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BioC 3.4: BUILD report for CopyNumber450k on moscato1

This page was generated on 2016-09-21 03:45:33 -0700 (Wed, 21 Sep 2016).

Package 254/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CopyNumber450k 1.9.0
Simon Papillon-Cavanagh
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CopyNumber450k
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  ERROR  skipped 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded [ ERROR ] skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: CopyNumber450k
Version: 1.9.0
Command: chmod a+r CopyNumber450k -R && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data CopyNumber450k
StartedAt: 2016-09-20 00:32:56 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 00:33:58 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 61.9 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r CopyNumber450k -R && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data CopyNumber450k
###
##############################################################################
##############################################################################


* checking for file 'CopyNumber450k/DESCRIPTION' ... OK
* preparing 'CopyNumber450k':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"D:/biocbld/bbs-3.4-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
 ERROR
Loading required package: Biobase
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, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

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

Loading required package: minfi
Loading required package: lattice
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: DNAcopy
Loading required package: preprocessCore
Warning: multiple methods tables found for 'plotPCA'

Attaching package: 'CopyNumber450k'

The following object is masked from 'package:DNAcopy':

    plotSample

The following object is masked from 'package:bumphunter':

    getSegments

The following object is masked from 'package:BiocGenerics':

    plotPCA

Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19

Error: processing vignette 'CopyNumber450k.Rnw' failed with diagnostics:
 chunk 4 (label = createobject) 
Error in fun(RGset)[ctrlAddress, ] : subscript out of bounds
Execution halted