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BioC experimental data: BUILD report for CopyNumber450kData on malbec2

This page was generated on 2017-10-18 15:09:41 -0400 (Wed, 18 Oct 2017).

Package 61/314HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CopyNumber450kData 1.12.0
Simon Papillon-Cavanagh
Snapshot Date: 2017-10-18 09:00:07 -0400 (Wed, 18 Oct 2017)
URL: https://git.bioconductor.org/packages/CopyNumber450kData
Branch: RELEASE_3_5
Last Commit: 4e7fb02
Last Changed Date: 2017-08-16 14:52:11 -0400 (Wed, 16 Aug 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded [ ERROR ] skipped 

Summary

Package: CopyNumber450kData
Version: 1.12.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data CopyNumber450kData
StartedAt: 2017-10-18 10:14:08 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 10:16:58 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 170.2 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data CopyNumber450kData
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* checking for file ‘CopyNumber450kData/DESCRIPTION’ ... OK
* preparing ‘CopyNumber450kData’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: CopyNumber450kData
Loading required package: minfi
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, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
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: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

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

    anyMissing, rowMedians


Attaching package: ‘DelayedArray’

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply

Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

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

    type

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

    strsplit

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: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Warning: Package 'CopyNumber450kData' is deprecated and will be removed from
  Bioconductor version 3.6

Error: processing vignette 'CopyNumber450kData.Rnw' failed with diagnostics:
 chunk 2 (label = load) 
Error in colData(object) : 
  no slot of name "colData" for this object of class "RGChannelSet"
Execution halted