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### Running command:
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###   chmod a+r TitanCNA -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data TitanCNA
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* checking for file 'TitanCNA/DESCRIPTION' ... OK
* preparing 'TitanCNA':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'TitanCNA.Rnw' using Sweave
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::desc' by 'dplyr::desc' when loading 'TitanCNA'
Warning: replacing previous import 'BiocGenerics::setequal' by 'dplyr::setequal' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::slice' by 'dplyr::slice' when loading 'TitanCNA'
Warning: replacing previous import 'GenomeInfoDb::intersect' by 'dplyr::intersect' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'TitanCNA'
Warning: replacing previous import 'BiocGenerics::combine' by 'dplyr::combine' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::collapse' by 'dplyr::collapse' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'TitanCNA'
Warning: replacing previous import 'dplyr::select' by 'VariantAnnotation::select' when loading 'TitanCNA'
titan: Loading data E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpWeYqQ6/Rinst160d038932472/TitanCNA/extdata/test_alleleCounts_chr2.txt
Reading GC and mappability files
Slurping: E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpWeYqQ6/Rinst160d038932472/TitanCNA/extdata/gc_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Slurping: E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpWeYqQ6/Rinst160d038932472/TitanCNA/extdata/map_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Loading tumour file:E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpWeYqQ6/Rinst160d038932472/TitanCNA/extdata/test_tum_chr2.wig
Slurping: E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpWeYqQ6/Rinst160d038932472/TitanCNA/extdata/test_tum_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Loading normal file:E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpWeYqQ6/Rinst160d038932472/TitanCNA/extdata/test_norm_chr2.wig
Slurping: E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpWeYqQ6/Rinst160d038932472/TitanCNA/extdata/test_norm_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Warning in .replace_seqlevels_style(x_seqlevels, value) :
  found more than one best sequence renaming map compatible with seqname style "NCBI" for this object, using the first one
Warning in .replace_seqlevels_style(x_seqlevels, value) :
  found more than one best sequence renaming map compatible with seqname style "NCBI" for this object, using the first one
Warning in .replace_seqlevels_style(x_seqlevels, value) :
  found more than one best sequence renaming map compatible with seqname style "NCBI" for this object, using the first one
Warning in .replace_seqlevels_style(x_seqlevels, value) :
  found more than one best sequence renaming map compatible with seqname style "NCBI" for this object, using the first one
Correcting Tumour
Applying filter on data...
Correcting for GC bias...
Correcting for mappability bias...
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Correcting Normal
Applying filter on data...
Correcting for GC bias...
Correcting for mappability bias...
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Normalizing Tumour by Normal
Removed Chrs: 
titan: Running HMM...
fwdBack: Iteration 1 chr: Warning: executing %dopar% sequentially: no parallel backend registered
1 
Using Coordinate Descent iteration 11 with Fval=-30499 and n=0.3982 (map), s=[0.0083,0.3774], phi=1.501
fwdBack: loglik=-34155.3905
fwdBack: priorN=0.3631
fwdBack: priorS=-2.6658
fwdBack: priorVar=-436.5228
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.0987
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 1 complete loglik=-34533.9710
fwdBack: Elapsed time for iteration 1: 0.0643m
fwdBack: Iteration 2 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26846 and n=0.2536 (map), s=[0.0092,0.4330], phi=1.467
fwdBack: loglik=-28997.5065
fwdBack: priorN=0.1274
fwdBack: priorS=-2.5189
fwdBack: priorVar=-747.0567
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.2661
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 2 complete loglik=-29686.8772
fwdBack: Elapsed time for iteration 2: 0.0628m
fwdBack: Iteration 3 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26086 and n=0.2117 (map), s=[0.0069,0.4527], phi=1.481
fwdBack: loglik=-26362.4549
fwdBack: priorN=0.0012
fwdBack: priorS=-2.7978
fwdBack: priorVar=-816.7250
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.1915
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 3 complete loglik=-27121.8243
fwdBack: Elapsed time for iteration 3: 0.0650m
fwdBack: Total elapsed time: 0.2855m
outputTitanResults: Correcting results...
outputTitanResults: Recomputing log-likelihood.
titan: Running HMM...
fwdBack: Iteration 1 chr: 1