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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data R453Plus1Toolbox
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* checking for file ‘R453Plus1Toolbox/DESCRIPTION’ ... OK
* preparing ‘R453Plus1Toolbox’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘vignette.Rnw’ using Sweave
Loading required package: VariantAnnotation
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: 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 required package: pwalign

Attaching package: ‘pwalign’

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

    PairwiseAlignments,
    PairwiseAlignmentsSingleSubject, aligned,
    alignedPattern, alignedSubject, compareStrings,
    deletion, errorSubstitutionMatrices, indel,
    insertion, mismatchSummary, mismatchTable, nedit,
    nindel, nucleotideSubstitutionMatrix,
    pairwiseAlignment, pid,
    qualitySubstitutionMatrices, stringDist,
    unaligned, writePairwiseAlignments

Warning in .local(dirname) : 'AVASet(dirname)' is deprecated.
Use 'AVASet(dirname, avaBin)' instead.
See help("Deprecated")
Reading sample data ... done
Reading reference sequences ... done
Reading variant data ... done
Reading amplicon data ... done
Variants: 

Amplicons: 
assayDataAmp:4 features,  6 samples
  element names:forwCountrevCount
featureDataAmp: 

Reference sequences: 
Loading required package: BiocParallel
Loading required package: GenomicAlignments
combined forward & reverse filter set to 0.05
forward filter set to 0.1
reverse filter set to 0.05
combined forward & reverse filter set to 0
combined forward & reverse filter set to 0
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
Reading data ... 
... from /home/biocbuild/tmp/RtmpDwqMWC/Rinst1df7f278006d48/R453Plus1Toolbox/extdata/MapperSet/N01
... from /home/biocbuild/tmp/RtmpDwqMWC/Rinst1df7f278006d48/R453Plus1Toolbox/extdata/MapperSet/N03
... from /home/biocbuild/tmp/RtmpDwqMWC/Rinst1df7f278006d48/R453Plus1Toolbox/extdata/MapperSet/N04
done
Extrating chimeric reads with exactly two local alignments.
Removing reads that do not align to the target region.
Removing reads with a linker sequence in the middle.
Removing reads with close local alignments (perhaps small indels).
Removing duplicated reads (perhaps duplication due to PCR).
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’

Error: processing vignette 'vignette.Rnw' failed with diagnostics:
 chunk 50 (label = detectBreakpoints) 
Error in detectBreakpoints(filterReads, minClusterSize = 1) : 
  library BSgenome.Hsapiens.UCSC.hg19 not found (please try to pass your own genome via function parameters)

--- failed re-building ‘vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘vignette.Rnw’

Error: Vignette re-building failed.
Execution halted