BioC 3.5: BUILD report for SomaticSignatures on oaxaca

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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 SomaticSignatures
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* checking for file ‘SomaticSignatures/DESCRIPTION’ ... OK
* preparing ‘SomaticSignatures’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: VariantAnnotation
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: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
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: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    type


Attaching package: 'VariantAnnotation'

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

    tabulate

Loading required package: BSgenome
Loading required package: rtracklayer
Quitting from lines 371-387 (SomaticSignatures-vignette.Rhtml) 
Error: processing vignette 'SomaticSignatures-vignette.Rhtml' failed with diagnostics:
The following seqlevels are to be dropped but are currently in
  use (i.e. have ranges on them): X, Y, MT, GL000241.1,
  GL000237.1, GL000191.1, GL000214.1, GL000221.1, GL000209.1,
  GL000218.1, GL000220.1, GL000213.1, GL000211.1, GL000205.1,
  GL000219.1, GL000223.1, GL000195.1, GL000193.1, GL000194.1,
  GL000192.1. Please use the 'pruning.mode' argument to control
  how to prune 'x', that is, how to remove the ranges in 'x'
  that are on these sequences. For example, do something like:
  
  seqlevels(x, pruning.mode="coarse") <- new_seqlevels
  
  or
  
  keepSeqlevels(x, new_seqlevels, pruning.mode="coarse")
  
  See ?seqinfo for a description of the pruning modes.
Execution halted
BioC 3.5: BUILD report for SomaticSignatures on oaxaca

Summary

Command output
