############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scDD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scDD_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/scDD.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scDD/DESCRIPTION’ ... OK * this is package ‘scDD’ version ‘1.28.0’ * 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 ‘scDD’ 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 dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘grDevices’ ‘graphics’ ‘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 calcMV: no visible global function definition for ‘var’ classifyDD: no visible global function definition for ‘quantile’ classifyDD: no visible global function definition for ‘rt’ classifyDD: no visible global function definition for ‘lm’ classifyDD: no visible global function definition for ‘t.test’ feDP: no visible global function definition for ‘runif’ feDP: no visible global function definition for ‘lm’ feDP: no visible global function definition for ‘t.test’ feDP: no visible global function definition for ‘fisher.test’ feDP: no visible global function definition for ‘p.adjust’ findFC : createFindFC: no visible global function definition for ‘quantile’ findFC : createFindFC : f: no visible global function definition for ‘runif’ findFC: no visible global function definition for ‘par’ findFC: no visible global function definition for ‘points’ mclustRestricted: no visible global function definition for ‘runif’ permMclustCov: no visible global function definition for ‘model.matrix’ permMclustCov: no visible global function definition for ‘lm’ permMclustCov : getPerm: no visible global function definition for ‘residuals’ permMclustGene: no visible global function definition for ‘model.matrix’ permMclustGene: no visible global function definition for ‘lm’ permMclustGene: no visible global function definition for ‘residuals’ scDD: no visible global function definition for ‘p.adjust’ scDD : fishersCombinedPval: no visible global function definition for ‘pchisq’ sideHist : ggplotColours: no visible global function definition for ‘hcl’ sideHist: no visible global function definition for ‘hist’ sideHist: no visible global function definition for ‘axis’ sideHist: no visible global function definition for ‘rect’ sideHist: no visible global function definition for ‘lines’ sideHist: no visible global function definition for ‘density’ simuDB: no visible global function definition for ‘rnbinom’ simuDE: no visible global function definition for ‘rnbinom’ simuDE: no visible global function definition for ‘var’ simuDM: no visible global function definition for ‘rnbinom’ simuDP: no visible global function definition for ‘rbinom’ simuDP: no visible global function definition for ‘rnbinom’ simulateSet: no visible global function definition for ‘pdf’ simulateSet: no visible global function definition for ‘dev.off’ simulateSet: no visible global function definition for ‘runif’ singleCellSimu: no visible global function definition for ‘var’ singleCellSimu: no visible global function definition for ‘lm’ testKS : onegene: no visible global function definition for ‘ks.test’ testKS: no visible global function definition for ‘p.adjust’ testZeroes : onegene: no visible global function definition for ‘binomial’ validation : : no visible global function definition for ‘var’ validation: no visible binding for global variable ‘var’ validation: no visible global function definition for ‘par’ validation: no visible global function definition for ‘abline’ validation: no visible global function definition for ‘points’ Undefined global functions or variables: abline axis binomial density dev.off fisher.test hcl hist ks.test lines lm model.matrix p.adjust par pchisq pdf points quantile rbinom rect residuals rnbinom rt runif t.test var Consider adding importFrom("grDevices", "dev.off", "hcl", "pdf") importFrom("graphics", "abline", "axis", "hist", "lines", "par", "points", "rect") importFrom("stats", "binomial", "density", "fisher.test", "ks.test", "lm", "model.matrix", "p.adjust", "pchisq", "quantile", "rbinom", "residuals", "rnbinom", "rt", "runif", "t.test", "var") 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed scDD 108.189 4.738 36.692 simulateSet 28.010 5.067 9.209 results 13.453 1.675 12.558 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/scDD.Rcheck/00check.log’ for details.