no visible global function definition for 'dev.new' plotAllele: no visible global function definition for 'devAskNewPage' plotAllele: no visible global function definition for 'quantile' plotAllele: no visible global function definition for 'par' plotAllele: no visible global function definition for 'legend' plotAllele: no visible global function definition for 'title' plotAllele: no visible global function definition for 'graphics.off' plotChrom: no visible global function definition for 'pdf' plotChrom: no visible global function definition for 'dev.cur' plotChrom: no visible global function definition for 'dev.new' plotChrom: no visible global function definition for 'devAskNewPage' plotChrom: no visible global function definition for 'quantile' plotChrom: no visible global function definition for 'par' plotChrom: no visible global function definition for 'legend' plotChrom: no visible global function definition for 'title' plotChrom: no visible global function definition for 'graphics.off' plotCircle: no visible global function definition for 'par' plotCircle: no visible global function definition for 'text' plotCircle: no visible global function definition for 'xspline' plotCircle: no visible global function definition for 'lines' plotGamma: no visible global function definition for 'quantile' plotGamma: no visible global function definition for 'col2rgb' plotGamma: no visible global function definition for 'rgb' plotGamma: no visible global function definition for 'dev.cur' plotGamma: no visible global function definition for 'dev.new' plotGamma: no visible global function definition for 'par' plotGamma: no visible global function definition for 'axis' plotGamma: no visible global function definition for 'box' plotGamma: no visible global function definition for 'legend' plotGamma: no visible global function definition for 'barplot' plotGamma: no visible global function definition for 'abline' plotGamma: no visible global function definition for 'mtext' plotGamma: no visible global function definition for 'points' plotGenome: no visible global function definition for 'quantile' plotGenome: no visible global function definition for 'pdf' plotGenome: no visible global function definition for 'dev.cur' plotGenome: no visible global function definition for 'dev.new' plotGenome: no visible global function definition for 'par' plotGenome: no visible global function definition for 'legend' plotGenome: no visible global function definition for 'title' plotGenome: no visible global function definition for 'devAskNewPage' plotGenome: no visible global function definition for 'graphics.off' plotIdeogram: no visible global function definition for 'rect' plotIdeogram: no visible global function definition for 'mtext' plotObs: no visible global function definition for 'par' plotSample: no visible global function definition for 'pdf' plotSample: no visible global function definition for 'dev.cur' plotSample: no visible global function definition for 'dev.new' plotSample: no visible global function definition for 'devAskNewPage' plotSample: no visible global function definition for 'quantile' plotSample: no visible global function definition for 'par' plotSample: no visible global function definition for 'legend' plotSample: no visible global function definition for 'title' plotSample: no visible global function definition for 'graphics.off' plotSegments: no visible global function definition for 'par' sawMarkM: no visible global function definition for 'quantile' subset.abe: no visible binding for global variable 'quantile' subsetData: no visible global function definition for 'read.table' subsetSegments: no visible global function definition for 'read.table' winsorize: no visible global function definition for 'read.table' winsorize: no visible global function definition for 'write.table' Undefined global functions or variables: abline axis barplot box col2rgb colorRampPalette dev.cur dev.new devAskNewPage graphics.off legend lines mad modifyList mtext par pdf points polygon quantile rainbow read.table rect rgb runmed segments text title write.table xspline Consider adding importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.cur", "dev.new", "devAskNewPage", "graphics.off", "pdf", "rainbow", "rgb") importFrom("graphics", "abline", "axis", "barplot", "box", "legend", "lines", "mtext", "par", "points", "polygon", "rect", "segments", "text", "title", "xspline") importFrom("stats", "mad", "quantile", "runmed") importFrom("utils", "modifyList", "read.table", "write.table") to your NAMESPACE file. * 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 R/sysdata.rda ... OK * checking installed files from 'inst/doc' ... 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 ... 'copynumber.rnw'... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See 'C:/msys64/home/tomas/utf/ucrt64/inst_all/copynumber.Rcheck/00check.log' for details.