Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2024-06-24 11:38 -0400 (Mon, 24 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4690
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4404
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 1349/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multiWGCNA 1.3.1  (landing page)
Dario Tommasini
Snapshot Date: 2024-06-23 14:00 -0400 (Sun, 23 Jun 2024)
git_url: https://git.bioconductor.org/packages/multiWGCNA
git_branch: devel
git_last_commit: 6e4e30e
git_last_commit_date: 2024-05-04 21:10:07 -0400 (Sat, 04 May 2024)
nebbiolo2Linux (Ubuntu 22.04.3 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


CHECK results for multiWGCNA on nebbiolo2

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.

raw results


Summary

Package: multiWGCNA
Version: 1.3.1
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:multiWGCNA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings multiWGCNA_1.3.1.tar.gz
StartedAt: 2024-06-24 01:19:56 -0400 (Mon, 24 Jun 2024)
EndedAt: 2024-06-24 01:33:01 -0400 (Mon, 24 Jun 2024)
EllapsedTime: 784.5 seconds
RetCode: 0
Status:   OK  
CheckDir: multiWGCNA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:multiWGCNA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings multiWGCNA_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/multiWGCNA.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘multiWGCNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘multiWGCNA’ version ‘1.3.1’
* 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 63.097  2.772  66.177
preservationComparisons    59.268  3.136  62.741
constructNetworks          32.966  1.420  34.655
moduleComparisonPlot       15.674  0.898  16.864
drawMultiWGCNAnetwork       8.801  0.540   9.685
iterate                     8.407  0.888   9.614
runDME                      8.353  0.560   9.291
overlapComparisons          7.064  0.439   7.768
diffModuleExpression        4.617  0.355   5.388
* 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-3.20-bioc/meat/multiWGCNA.Rcheck/00check.log’
for details.


Installation output

multiWGCNA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL multiWGCNA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘multiWGCNA’ ...
** 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 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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 
 99.517   2.748 102.629 

Example timings

multiWGCNA.Rcheck/multiWGCNA-Ex.timings

nameusersystemelapsed
GetDatExpr4.1870.3484.970
PreservationPermutationTest000
PreservationScoreDistribution0.0490.0200.070
bidirectionalBestMatches3.7560.3764.439
cleanDatExpr2.0070.2692.539
coexpressionLineGraph2.7260.2963.286
computeOverlapsFromWGCNA3.5370.3524.161
constructNetworks32.966 1.42034.655
diffCoexpression1.9190.1242.337
diffModuleExpression4.6170.3555.388
drawMultiWGCNAnetwork8.8010.5409.685
iterate8.4070.8889.614
makeTraitTable0.0010.0020.002
moduleComparisonPlot15.674 0.89816.864
moduleExpressionPlot3.5360.2684.146
moduleToModuleHeatmap3.3150.2764.027
name3.3500.3954.011
overlapComparisons7.0640.4397.768
preservationComparisonPlot63.097 2.77266.177
preservationComparisons59.268 3.13662.741
runDME8.3530.5609.291
topNGenes2.5060.1323.001