############################################################################## ############################################################################## ### ### 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_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/viper.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘viper/DESCRIPTION’ ... OK * this is package ‘viper’ version ‘1.34.0’ * 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 R 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 documentation object 'viper' ‘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 34.832 2.903 48.230 shadow 25.655 1.363 35.024 bootstrapViper 24.624 1.379 35.320 msviperSynergy 17.668 1.166 24.025 msviperCombinatorial 15.022 0.648 19.964 viperRPT 13.039 0.981 18.289 msviper 13.222 0.626 19.234 plot.msviper 12.859 0.686 17.742 viper 11.631 0.961 17.019 bootstrapmsviper 9.421 0.477 13.663 bootstrapTtest-methods 7.233 0.353 10.171 ttestNull-methods 6.949 0.478 9.596 ledge 7.132 0.220 10.014 msviperAnnot 5.363 0.227 7.671 aracne2regulon 4.187 0.392 6.196 msviperClass 3.803 0.153 5.324 aracne2regulon4cnv 3.570 0.243 5.036 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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-3.17-bioc/meat/viper.Rcheck/00check.log’ for details.