############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:multiWGCNA.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings multiWGCNA_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/multiWGCNA.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * 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 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 61.172 1.165 62.559 preservationComparisons 56.211 2.039 58.516 constructNetworks 32.270 0.769 33.264 moduleComparisonPlot 15.246 0.701 16.171 iterate 7.486 2.162 9.872 drawMultiWGCNAnetwork 8.693 0.251 9.238 runDME 8.032 0.269 8.633 overlapComparisons 7.006 0.236 7.465 GetDatExpr 4.175 0.445 5.009 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/multiWGCNA.Rcheck/00check.log’ for details.