############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CNAnorm.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CNAnorm_1.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CNAnorm.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘CNAnorm/DESCRIPTION’ ... OK * this is package ‘CNAnorm’ version ‘1.52.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘CNAnorm’ can be installed ... OK * used Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 code 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .OTquantileWeights: no visible global function definition for ‘median’ .OTquantileWeights: no visible global function definition for ‘quantile’ .TTquantileWeights: no visible global function definition for ‘median’ .TTquantileWeights: no visible global function definition for ‘quantile’ .exportTable: no visible global function definition for ‘write.table’ .gaussianWeights: no visible global function definition for ‘median’ .gaussianWeights: no visible global function definition for ‘sd’ .guessPeaksAndPloidy: no visible global function definition for ‘density’ .guessPeaksAndPloidy: no visible global function definition for ‘median’ .peakPloidy: no visible global function definition for ‘median’ .plotGenome: no visible global function definition for ‘text’ .plotGenome: no visible global function definition for ‘par’ .plotGenome: no visible global function definition for ‘points’ .plotGenome: no visible global function definition for ‘axis’ .plotGenome: no visible global function definition for ‘axTicks’ .plotGenome: no visible global function definition for ‘title’ .plotGenome: no visible global function definition for ‘mtext’ .plotGenome: no visible global function definition for ‘abline’ .plotGenome: no visible global function definition for ‘data’ .plotGenome: no visible global function definition for ‘lines’ .plotPeaks: no visible global function definition for ‘density’ .plotPeaks: no visible global function definition for ‘median’ .plotPeaks: no visible global function definition for ‘lines’ .plotPeaks: no visible global function definition for ‘abline’ .plotPeaks: no visible global function definition for ‘text’ .plotPeaks: no visible global function definition for ‘legend’ .plotPeaks_old: no visible global function definition for ‘median’ .plotPeaks_old: no visible global function definition for ‘lines’ .plotPeaks_old: no visible global function definition for ‘abline’ .plotPeaks_old: no visible global function definition for ‘text’ .plotPeaks_old: no visible global function definition for ‘legend’ Rcheck: no visible global function definition for ‘lm’ bandseg: no visible global function definition for ‘filter’ brute.seg: no visible global function definition for ‘median’ findOutliers: no visible global function definition for ‘median’ findOutliers: no visible global function definition for ‘density’ gcNormalize: no visible global function definition for ‘loess’ gcNormalize: no visible global function definition for ‘predict’ gcNormalize: no visible global function definition for ‘median’ get.initial.values: no visible global function definition for ‘var’ get.initial.values: no visible global function definition for ‘quantile’ getMQR: no visible global function definition for ‘lm’ global.norm: no visible global function definition for ‘lm’ global.norm: no visible global function definition for ‘predict’ medianWinSize: no visible global function definition for ‘median’ myDensity: no visible global function definition for ‘median’ myDensity: no visible global function definition for ‘sd’ myDensity: no visible global function definition for ‘density’ myPeaks: no visible global function definition for ‘embed’ pdetect: no visible global function definition for ‘rnorm’ pdetect: no visible global function definition for ‘density’ pdetect: no visible global function definition for ‘var’ pdetect: no visible global function definition for ‘quantile’ pdetect: no visible global function definition for ‘dnorm’ pdetect: no visible global function definition for ‘median’ pdetect.iter: no visible global function definition for ‘var’ pdetect.iter: no visible global function definition for ‘dnorm’ pdetect.iter: no visible global function definition for ‘median’ plotPeaksMixture: no visible global function definition for ‘median’ plotPeaksMixture: no visible global function definition for ‘hist’ plotPeaksMixture: no visible global function definition for ‘abline’ rseg: no visible global function definition for ‘median’ smoothseg: no visible global function definition for ‘lines’ exportTable,CNAnorm: no visible global function definition for ‘write.table’ peakPloidy,CNAnorm: no visible global function definition for ‘median’ plotGenome,CNAnorm: no visible global function definition for ‘text’ plotGenome,CNAnorm: no visible global function definition for ‘par’ plotGenome,CNAnorm: no visible global function definition for ‘points’ plotGenome,CNAnorm: no visible global function definition for ‘axis’ plotGenome,CNAnorm: no visible global function definition for ‘axTicks’ plotGenome,CNAnorm: no visible global function definition for ‘title’ plotGenome,CNAnorm: no visible global function definition for ‘mtext’ plotGenome,CNAnorm: no visible global function definition for ‘abline’ plotGenome,CNAnorm: no visible global function definition for ‘data’ plotGenome,CNAnorm: no visible global function definition for ‘lines’ plotPeaks,CNAnorm: no visible global function definition for ‘density’ plotPeaks,CNAnorm: no visible global function definition for ‘median’ plotPeaks,CNAnorm: no visible global function definition for ‘lines’ plotPeaks,CNAnorm: no visible global function definition for ‘abline’ plotPeaks,CNAnorm: no visible global function definition for ‘text’ plotPeaks,CNAnorm: no visible global function definition for ‘legend’ Undefined global functions or variables: abline axTicks axis data density dnorm embed filter hist legend lines lm loess median mtext par points predict quantile rnorm sd text title var write.table Consider adding importFrom("graphics", "abline", "axTicks", "axis", "hist", "legend", "lines", "mtext", "par", "points", "text", "title") importFrom("stats", "density", "dnorm", "embed", "filter", "lm", "loess", "median", "predict", "quantile", "rnorm", "sd", "var") importFrom("utils", "data", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) peakPloidy.Rd:67-68: Lost braces 67 | \bold{peakRatio}{Threshold used to call a peak. Peaks smaller than | ^ checkRd: (-1) peakPloidy.Rd:70-73: Lost braces 70 | \bold{spacingTolerance}{A parameter smaller than 1 which describes how | ^ checkRd: (-1) peakPloidy.Rd:75-76: Lost braces 75 | \bold{interceptRatio}{Minimum value for the intercept of the linear model. | ^ * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking usage of KIND in Fortran files ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed peakPloidy 9.05 0.043 9.093 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/CNAnorm.Rcheck/00check.log’ for details.