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This page was generated on 2025-08-30 12:09 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1399/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multiWGCNA 1.7.0  (landing page)
Dario Tommasini
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 2025)
git_url: https://git.bioconductor.org/packages/multiWGCNA
git_branch: devel
git_last_commit: b6102c0
git_last_commit_date: 2025-04-15 13:18:26 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for multiWGCNA on taishan

To the developers/maintainers of the multiWGCNA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/multiWGCNA.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: multiWGCNA
Version: 1.7.0
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
StartedAt: 2025-08-29 09:33:16 -0000 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 09:45:01 -0000 (Fri, 29 Aug 2025)
EllapsedTime: 704.1 seconds
RetCode: 0
Status:   OK  
CheckDir: multiWGCNA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 94.427  0.632  98.439
preservationComparisons    90.930  0.524  94.853
constructNetworks          31.589  0.282  34.601
moduleComparisonPlot       17.315  0.121  20.455
drawMultiWGCNAnetwork      12.055  0.230  16.253
iterate                    11.120  0.443  14.562
runDME                     10.820  0.099  15.371
overlapComparisons         10.049  0.083  12.658
diffModuleExpression        5.996  0.151   9.457
GetDatExpr                  4.624  0.152   8.417
moduleToModuleHeatmap       4.330  0.098   7.461
moduleExpressionPlot        4.234  0.080   7.432
bidirectionalBestMatches    4.140  0.135   6.837
coexpressionLineGraph       3.538  0.136   6.647
computeOverlapsFromWGCNA    3.212  0.120   5.743
topNGenes                   2.720  0.040   6.396
name                        2.655  0.087   5.203
cleanDatExpr                2.407  0.211   5.058
diffCoexpression            2.136  0.092   5.102
* 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.


Installation output

multiWGCNA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL multiWGCNA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘multiWGCNA’ ...
** this is package ‘multiWGCNA’ version ‘1.7.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (multiWGCNA)

Tests output

multiWGCNA.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(multiWGCNA)
Loading required package: ggalluvial
Loading required package: ggplot2

