############################################################################## ############################################################################## ### ### 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_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/multiWGCNA.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 ‘1.5.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 22.164 2.752 25.074 preservationComparisons 21.739 2.560 24.510 constructNetworks 13.901 0.077 14.186 moduleComparisonPlot 4.900 0.100 5.161 * 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-3.21-bioc/meat/multiWGCNA.Rcheck/00check.log’ for details.