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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 VariantFiltering
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* checking for file ‘VariantFiltering/DESCRIPTION’ ... OK
* preparing ‘VariantFiltering’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘usingVariantFiltering.Rnw’ using Sweave
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

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: 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
Loading annotation package phastCons100way.UCSC.hg19
Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'phastCons100way.UCSC.hg19'
Fetching annotation object humanGenesPhylostrata
Assuming the genome build of the input variants is hs37d5.
Switching to the UCSC chromosome-name style from the transcript-centric annotation package.
Chromosome chrM has different lengths between the input VCF and the input TxDb pakage. This chromosome will be discarded from further analysis
Assumming hs37d5 and hg19 represent the same genome build.
Discarding scaffold sequences.
Annotating variant type (SNV, Insertion, Deletion, MNV, Delins)
Annotating dbSNP identifiers with SNPlocs.Hsapiens.dbSNP144.GRCh37
Annotating location with VariantAnnotation::locateVariants()
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1584 out-of-bound ranges located on sequences 149424,
  352968, 353841, 353842, 353844, 353847, 354577, 354579, 350613, 350614,
  351302, 356894, 360192, 357985, 365217, 365219, 365220, 365221, 361924,
  362299, 362780, 363498, 363856, 363858, 363860, 364702, 373666, 373667,
  373668, 373669, 373671, 373672, 373673, 373674, 373675, 373676, 373677,
  373678, 373679, 373680, 373681, 373686, 373689, 373690, 373691, 373694,
  373695, 374290, and 374291. Note that ranges located on a sequence whose
  length is unknown (NA) or on a circular sequence are not considered
  out-of-bound (use seqlengths() and isCircular() to get the lengths and
  circularity flags of the underlying sequences). You can use trim() to trim
  these ranges. See ?`trim,GenomicRanges-method` for more information.

Error: processing vignette 'usingVariantFiltering.Rnw' failed with diagnostics:
 chunk 5 
Error : unable to open database file

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

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

Error: Vignette re-building failed.
Execution halted