############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:multiWGCNA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings multiWGCNA_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/multiWGCNA.Rcheck’ * using R version 4.4.3 (2025-02-28) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘multiWGCNA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘multiWGCNA’ version ‘1.4.0’ * 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 ‘multiWGCNA’ can be installed ... OK * 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 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 TOMFlowPlot: no visible global function definition for ‘as.dist’ TOMFlowPlot: no visible binding for global variable ‘module’ TOMFlowPlot: no visible binding for global variable ‘Count’ TOMFlowPlot: no visible binding for global variable ‘one.gene’ TOMFlowPlot: no visible binding for global variable ‘two.gene’ TOMFlowPlot: no visible binding for global variable ‘stratum’ bidirectionalBestMatches: no visible binding for global variable ‘mod1’ bidirectionalBestMatches: no visible binding for global variable ‘mod2’ bidirectionalBestMatches: no visible binding for global variable ‘overlap’ coexpressionLineGraph: no visible binding for global variable ‘Var1’ coexpressionLineGraph: no visible binding for global variable ‘value’ coexpressionLineGraph: no visible binding for global variable ‘Var2’ computeOverlapsFromWGCNA: no visible binding for global variable ‘mod1’ computeOverlapsFromWGCNA: no visible binding for global variable ‘mod2’ continuousFlowPlot: no visible global function definition for ‘ulist’ continuousFlowPlot: no visible binding for global variable ‘uniqueSortedData’ continuousFlowPlot: no visible binding for global variable ‘stratum’ continuousFlowPlot: no visible global function definition for ‘error’ correlationComparisonBoxplot: no visible binding for global variable ‘Status’ correlationComparisonBoxplot: no visible binding for global variable ‘Correlation’ correlationComparisonHeatmaps: no visible binding for global variable ‘Var1’ correlationComparisonHeatmaps: no visible binding for global variable ‘Var2’ correlationComparisonHeatmaps: no visible binding for global variable ‘value’ diffCoexpression: no visible binding for global variable ‘layout_with_fr’ diffCoexpression: no visible binding for global variable ‘p.adj’ diffModuleExpression: no visible binding for global variable ‘Sample’ drawNetwork: no visible binding for global variable ‘layout_with_fr’ expressionHeatmap: no visible binding for global variable ‘Sample’ expressionHeatmap: no visible binding for global variable ‘Gene’ expressionHeatmap: no visible binding for global variable ‘Zscore’ findOutlierModules: no visible global function definition for ‘zScoreMatrix’ getPreservation: no visible binding for global variable ‘name2’ moduleComparisonPlot: no visible binding for global variable ‘overlap’ moduleComparisonPlot: no visible binding for global variable ‘mod1’ moduleComparisonPlot: no visible binding for global variable ‘mod2’ moduleComparisonPlot: no visible binding for global variable ‘p.adj’ moduleComparisonPlot: no visible binding for global variable ‘stratum’ moduleExpressionPlot: no visible binding for global variable ‘Sample’ moduleExpressionPlot: no visible binding for global variable ‘Expression’ moduleToModuleHeatmap: no visible binding for global variable ‘mod1’ moduleToModuleHeatmap: no visible binding for global variable ‘mod2’ moduleToModuleHeatmap: no visible binding for global variable ‘p.adj’ moduleToModuleHeatmap: no visible binding for global variable ‘overlap’ preservationComparisonPlot: no visible binding for global variable ‘log10Pvalue’ preservationComparisonPlot: no visible binding for global variable ‘Zsum’ preservationComparisonPlot: no visible binding for global variable ‘trait’ preservationComparisonPlot: no visible binding for global variable ‘Module’ topNGenes: no visible binding for global variable ‘kWithin’ Undefined global functions or variables: Correlation Count Expression Gene Module Sample Status Var1 Var2 Zscore Zsum as.dist error kWithin layout_with_fr log10Pvalue mod1 mod2 module name2 one.gene overlap p.adj stratum trait two.gene ulist uniqueSortedData value zScoreMatrix Consider adding importFrom("stats", "as.dist") 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 ... 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed preservationComparisonPlot 78.462 10.309 90.273 preservationComparisons 74.071 10.234 85.782 constructNetworks 45.879 0.332 47.007 moduleComparisonPlot 16.679 0.357 17.987 iterate 9.127 2.297 12.369 runDME 10.241 1.101 12.752 drawMultiWGCNAnetwork 10.515 0.648 12.280 overlapComparisons 7.924 0.488 9.261 GetDatExpr 7.190 0.790 9.527 diffModuleExpression 5.885 0.295 7.285 moduleToModuleHeatmap 5.170 0.223 6.162 bidirectionalBestMatches 4.641 0.189 5.616 moduleExpressionPlot 4.247 0.198 5.381 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/multiWGCNA.Rcheck/00check.log’ for details.