Error(s) in re-building vignettes:
--- re-building 'pcalgDoc.Rnw' using Sweave
Loading required package: Rgraphviz
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: grid
Warning: multiple methods tables found for 'plot'

Error: processing vignette 'pcalgDoc.Rnw' failed with diagnostics:
 chunk 6 (label = exIntroPlot) 
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'

--- failed re-building 'pcalgDoc.Rnw'

--- re-building 'vignette2018.Rnw' using Sweave
Loading required package: Rgraphviz
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: grid
Warning: multiple methods tables found for 'plot'

Error: processing vignette 'vignette2018.Rnw' failed with diagnostics:
 chunk 7 (label = exIntroPlot) 
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'

--- failed re-building 'vignette2018.Rnw'

SUMMARY: processing the following files failed:
  'pcalgDoc.Rnw' 'vignette2018.Rnw'

Error: Vignette re-building failed.
Execution halted