BioC 3.5: BUILD report for conumee on oaxaca

##############################################################################
##############################################################################
###
### 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, 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
matrixStats v0.51.0 (2016-10-08) successfully loaded. See ?matrixStats for help.

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, rowMaxs

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

    apply


Attaching package: 'SummarizedExperiment'

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

    rowRanges

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    type

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
Loading required package: IlluminaHumanMethylationEPICmanifest
Loading required package: IlluminaHumanMethylationEPICanno.ilm10b2.hg19

Attaching package: 'IlluminaHumanMethylationEPICanno.ilm10b2.hg19'

The following objects are masked from 'package:IlluminaHumanMethylation450kanno.ilmn12.hg19':

    Islands.UCSC, Locations, Manifest, Other,
    SNPs.132CommonSingle, SNPs.135CommonSingle,
    SNPs.137CommonSingle, SNPs.138CommonSingle,
    SNPs.141CommonSingle, SNPs.142CommonSingle,
    SNPs.144CommonSingle, SNPs.146CommonSingle,
    SNPs.147CommonSingle, SNPs.Illumina

downloading 6042324037_R05C02_Grn.idat - done.
downloading 6042324037_R05C02_Red.idat - done.
downloading 6042324037_R06C01_Grn.idat - done.
downloading 6042324037_R06C01_Red.idat - done.
Quitting from lines 59-62 (conumee.Rmd) 
Error: processing vignette 'conumee.Rmd' failed with diagnostics:
'assay(<RGChannelSet>, i="character", ...)' invalid subscript 'i'
no slot of name "assays" for this object of class "RGChannelSet"
Execution halted
BioC 3.5: BUILD report for conumee on oaxaca

Summary

Command output
