############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:viper.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings viper_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/viper.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘viper/DESCRIPTION’ ... OK * this is package ‘viper’ version ‘1.39.0’ * 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed viperSignature-methods 29.143 0.039 29.253 bootstrapViper 22.143 0.343 22.535 shadow 19.658 0.068 19.771 msviperSynergy 14.191 0.036 14.260 msviperCombinatorial 11.900 0.052 11.985 msviper 10.499 0.031 10.558 plot.msviper 10.355 0.052 10.429 viperRPT 10.323 0.028 10.374 viper 9.281 0.080 9.384 bootstrapmsviper 7.883 0.052 7.953 bootstrapTtest-methods 7.533 0.072 7.628 ttestNull-methods 7.210 0.012 7.236 ledge 5.465 0.016 5.493 aracne2regulon 5.237 0.052 5.300 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/viper.Rcheck/00check.log’ for details.