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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:multiWGCNA.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings multiWGCNA_1.5.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/multiWGCNA.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 ... 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 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 84.44  11.31   95.86
preservationComparisons    78.29  11.88   90.27
constructNetworks          41.61   0.39   42.23
moduleComparisonPlot       19.84   0.69   20.69
iterate                    10.68   1.59   12.47
drawMultiWGCNAnetwork      11.30   0.91   12.35
runDME                     11.17   0.96   12.44
overlapComparisons          9.17   0.47    9.76
GetDatExpr                  7.62   1.98   10.30
diffModuleExpression        5.61   0.61    6.36
moduleToModuleHeatmap       4.83   0.32    5.22
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/multiWGCNA.Rcheck/00check.log'
for details.