Dario Tommasini
| Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 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) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-20 11:32:16 -0400 (Mon, 20 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
| 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 1343/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| multiWGCNA 1.3.1 (landing page) Dario Tommasini
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the multiWGCNA package: - 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. |
| Package: multiWGCNA |
| Version: 1.3.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:multiWGCNA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings multiWGCNA_1.3.1.tar.gz |
| StartedAt: 2024-05-19 20:32:36 -0400 (Sun, 19 May 2024) |
| EndedAt: 2024-05-19 20:43:53 -0400 (Sun, 19 May 2024) |
| EllapsedTime: 677.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: multiWGCNA.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:multiWGCNA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings multiWGCNA_1.3.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/multiWGCNA.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multiWGCNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘multiWGCNA’ version ‘1.3.1’
* 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 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 75.362 9.194 86.256
preservationComparisons 71.506 8.788 81.599
constructNetworks 44.610 0.288 45.728
moduleComparisonPlot 17.260 0.402 18.696
runDME 10.800 0.883 13.234
iterate 9.219 1.994 12.248
drawMultiWGCNAnetwork 9.921 0.520 11.656
overlapComparisons 7.893 0.495 9.243
GetDatExpr 6.456 0.821 8.939
diffModuleExpression 6.503 0.292 8.016
bidirectionalBestMatches 4.885 0.206 5.919
moduleToModuleHeatmap 4.752 0.207 6.034
moduleExpressionPlot 4.720 0.195 5.938
computeOverlapsFromWGCNA 4.335 0.282 5.447
* 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
‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/multiWGCNA.Rcheck/00check.log’
for details.
multiWGCNA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL multiWGCNA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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)
multiWGCNA.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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
115.903 1.872 119.406
multiWGCNA.Rcheck/multiWGCNA-Ex.timings
| name | user | system | elapsed | |
| GetDatExpr | 6.456 | 0.821 | 8.939 | |
| PreservationPermutationTest | 0.000 | 0.000 | 0.001 | |
| PreservationScoreDistribution | 0.028 | 0.001 | 0.030 | |
| bidirectionalBestMatches | 4.885 | 0.206 | 5.919 | |
| cleanDatExpr | 2.111 | 0.620 | 3.608 | |
| coexpressionLineGraph | 3.652 | 0.172 | 4.665 | |
| computeOverlapsFromWGCNA | 4.335 | 0.282 | 5.447 | |
| constructNetworks | 44.610 | 0.288 | 45.728 | |
| diffCoexpression | 2.453 | 0.176 | 3.640 | |
| diffModuleExpression | 6.503 | 0.292 | 8.016 | |
| drawMultiWGCNAnetwork | 9.921 | 0.520 | 11.656 | |
| iterate | 9.219 | 1.994 | 12.248 | |
| makeTraitTable | 0.002 | 0.000 | 0.003 | |
| moduleComparisonPlot | 17.260 | 0.402 | 18.696 | |
| moduleExpressionPlot | 4.720 | 0.195 | 5.938 | |
| moduleToModuleHeatmap | 4.752 | 0.207 | 6.034 | |
| name | 3.301 | 0.209 | 4.345 | |
| overlapComparisons | 7.893 | 0.495 | 9.243 | |
| preservationComparisonPlot | 75.362 | 9.194 | 86.256 | |
| preservationComparisons | 71.506 | 8.788 | 81.599 | |
| runDME | 10.800 | 0.883 | 13.234 | |
| topNGenes | 3.331 | 0.161 | 4.528 | |