> 
> test_check("multiWGCNA")
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
multiWGCNAdata not installed.
  Full functionality, documentation, and loading of data might not be possible without installing
loading from cache
require("SummarizedExperiment")
 Flagging genes and samples with too many missing values...
  ..step 1
 Calculating module eigengenes block-wise from all genes
   Flagging genes and samples with too many missing values...
    ..step 1
 ..Working on block 1 .
    TOM calculation: adjacency..
    ..will not use multithreading.
     Fraction of slow calculations: 0.000000
    ..connectivity..
    ..matrix multiplication (system BLAS)..
    ..normalization..
    ..done.
 ....clustering..
 ....detecting modules..
 ....calculating module eigengenes..
 ....checking kME in modules..
     ..removing 163 genes from module 1 because their KME is too low.
     ..removing 126 genes from module 2 because their KME is too low.
     ..removing 59 genes from module 3 because their KME is too low.
     ..removing 18 genes from module 4 because their KME is too low.
     ..removing 28 genes from module 5 because their KME is too low.
     ..removing 24 genes from module 6 because their KME is too low.
     ..removing 9 genes from module 7 because their KME is too low.
 ..merging modules that are too close..
     mergeCloseModules: Merging modules whose distance is less than 0.1
       Calculating new MEs...
 softConnectivity: FYI: connecitivty of genes with less than 20 valid samples will be returned as NA.
 ..calculating connectivities.. 
 Flagging genes and samples with too many missing values...
  ..step 1
 Calculating module eigengenes block-wise from all genes
   Flagging genes and samples with too many missing values...
    ..step 1
 ..Working on block 1 .
    TOM calculation: adjacency..
    ..will not use multithreading.
     Fraction of slow calculations: 0.000000
    ..connectivity..
    ..matrix multiplication (system BLAS)..
    ..normalization..
    ..done.
 ....clustering..
 ....detecting modules..
 ....calculating module eigengenes..
 ....checking kME in modules..
     ..removing 139 genes from module 1 because their KME is too low.
     ..removing 82 genes from module 2 because their KME is too low.
     ..removing 95 genes from module 3 because their KME is too low.
     ..removing 37 genes from module 4 because their KME is too low.
     ..removing 35 genes from module 5 because their KME is too low.
     ..removing 36 genes from module 6 because their KME is too low.
     ..removing 27 genes from module 7 because their KME is too low.
 ..merging modules that are too close..
     mergeCloseModules: Merging modules whose distance is less than 0.1
       Calculating new MEs...
 softConnectivity: FYI: connecitivty of genes with less than 10 valid samples will be returned as NA.
 ..calculating connectivities.. 
 Flagging genes and samples with too many missing values...
  ..step 1
 Calculating module eigengenes block-wise from all genes
   Flagging genes and samples with too many missing values...
    ..step 1
 ..Working on block 1 .
    TOM calculation: adjacency..
    ..will not use multithreading.
     Fraction of slow calculations: 0.000000
    ..connectivity..
    ..matrix multiplication (system BLAS)..
    ..normalization..
    ..done.
 ....clustering..
 ....detecting modules..
 ....calculating module eigengenes..
 ....checking kME in modules..
     ..removing 164 genes from module 1 because their KME is too low.
     ..removing 138 genes from module 2 because their KME is too low.
     ..removing 86 genes from module 3 because their KME is too low.
     ..removing 33 genes from module 4 because their KME is too low.
     ..removing 35 genes from module 5 because their KME is too low.
     ..removing 34 genes from module 6 because their KME is too low.
     ..removing 19 genes from module 7 because their KME is too low.
 ..merging modules that are too close..
     mergeCloseModules: Merging modules whose distance is less than 0.1
       Calculating new MEs...
 softConnectivity: FYI: connecitivty of genes with less than 11 valid samples will be returned as NA.
 ..calculating connectivities.. 
 Flagging genes and samples with too many missing values...
  ..step 1
 Calculating module eigengenes block-wise from all genes
   Flagging genes and samples with too many missing values...
    ..step 1
 ..Working on block 1 .
    TOM calculation: adjacency..
    ..will not use multithreading.
     Fraction of slow calculations: 0.000000
    ..connectivity..
    ..matrix multiplication (system BLAS)..
    ..normalization..
    ..done.
 ....clustering..
 ....detecting modules..
 ....calculating module eigengenes..
 ....checking kME in modules..
     ..removing 163 genes from module 1 because their KME is too low.
     ..removing 126 genes from module 2 because their KME is too low.
     ..removing 59 genes from module 3 because their KME is too low.
     ..removing 18 genes from module 4 because their KME is too low.
     ..removing 28 genes from module 5 because their KME is too low.
     ..removing 24 genes from module 6 because their KME is too low.
     ..removing 9 genes from module 7 because their KME is too low.
 ..merging modules that are too close..
     mergeCloseModules: Merging modules whose distance is less than 0.1
       Calculating new MEs...
 softConnectivity: FYI: connecitivty of genes with less than 20 valid samples will be returned as NA.
 ..calculating connectivities.. 
 Flagging genes and samples with too many missing values...
  ..step 1
 Calculating module eigengenes block-wise from all genes
   Flagging genes and samples with too many missing values...
    ..step 1
 ..Working on block 1 .
    TOM calculation: adjacency..
    ..will not use multithreading.
     Fraction of slow calculations: 0.000000
    ..connectivity..
    ..matrix multiplication (system BLAS)..
    ..normalization..
    ..done.
 ....clustering..
 ....detecting modules..
 ....calculating module eigengenes..
 ....checking kME in modules..
     ..removing 139 genes from module 1 because their KME is too low.
     ..removing 82 genes from module 2 because their KME is too low.
     ..removing 95 genes from module 3 because their KME is too low.
     ..removing 37 genes from module 4 because their KME is too low.
     ..removing 35 genes from module 5 because their KME is too low.
     ..removing 36 genes from module 6 because their KME is too low.
     ..removing 27 genes from module 7 because their KME is too low.
 ..merging modules that are too close..
     mergeCloseModules: Merging modules whose distance is less than 0.1
       Calculating new MEs...
 softConnectivity: FYI: connecitivty of genes with less than 10 valid samples will be returned as NA.
 ..calculating connectivities.. 
 Flagging genes and samples with too many missing values...
  ..step 1
 Calculating module eigengenes block-wise from all genes
   Flagging genes and samples with too many missing values...
    ..step 1
 ..Working on block 1 .
    TOM calculation: adjacency..
    ..will not use multithreading.
     Fraction of slow calculations: 0.000000
    ..connectivity..
    ..matrix multiplication (system BLAS)..
    ..normalization..
    ..done.
 ....clustering..
 ....detecting modules..
 ....calculating module eigengenes..
 ....checking kME in modules..
     ..removing 164 genes from module 1 because their KME is too low.
     ..removing 138 genes from module 2 because their KME is too low.
     ..removing 86 genes from module 3 because their KME is too low.
     ..removing 33 genes from module 4 because their KME is too low.
     ..removing 35 genes from module 5 because their KME is too low.
     ..removing 34 genes from module 6 because their KME is too low.
     ..removing 19 genes from module 7 because their KME is too low.
 ..merging modules that are too close..
     mergeCloseModules: Merging modules whose distance is less than 0.1
       Calculating new MEs...
 softConnectivity: FYI: connecitivty of genes with less than 11 valid samples will be returned as NA.
 ..calculating connectivities.. 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
 80.948   0.973  86.527 

Example timings

multiWGCNA.Rcheck/multiWGCNA-Ex.timings

nameusersystemelapsed
GetDatExpr4.6240.1528.417
PreservationPermutationTest0.0010.0000.000
PreservationScoreDistribution0.0320.0040.037
bidirectionalBestMatches4.1400.1356.837
cleanDatExpr2.4070.2115.058
coexpressionLineGraph3.5380.1366.647
computeOverlapsFromWGCNA3.2120.1205.743
constructNetworks31.589 0.28234.601
diffCoexpression2.1360.0925.102
diffModuleExpression5.9960.1519.457
drawMultiWGCNAnetwork12.055 0.23016.253
iterate11.120 0.44314.562
makeTraitTable0.0010.0020.003
moduleComparisonPlot17.315 0.12120.455
moduleExpressionPlot4.2340.0807.432
moduleToModuleHeatmap4.3300.0987.461
name2.6550.0875.203
overlapComparisons10.049 0.08312.658
preservationComparisonPlot94.427 0.63298.439
preservationComparisons90.930 0.52494.853
runDME10.820 0.09915.371
topNGenes2.7200.0406.396