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 | |
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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