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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 MethTargetedNGS
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* checking for file ‘MethTargetedNGS/DESCRIPTION’ ... OK
* preparing ‘MethTargetedNGS’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MethTargetedNGS.Rnw’ using Sweave
Loading required package: stringr
Loading required package: seqinr
Loading required package: gplots

Attaching package: ‘gplots’

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

    lowess

Loading required package: Biostrings
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:gplots’:

    space

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: XVector
Loading required package: GenomeInfoDb

Attaching package: ‘Biostrings’

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

    translate

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

    strsplit

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, pattern, pid, qualitySubstitutionMatrices,
    stringDist, unaligned, writePairwiseAlignments


Error: processing vignette 'MethTargetedNGS.Rnw' failed with diagnostics:
 chunk 2 (label = Aligning samples to reference sequence) 
Error in unlist(substitutionMatrix, substitutionMatrix) : 
  'recursive' must be a length-1 vector

--- failed re-building ‘MethTargetedNGS.Rnw’

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

Error: Vignette re-building failed.
Execution halted