############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ABSSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ABSSeq_1.59.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ABSSeq.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ABSSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ABSSeq’ version ‘1.59.0’ * 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 ‘ABSSeq’ 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 'library' or 'require' call to ‘edgeR’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: ‘methods’ 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 ABSDataSet: no visible global function definition for ‘new’ ABSSeqlm: no visible global function definition for ‘pnorm’ ABSSeqlm: no visible global function definition for ‘p.adjust’ ReplaceOutliersByMAD: no visible global function definition for ‘is’ ReplaceOutliersByMAD: no visible global function definition for ‘model.matrix’ ReplaceOutliersByMAD: no visible global function definition for ‘predict’ aFoldcomplexDesign: no visible binding for global variable ‘sd’ aFoldcomplexDesign: no visible binding for global variable ‘var’ aFoldcomplexDesign: no visible global function definition for ‘sd’ callDEs: no visible global function definition for ‘is’ callDEs: no visible binding for global variable ‘p.adjust.methods’ callDEs: no visible global function definition for ‘pnorm’ callDEs: no visible global function definition for ‘pnbinom’ callDEs: no visible global function definition for ‘p.adjust’ callParameter: no visible global function definition for ‘is’ callParameter: no visible binding for global variable ‘var’ callParameter: no visible global function definition for ‘quantile’ callParameter: no visible global function definition for ‘predict’ callParameter: no visible global function definition for ‘model.matrix’ callParameterwithoutReplicates: no visible global function definition for ‘is’ callParameterwithoutReplicates: no visible binding for global variable ‘sd’ callParameterwithoutReplicates: no visible global function definition for ‘predict’ callParameterwithoutReplicates: no visible binding for global variable ‘var’ callParameterwithoutReplicates: no visible global function definition for ‘quantile’ callParameterwithoutReplicates: no visible global function definition for ‘model.matrix’ callPergroup: no visible binding for global variable ‘var’ estimateSizeFactorsForMatrix: no visible binding for global variable ‘median’ genAFold: no visible binding for global variable ‘var’ genAFold: no visible binding for global variable ‘sd’ genAFold: no visible global function definition for ‘sd’ normalFactors: no visible global function definition for ‘is’ normalFactors: no visible global function definition for ‘validObject’ normalFactors : rowQuar: no visible global function definition for ‘quantile’ normalFactors: no visible global function definition for ‘calcNormFactors’ plotDifftoBase: no visible global function definition for ‘is’ preAFold: no visible global function definition for ‘quantile’ preAFold: no visible global function definition for ‘var’ preAFold: no visible global function definition for ‘predict’ preAFoldComplex: no visible global function definition for ‘quantile’ preAFoldComplex: no visible global function definition for ‘var’ preAFoldComplex: no visible global function definition for ‘predict’ qtotalNormalized : rowQuar: no visible global function definition for ‘quantile’ qtotalNormalized : rowQuar: no visible global function definition for ‘sd’ qtotalNormalized : rowQuar: no visible global function definition for ‘median’ qtotalNormalized : rowQuar : : no visible global function definition for ‘median’ replaceByrow: no visible global function definition for ‘median’ replaceByrow: no visible global function definition for ‘mad’ LevelstoNormFC<-,ABSDataSet-numeric: no visible global function definition for ‘validObject’ [[<-,SumInfo-character-missing: no visible global function definition for ‘as’ counts<-,ABSDataSet-matrix: no visible global function definition for ‘validObject’ excounts<-,ABSDataSet-matrix: no visible global function definition for ‘validObject’ groups<-,ABSDataSet-factor: no visible global function definition for ‘validObject’ maxRates<-,ABSDataSet-numeric: no visible global function definition for ‘validObject’ minRates<-,ABSDataSet-numeric: no visible global function definition for ‘validObject’ minimalDispersion<-,ABSDataSet-numeric: no visible global function definition for ‘validObject’ normMethod<-,ABSDataSet-character: no visible global function definition for ‘validObject’ paired<-,ABSDataSet-logical: no visible global function definition for ‘validObject’ sFactors<-,ABSDataSet-numeric: no visible global function definition for ‘validObject’ Undefined global functions or variables: as calcNormFactors is mad median model.matrix new p.adjust p.adjust.methods pnbinom pnorm predict quantile sd validObject var Consider adding importFrom("methods", "as", "is", "new", "validObject") importFrom("stats", "mad", "median", "model.matrix", "p.adjust", "p.adjust.methods", "pnbinom", "pnorm", "predict", "quantile", "sd", "var") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 callParameter 19.392 0.870 21.937 plotDifftoBase 19.266 0.847 20.909 callDEs 19.098 0.878 21.187 ABSSeq 19.090 0.836 20.973 results 18.949 0.819 20.660 excounts 14.202 0.942 15.726 ReplaceOutliersByMAD 14.174 0.714 16.133 ABSSeqlm 10.355 0.605 11.440 genAFold 7.255 0.482 8.098 aFoldcomplexDesign 6.862 0.404 8.064 * 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-3.20-bioc/meat/ABSSeq.Rcheck/00check.log’ for details.