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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data VariantFiltering
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* checking for file ‘VariantFiltering/DESCRIPTION’ ... OK
* preparing ‘VariantFiltering’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘usingVariantFiltering.Rnw’ using Sweave
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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, aperm, 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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: VariantAnnotation
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

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

    findMatches

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

    I, expand.grid, unname

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")'.


Attaching package: ‘Biobase’

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

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

    strsplit


Attaching package: ‘VariantAnnotation’

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

    tabulate

Loading BSgenome annotation package BSgenome.Hsapiens.1000genomes.hs37d5
Loading OrgDb annotation package org.Hs.eg.db
Loading TxDb annotation package TxDb.Hsapiens.UCSC.hg19.knownGene
Loading SNPlocs annotation package SNPlocs.Hsapiens.dbSNP144.GRCh37
Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'SNPlocs.Hsapiens.dbSNP144.GRCh37'
Loading annotation package MafDb.1Kgenomes.phase1.hs37d5
Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'MafDb.1Kgenomes.phase1.hs37d5'
Loading annotation package PolyPhen.Hsapiens.dbSNP131
Loading annotation package SIFT.Hsapiens.dbSNP137

Error: processing vignette 'usingVariantFiltering.Rnw' failed with diagnostics:
 chunk 3 
Error in VariantFilteringParam(CEUvcf) : 
  please install the Bioconductor package phastCons100way.UCSC.hg19.

--- failed re-building 'usingVariantFiltering.Rnw'

SUMMARY: processing the following file failed:
  'usingVariantFiltering.Rnw'

Error: Vignette re-building failed.
Execution halted