############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CoRegNet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CoRegNet_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CoRegNet.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘CoRegNet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CoRegNet’ version ‘1.42.0’ * 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 ‘CoRegNet’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘RColorBrewer’ ‘gplots’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .descriptionUpdate: no visible global function definition for ‘vcount’ .descriptionUpdate: no visible global function definition for ‘fisher.test’ .distfun: no visible global function definition for ‘as.dist’ .distfun: no visible global function definition for ‘cor’ .fitGRN : : no visible global function definition for ‘lm’ .fitGRN : : no visible global function definition for ‘coef’ .fitGRN: no visible global function definition for ‘cor’ .fitGRN: no visible global function definition for ‘lm’ .fitGRN: no visible global function definition for ‘coef’ .hclustfun: no visible global function definition for ‘hclust’ .heatplot: no visible global function definition for ‘rainbow’ .heatplot : distf: no visible global function definition for ‘as.dist’ .heatplot : distf: no visible global function definition for ‘cor’ .heatplot : hclustf: no visible global function definition for ‘hclust’ .heatplot: no visible global function definition for ‘colorRampPalette’ .heatplot: no visible global function definition for ‘heatmap.2’ .heatplot: no visible global function definition for ‘quantile’ .tfPlot: no visible global function definition for ‘colorRampPalette’ .tfPlot: no visible global function definition for ‘rainbow’ .tfPlot: no visible global function definition for ‘par’ .tfPlot: no visible global function definition for ‘mtext’ .tfPlot: no visible global function definition for ‘quantile’ .traits : : no visible global function definition for ‘lines’ .traits: no visible global function definition for ‘abline’ automaticParameters: no visible global function definition for ‘quantile’ automaticParameters : : no visible global function definition for ‘pnorm’ automaticParameters: no visible global function definition for ‘abline’ automaticParameters: no visible global function definition for ‘sd’ coregnet : : no visible global function definition for ‘cor’ coregnet: no visible global function definition for ‘cor’ directedNetworkEnrichment: no visible global function definition for ‘fisher.test’ discretizeExpressionData: no visible global function definition for ‘sd’ fishersMethod: no visible global function definition for ‘pchisq’ legendPlot: no visible global function definition for ‘par’ legendPlot: no visible global function definition for ‘colorRampPalette’ legendPlot: no visible global function definition for ‘axis’ legendPlot: no visible global function definition for ‘rainbow’ list.enriched: no visible global function definition for ‘wilcox.test’ networkLegendPlot: no visible global function definition for ‘par’ networkLegendPlot: no visible global function definition for ‘symbols’ networkLegendPlot: no visible global function definition for ‘text’ networkLegendPlot: no visible global function definition for ‘rainbow’ networkLegendPlot: no visible global function definition for ‘segments’ networkLegendPlot: no visible global function definition for ‘arrows’ reactiveAdjacencyMatrix : : no visible global function definition for ‘rainbow’ set.overlap: no visible global function definition for ‘fisher.test’ undirectedNetworkEnrichment: no visible global function definition for ‘fisher.test’ updateData : : : no visible global function definition for ‘t.test’ activators,coregnet: no visible global function definition for ‘na.omit’ coregulators,coregnet: no visible global function definition for ‘p.adjust’ coregulators,coregnet : : no visible global function definition for ‘fisher.test’ refine,coregnet: no visible global function definition for ‘glm’ refine,coregnet: no visible global function definition for ‘abline’ regulatorInfluence,coregnet : : : no visible global function definition for ‘t.test’ regulators,coregnet: no visible global function definition for ‘na.omit’ repressors,coregnet: no visible global function definition for ‘na.omit’ targets,coregnet: no visible global function definition for ‘na.omit’ Undefined global functions or variables: abline arrows as.dist axis coef colorRampPalette cor fisher.test glm hclust heatmap.2 lines lm mtext na.omit p.adjust par pchisq pnorm quantile rainbow sd segments symbols t.test text vcount wilcox.test Consider adding importFrom("grDevices", "colorRampPalette", "rainbow") importFrom("graphics", "abline", "arrows", "axis", "lines", "mtext", "par", "segments", "symbols", "text") importFrom("stats", "as.dist", "coef", "cor", "fisher.test", "glm", "hclust", "lm", "na.omit", "p.adjust", "pchisq", "pnorm", "quantile", "sd", "t.test", "wilcox.test") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) discretizeExpressionData.Rd:73: Lost braces; missing escapes or markup? 73 | A matrix of integers with the same number of rows and the same number of column as the input numericalExpression. Values in the output matrix are in {-1,0,1}. | ^ checkRd: (-1) hLICORN.Rd:32: Lost braces; missing escapes or markup? 32 | optional. Should be in exactly the same format as \code{numericalExpression} (dimensions, colnames and rownames) and should contain value only in {-1,0,1} with -1 for under-expressed, 0 for no change and 1 for over expressed. For default value see details. | ^ * checking Rd metadata ... NOTE Invalid package aliases in Rd file 'coRegnet-package.Rd': ‘coRegnet-package’ * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed hLICORN 45.007 3.973 32.507 masterRegulator 17.332 1.258 11.730 * checking for unstated dependencies in ‘tests’ ... WARNING '::' or ':::' import not declared from: ‘BiocGenerics’ * checking tests ... Running ‘runTests.R’ OK * 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, 5 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/CoRegNet.Rcheck/00check.log’ for details.