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BUILD report for ProCoNA on celaya2

This page was generated on 2019-10-16 12:52:02 -0400 (Wed, 16 Oct 2019).

Package 1254/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ProCoNA 1.22.0
David L Gibbs
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ProCoNA
Branch: RELEASE_3_9
Last Commit: bf9b180
Last Changed Date: 2019-05-02 11:53:45 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK [ ERROR ] skipped  skipped 

Summary

Package: ProCoNA
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ProCoNA
StartedAt: 2019-10-15 20:59:16 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 21:00:20 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 64.3 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
--- re-building ‘ProCoNA_Vignette.Rnw’ using Sweave
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, 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, 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 2.10.1 
  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

Warning: Package 'ProCoNA' is deprecated and will be removed from
  Bioconductor version 3.10

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.'

--- failed re-building ‘ProCoNA_Vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘ProCoNA_Vignette.Rnw’

Error: Vignette re-building failed.
Execution halted