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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 cn.mops
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* checking for file ‘cn.mops/DESCRIPTION’ ... OK
* preparing ‘cn.mops’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘cn.mops.Rnw’ using Sweave
Loading required package: parallel
Loading required package: GenomicRanges
Loading required package: stats4
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, 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.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb

Attaching package: ‘cn.mops’

The following object is masked from ‘package:S4Vectors’:

    params

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:cn.mops’:

    sampleNames

Normalizing...
Starting local modeling, please be patient...  
Reference sequence:  chrA
Starting segmentation algorithm...
Using "fastseg" for segmentation.
Identified the following reference sequences:  20
Missing "refSeqNames"! Selecting all identified reference sequence for analysis.

 PLEASE BE PATIENT... this might take a while. Consider using the parallel version of this function

Segplot might not work because of special characters in the sample names. Use only A-Z,a-z and 0-9! 
 There is a hidden function cn.mops:::.replaceNames that replaces the names in the "CNVDetectionResult" object.
Normalizing...
Starting local modeling, please be patient...  
Reference sequence:  22
Starting segmentation algorithm...
Using "fastseg" for segmentation.
NOTE: The default parameters are adjusted for "tumor-vs-normal"!
Normalizing...
Starting local modeling, please be patient...  
Reference sequence:  undef
Starting segmentation algorithm...
Using "DNAcopy" for segmentation.
Loading required namespace: DNAcopy
Failed with error:  ‘there is no package called ‘DNAcopy’’

Error: processing vignette 'cn.mops.Rnw' failed with diagnostics:
 chunk 33 
Error in loadNamespace(x) : there is no package called ‘DNAcopy’

--- failed re-building ‘cn.mops.Rnw’

SUMMARY: processing the following file failed:
  ‘cn.mops.Rnw’

Error: Vignette re-building failed.
Execution halted