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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ADaCGH2
###
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* checking for file ‘ADaCGH2/DESCRIPTION’ ... OK
* preparing ‘ADaCGH2’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ADaCGH2.Rnw’ using Sweave
Loading required package: parallel
Loading required package: ff
Loading required package: bit

Attaching package: ‘bit’

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

    xor

Attaching package ff
- getOption("fftempdir")=="/tmp/Rtmpgd5vbU/ff"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system


Attaching package: ‘ff’

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

    write.csv, write.csv2

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

    is.factor, is.ordered

Loading required package: GLAD

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Have fun with GLAD

For smoothing it is possible to use either
the AWS algorithm (Polzehl and Spokoiny, 2002,
or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics,  2008,

If you use the package with AWS, please cite:
Hupe et al. (Bioinformatics, 2004, and Polzehl and Spokoiny (2002,

If you use the package with HaarSeg, please cite:
Hupe et al. (Bioinformatics, 2004, and (Ben-Yaacov and Eldar, Bioinformatics, 2008,

For fast computation it is recommanded to use
the daglad function with smoothfunc=haarseg

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New options are available in daglad: see help for details.

Read 500 records
Read 500 records
Read 500 records
Read 500 records
Read 500 records
Read 500 records
Read 500 records
Read 500 records
Read 500 records
Warning in mclapply(X, FUN, ..., mc.preschedule = TRUE, mc.cores = mc.cores,  :
  all scheduled cores encountered errors in user code

Error: processing vignette 'ADaCGH2.Rnw' failed with diagnostics:
 chunk 7 
Error in out[[1]]$smoothed : $ operator is invalid for atomic vectors

--- failed re-building ‘ADaCGH2.Rnw’

SUMMARY: processing the following file failed:
  ‘ADaCGH2.Rnw’

Error: Vignette re-building failed.
Execution halted