############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:viper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings viper_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/viper.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-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 Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘viper/DESCRIPTION’ ... OK * this is package ‘viper’ version ‘1.38.0’ * 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 ‘viper’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE TFmode1: no visible global function definition for ‘cor’ TFmode2: no visible global function definition for ‘cor’ TFscore : : no visible global function definition for ‘pnorm’ aREA: no visible global function definition for ‘qnorm’ aREA: no visible global function definition for ‘txtProgressBar’ aREA : : no visible global function definition for ‘setTxtProgressBar’ aecdf: no visible global function definition for ‘quantile’ aecdf: no visible global function definition for ‘ecdf’ aecdf: no visible global function definition for ‘lm’ aecdf: no visible global function definition for ‘approxfun’ aecdf : dnull: no visible global function definition for ‘predict’ aecdf : dnull: no visible global function definition for ‘qnorm’ aecdf1: no visible global function definition for ‘quantile’ aecdf1: no visible global function definition for ‘ecdf’ aecdf1: no visible binding for global variable ‘tl2’ aecdf1: no visible binding for global variable ‘iq2’ aecdf1: no visible global function definition for ‘epd’ aecdf1: no visible global function definition for ‘lm’ aecdf1: no visible global function definition for ‘predict’ aecdf1: no visible global function definition for ‘qnorm’ approxk2d: no visible binding for global variable ‘quantile’ bootstrapViper : : : no visible global function definition for ‘qnorm’ bootstrapViper : : no visible global function definition for ‘txtProgressBar’ bootstrapViper : : : no visible global function definition for ‘setTxtProgressBar’ bootstrapmsviper: no visible binding for global variable ‘median’ bootstrapmsviper: no visible global function definition for ‘pnorm’ distMode: no visible global function definition for ‘density’ groupPwea3: no visible global function definition for ‘qnorm’ groupPwea3: no visible global function definition for ‘txtProgressBar’ groupPwea3 : : no visible global function definition for ‘setTxtProgressBar’ groupPwea3 : : no visible global function definition for ‘qnorm’ groupPwea3: no visible global function definition for ‘pnorm’ msviper: no visible global function definition for ‘txtProgressBar’ msviper : : no visible global function definition for ‘setTxtProgressBar’ msviper: no visible global function definition for ‘pnorm’ msviperClass: no visible global function definition for ‘pnorm’ msviperCombinatorial: no visible global function definition for ‘combn’ msviperSynergy : : no visible global function definition for ‘qnorm’ msviperSynergy : : no visible global function definition for ‘quantile’ msviperSynergy : : no visible global function definition for ‘ecdf’ msviperSynergy : : no visible global function definition for ‘knots’ msviperSynergy : : no visible global function definition for ‘smooth.spline’ msviperSynergy : : no visible global function definition for ‘predict’ msviperSynergy: no visible global function definition for ‘txtProgressBar’ msviperSynergy : : no visible global function definition for ‘setTxtProgressBar’ plot.msviper: no visible global function definition for ‘par’ plot.msviper: no visible global function definition for ‘layout’ plot.msviper: no visible global function definition for ‘rgb2hsv’ plot.msviper: no visible global function definition for ‘col2rgb’ plot.msviper: no visible global function definition for ‘hsv’ plot.msviper: no visible global function definition for ‘lines’ plot.msviper: no visible global function definition for ‘smooth.spline’ plot.msviper: no visible global function definition for ‘text’ plot.msviper: no visible global function definition for ‘axis’ plot.msviper: no visible global function definition for ‘abline’ plot.msviper: no visible global function definition for ‘image’ plot.msviper: no visible global function definition for ‘box’ plot.msviper: no visible global function definition for ‘grid’ ppwea3NULLf : : : no visible global function definition for ‘pnorm’ pwea3NULLf : : no visible global function definition for ‘quantile’ pwea3NULLf : : no visible global function definition for ‘ecdf’ pwea3NULLf : : no visible global function definition for ‘knots’ pwea3NULLf : : no visible global function definition for ‘smooth.spline’ pwea3NULLf : : : no visible global function definition for ‘predict’ pwea3NULLf : : : no visible global function definition for ‘qnorm’ pwea3NULLf: no visible global function definition for ‘txtProgressBar’ pwea3NULLf : : no visible global function definition for ‘setTxtProgressBar’ pwea3NULLgroups: no visible global function definition for ‘qnorm’ pwea3NULLgroups: no visible global function definition for ‘txtProgressBar’ pwea3NULLgroups : : no visible global function definition for ‘setTxtProgressBar’ regulonDist : : no visible global function definition for ‘fisher.test’ scaleGroups : : no visible global function definition for ‘qnorm’ scaleGroups: no visible global function definition for ‘runif’ selectTFs : : no visible global function definition for ‘combn’ shadow: no visible global function definition for ‘combn’ shadow : : no visible global function definition for ‘quantile’ shadow : : no visible global function definition for ‘ecdf’ shadow : : no visible global function definition for ‘knots’ shadow : : no visible global function definition for ‘smooth.spline’ shadow : : no visible global function definition for ‘predict’ shadow: no visible global function definition for ‘txtProgressBar’ shadow : : no visible global function definition for ‘setTxtProgressBar’ shadowRegulon: no visible global function definition for ‘pnorm’ shadowRegulon : : no visible global function definition for ‘qnorm’ shadowRegulon : : no visible global function definition for ‘pnorm’ shadowRegulon: no visible global function definition for ‘combn’ signatureDistance: no visible global function definition for ‘qnorm’ summary.msviper: no visible global function definition for ‘p.adjust’ viper: no visible global function definition for ‘punif’ viper : : no visible global function definition for ‘median’ viper : : no visible global function definition for ‘mad’ viper : : no visible global function definition for ‘txtProgressBar’ viper : : : no visible global function definition for ‘setTxtProgressBar’ viperRPT : : no visible global function definition for ‘residuals’ viperRPT : : no visible global function definition for ‘lm’ viperRPT : : no visible global function definition for ‘smooth.spline’ viperSimilarity: no visible global function definition for ‘qnorm’ bootstrapTtest,matrix : : no visible global function definition for ‘qnorm’ bootstrapTtest,matrix : : no visible global function definition for ‘pt’ bootstrapTtest,matrix: no visible global function definition for ‘txtProgressBar’ bootstrapTtest,matrix : : no visible global function definition for ‘setTxtProgressBar’ rowTtest,matrix: no visible global function definition for ‘pt’ ttestNull,matrix : : no visible global function definition for ‘qnorm’ ttestNull,matrix : : no visible global function definition for ‘pt’ ttestNull,matrix: no visible global function definition for ‘txtProgressBar’ ttestNull,matrix : : no visible global function definition for ‘setTxtProgressBar’ viperSignature,matrix : : no visible global function definition for ‘qnorm’ viperSignature,matrix: no visible global function definition for ‘txtProgressBar’ viperSignature,matrix : : : no visible global function definition for ‘qnorm’ viperSignature,matrix : : no visible global function definition for ‘setTxtProgressBar’ viperSignature,matrix: no visible global function definition for ‘combn’ Undefined global functions or variables: abline approxfun axis box col2rgb combn cor density ecdf epd fisher.test grid hsv image iq2 knots layout lines lm mad median p.adjust par pnorm predict pt punif qnorm quantile residuals rgb2hsv runif setTxtProgressBar smooth.spline text tl2 txtProgressBar Consider adding importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv") importFrom("graphics", "abline", "axis", "box", "grid", "image", "layout", "lines", "par", "text") importFrom("stats", "approxfun", "cor", "density", "ecdf", "fisher.test", "knots", "lm", "mad", "median", "p.adjust", "pnorm", "predict", "pt", "punif", "qnorm", "quantile", "residuals", "runif", "smooth.spline") importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar") 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 ... WARNING Undocumented arguments in Rd file 'viper.Rd' ‘mvws’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... 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 viperSignature-methods 33.261 3.370 47.128 bootstrapViper 22.318 1.195 30.478 shadow 18.147 1.059 25.122 viperRPT 12.476 1.302 17.421 msviperSynergy 11.601 0.692 15.839 viper 10.948 1.069 15.254 msviperCombinatorial 9.747 0.535 13.085 plot.msviper 9.282 0.443 12.664 msviper 8.983 0.591 12.490 bootstrapmsviper 6.616 0.638 9.389 ttestNull-methods 4.438 0.408 6.203 bootstrapTtest-methods 4.406 0.254 6.023 ledge 4.366 0.205 5.976 * 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: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/viper.Rcheck/00check.log’ for details.