############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SCnorm.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SCnorm_1.31.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SCnorm.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘SCnorm/DESCRIPTION’ ... OK * this is package ‘SCnorm’ version ‘1.31.1’ * 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 ‘SCnorm’ 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 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 ... NOTE Namespace in Imports field not imported from: ‘stats’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GetTD: no visible global function definition for ‘poly’ GetTD: no visible binding for global variable ‘na.exclude’ GetTD: no visible global function definition for ‘predict’ SCnorm : : : no visible global function definition for ‘median’ SCnormFit: no visible global function definition for ‘density’ SCnormFit: no visible global function definition for ‘poly’ SCnormFit: no visible binding for global variable ‘na.exclude’ SCnormFit: no visible global function definition for ‘predict’ SCnormFit: no visible global function definition for ‘quantile’ correctWithin: no visible global function definition for ‘quantile’ correctWithin: no visible global function definition for ‘loess’ correctWithin: no visible global function definition for ‘predict’ correctWithin: no visible global function definition for ‘median’ evaluateK : : no visible global function definition for ‘median’ generateEvalPlot: no visible binding for global variable ‘median’ getDens: no visible global function definition for ‘density’ getDens: no visible global function definition for ‘na.omit’ plotCountDepth : : : no visible global function definition for ‘median’ plotWithinFactor : : no visible global function definition for ‘median’ plotWithinFactor : : : no visible global function definition for ‘median’ scaleNormMultCont : : no visible global function definition for ‘median’ scaleNormMultCont: no visible global function definition for ‘median’ Undefined global functions or variables: density loess median na.exclude na.omit poly predict quantile Consider adding importFrom("stats", "density", "loess", "median", "na.exclude", "na.omit", "poly", "predict", "quantile") 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed getSlopes 5.93 0.696 4.683 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/SCnorm.Rcheck/00check.log’ for details.