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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GenomicAlignments
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* checking for file ‘GenomicAlignments/DESCRIPTION’ ... OK
* preparing ‘GenomicAlignments’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘WorkingWithAlignedNucleotides.Rmd’ using rmarkdown
Error: processing vignette 'WorkingWithAlignedNucleotides.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘WorkingWithAlignedNucleotides.Rmd’

--- re-building ‘GenomicAlignmentsIntroduction.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: 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: Seqinfo
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
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: 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: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

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

    strsplit

Loading required package: Rsamtools
--- finished re-building ‘GenomicAlignmentsIntroduction.Rnw’

--- re-building ‘OverlapEncodings.Rnw’ using Sweave
Warning in call_new_fun_in_cigarillo("cigarOpTable", "tabulate_cigar_ops",  :
  cigarOpTable() is formally deprecated in GenomicAlignments >= 1.45.5 and replaced with the
  tabulate_cigar_ops() function from the new cigarillo package
Warning in call_new_fun_in_cigarillo("cigarOpTable", "tabulate_cigar_ops",  :
  cigarOpTable() is formally deprecated in GenomicAlignments >= 1.45.5 and replaced with the
  tabulate_cigar_ops() function from the new cigarillo package
Warning in call_new_fun_in_cigarillo("cigarOpTable", "tabulate_cigar_ops",  :
  cigarOpTable() is formally deprecated in GenomicAlignments >= 1.45.5 and replaced with the
  tabulate_cigar_ops() function from the new cigarillo package
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: BSgenome
Loading required package: BiocIO
Loading required package: rtracklayer
--- finished re-building ‘OverlapEncodings.Rnw’

--- re-building ‘summarizeOverlaps.Rnw’ using Sweave
Loading required package: limma

Attaching package: ‘limma’

The following object is masked from ‘package:DESeq2’:

    plotMA

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

    plotMA

--- finished re-building ‘summarizeOverlaps.Rnw’

SUMMARY: processing the following file failed:
  ‘WorkingWithAlignedNucleotides.Rmd’

Error: Vignette re-building failed.
Execution halted