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BioC 3.3: BUILD report for conumee on oaxaca

This page was generated on 2016-10-13 13:01:37 -0700 (Thu, 13 Oct 2016).

Package 239/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
conumee 1.4.2
Volker Hovestadt
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/conumee
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  ERROR  skipped 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  ERROR  skipped  skipped 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded [ ERROR ] skipped  skipped 

Summary

Package: conumee
Version: 1.4.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data conumee
StartedAt: 2016-10-12 22:00:38 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 22:01:17 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 38.8 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data conumee
###
##############################################################################
##############################################################################


* checking for file ‘conumee/DESCRIPTION’ ... OK
* preparing ‘conumee’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
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

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

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: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
downloading 6042324037_R05C02_Grn.idat - done.
downloading 6042324037_R05C02_Red.idat - done.
downloading 6042324037_R06C01_Grn.idat - done.
downloading 6042324037_R06C01_Red.idat - done.
Warning: 'read.450k.exp' is deprecated.
Use 'read.metharray.exp' instead.
See help("Deprecated")
Warning: 'read.450k' is deprecated.
Use 'read.metharray' instead.
See help("Deprecated")
Quitting from lines 37-43 (conumee.Rmd) 
Error: processing vignette 'conumee.Rmd' failed with diagnostics:
Cannot read IDAT file. File format error. Unknown magic: <!DO
Execution halted