############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:viper.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings viper_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/viper.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * checking for file ‘viper/DESCRIPTION’ ... OK * this is package ‘viper’ version ‘1.35.0’ * 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 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed bootstrapViper 41.022 0.303 41.398 viperSignature-methods 28.644 0.079 28.778 shadow 19.526 0.068 19.633 msviperSynergy 14.122 0.084 14.235 msviperCombinatorial 11.251 0.107 11.382 viperRPT 10.831 0.035 10.885 plot.msviper 10.176 0.040 10.237 msviper 9.980 0.076 10.077 viper 9.638 0.052 9.708 bootstrapmsviper 8.124 0.056 8.197 ttestNull-methods 7.632 0.040 7.690 bootstrapTtest-methods 7.297 0.088 7.397 ledge 5.407 0.020 5.437 aracne2regulon 5.289 0.120 5.442 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘viper.Rnw’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/viper.Rcheck/00check.log’ for details.