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BUILD report for ProCoNA on merida1

This page was generated on 2019-04-16 11:57:09 -0400 (Tue, 16 Apr 2019).

Package 1194/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ProCoNA 1.20.0
David L Gibbs
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/ProCoNA
Branch: RELEASE_3_8
Last Commit: bd633f7
Last Changed Date: 2018-10-30 11:41:52 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  ERROR  skipped 
merida1 OS X 10.11.6 El Capitan / x86_64  OK [ ERROR ] skipped  skipped 

Summary

Package: ProCoNA
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ProCoNA
StartedAt: 2019-04-15 19:52:15 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 19:53:08 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 52.8 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ProCoNA
###
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* checking for file ‘ProCoNA/DESCRIPTION’ ... OK
* preparing ‘ProCoNA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: WGCNA
Loading required package: dynamicTreeCut
Loading required package: fastcluster

Attaching package: ‘fastcluster’

The following object is masked from ‘package:stats’:

    hclust



Attaching package: ‘WGCNA’

The following object is masked from ‘package:stats’:

    cor

Loading required package: MSnbase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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,
    append, as.data.frame, basename, cbind, colMeans, colSums,
    colnames, dirname, do.call, duplicated, eval, evalq, get,
    grep, grepl, intersect, is.unsorted, lapply, lengths,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rowMeans, rowSums, rownames,
    sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages
    'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: ProtGenerics

This is MSnbase version 2.8.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: ‘MSnbase’

The following object is masked from ‘package:stats’:

    smooth

The following object is masked from ‘package:base’:

    trimws

Loading required package: flashClust

Attaching package: ‘flashClust’

The following object is masked from ‘package:fastcluster’:

    hclust

The following object is masked from ‘package:stats’:

    hclust


Attaching package: ‘ProCoNA’

The following object is masked from ‘package:ProtGenerics’:

    peptides

The following object is masked from ‘package:Biobase’:

    samples

Removing peptides with more than 12 missing data points

Warning: executing %dopar% sequentially: no parallel backend registered
Constructing New ProCoNA Network Object
Computing soft threshold power
Using power: 14

Computing adjacency
Computing TOM
Clustering
Merging modules
Topological Overlap Permutation Test On Modules
Permuting module: 1

   dim of TOM: 139139

Permuting module: 2

   dim of TOM: 131131

Permuting module: 4

   dim of TOM: 9090

Permuting module: 3

   dim of TOM: 108108

DONE!
Permuting module: 1

   dim of TOM: 139139

Permuting module: 2

   dim of TOM: 131131

Permuting module: 4

   dim of TOM: 9090

Permuting module: 3

   dim of TOM: 108108


Error: processing vignette 'ProCoNA_Vignette.Rnw' failed with diagnostics:
 chunk 10 (label = Correlation of module eigenvectors with phenotypes.) 
Error in labeledHeatmap(Matrix = modCors[, mms], xLabels = names(phenotypes),  : 
  Length of 'xLabels' must equal the number of columns in 'Matrix.'
Execution halted