############################################################################## ############################################################################## ### ### 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_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/viper.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘viper/DESCRIPTION’ ... OK * this is package ‘viper’ version ‘1.40.0’ * 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 31.991 4.172 36.777 shadow 24.790 1.938 27.225 bootstrapViper 24.189 1.559 28.020 msviperSynergy 17.373 1.338 18.847 msviperCombinatorial 13.538 0.854 14.518 viperRPT 12.381 1.278 13.814 plot.msviper 12.509 0.991 14.147 msviper 12.756 0.463 13.584 viper 10.940 1.228 12.313 bootstrapmsviper 9.458 0.541 11.019 bootstrapTtest-methods 7.156 0.345 8.572 ttestNull-methods 6.747 0.581 7.367 ledge 6.741 0.218 6.983 msviperAnnot 5.341 0.145 5.500 * 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-3.20-bioc/meat/viper.Rcheck/00check.log’ for details.