Error in re-building vignettes:
  ...
Loading required package: copynumber
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, colMeans, colSums, colnames, dirname,
    do.call, duplicated, eval, evalq, get, grep,
    grepl, intersect, is.unsorted, lapply, lengths,
    mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rowMeans,
    rowSums, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max,
    which.min

Loading required package: squash
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  line 1 appears to contain embedded nulls
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  line 2 appears to contain embedded nulls
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  line 3 appears to contain embedded nulls
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  line 4 appears to contain embedded nulls
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  line 5 appears to contain embedded nulls
Warning in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  embedded nul(s) found in input
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  cols = 1 != length(data) = 3

Error: processing vignette 'sequenza.Rnw' failed with diagnostics:
 chunk 11 (label = depthRGCnormall) 
Error in split.default(x = x, f = gc) : first argument must be a vector
Execution halted