Multiple platform build/check report for BioC 3.11 - BUILD report for RCAS on celaya2

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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 RCAS
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* checking for file ‘RCAS/DESCRIPTION’ ... OK
* preparing ‘RCAS’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RCAS.metaAnalysis.vignette.Rmd’ using rmarkdown
--- finished re-building ‘RCAS.metaAnalysis.vignette.Rmd’

--- re-building ‘RCAS.vignette.Rmd’ using rmarkdown
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

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

    filter

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

    layout

Loading required package: DT
Loading required package: data.table
Loading required package: topGO
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: graph
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: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:data.table':

    first, second

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

    rename

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

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

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

    slice


Attaching package: 'AnnotationDbi'

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

    select


Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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

    members

Loading required package: motifRG
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    complement

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

    strsplit

Loading required package: seqLogo
Loading required package: grid

Attaching package: 'grid'

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

    depth

Loading required package: BSgenome
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

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

    export

Loading required package: BSgenome.Hsapiens.UCSC.hg19
Warning: Package 'motifRG' is deprecated and will be removed from Bioconductor
  version 3.12

Warning: Package 'RCAS' is deprecated and will be removed from Bioconductor
  version 3.12
Warning in .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
Warning in .local(target, windows, strand.aware) :
  111 windows fall off the target
Warning in .local(target, windows, strand.aware) :
  119 windows fall off the target
Warning in .local(target, windows, bin.num, bin.op, strand.aware) :
  114 windows fall off the target
Warning in .local(target, windows, bin.num, bin.op, strand.aware) :
  69 windows fall off the target
Warning in .local(target, windows, bin.num, bin.op, strand.aware) :
  122 windows fall off the target
Warning in .local(target, windows, bin.num, bin.op, strand.aware) :
  60 windows fall off the target
Warning in .local(target, windows, bin.num, bin.op, strand.aware) :
  47 windows fall off the target
Warning in .local(target, windows, bin.num, bin.op, strand.aware) :
  53 windows fall off the target
Warning in .local(target, windows, bin.num, bin.op, strand.aware) :
  61 windows fall off the target
Found 1968 query regions shorter than 15 bps. Resizing those regions to 15 bps
extracting peak sequences from fasta..
extracting background sequences from fasta..
running motifRG...
Quitting from lines 203-215 (RCAS.vignette.Rmd) 
Error: processing vignette 'RCAS.vignette.Rmd' failed with diagnostics:
RangedData objects are defunct. Please migrate your code to use GRanges
  or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData
--- failed re-building ‘RCAS.vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘RCAS.vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
BUILD report for RCAS on celaya2

Summary

Command output
