############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:multiWGCNA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings multiWGCNA_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/multiWGCNA.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘multiWGCNA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘multiWGCNA’ version ‘1.7.0’ * 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 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 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 96.271 1.322 102.715 preservationComparisons 96.049 1.019 102.913 constructNetworks 33.845 0.625 37.839 moduleComparisonPlot 18.370 0.662 23.143 drawMultiWGCNAnetwork 12.264 0.606 17.473 runDME 12.102 0.203 19.076 iterate 10.934 0.850 14.779 overlapComparisons 10.180 0.459 13.184 diffModuleExpression 6.225 0.463 10.480 moduleToModuleHeatmap 4.644 0.431 7.464 GetDatExpr 4.566 0.359 8.957 bidirectionalBestMatches 4.298 0.316 7.621 moduleExpressionPlot 4.280 0.275 7.861 coexpressionLineGraph 3.723 0.227 7.320 computeOverlapsFromWGCNA 3.349 0.268 6.112 name 2.804 0.195 5.963 topNGenes 2.813 0.175 6.679 cleanDatExpr 2.403 0.308 5.232 diffCoexpression 2.313 0.131 5.493 * 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 ‘/home/biocbuild/bbs-3.22-bioc/meat/multiWGCNA.Rcheck/00check.log’ for details.