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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/Rtmp46kIWn/Rinst1cc3c246814c0/TitanCNA/extdata/test_alleleCounts_chr2.txt
Reading GC and mappability files
Slurping: E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmp46kIWn/Rinst1cc3c246814c0/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/Rtmp46kIWn/Rinst1cc3c246814c0/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/Rtmp46kIWn/Rinst1cc3c246814c0/TitanCNA/extdata/test_tum_chr2.wig
Slurping: E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmp46kIWn/Rinst1cc3c246814c0/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/Rtmp46kIWn/Rinst1cc3c246814c0/TitanCNA/extdata/test_norm_chr2.wig
Slurping: E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmp46kIWn/Rinst1cc3c246814c0/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=-30500 and n=0.3978 (map), s=[0.0083,0.3770], phi=1.503
fwdBack: loglik=-34156.3637
fwdBack: priorN=0.3628
fwdBack: priorS=-2.6671
fwdBack: priorVar=-435.1733
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.0851
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 1 complete loglik=-34533.5828
fwdBack: Elapsed time for iteration 1: 0.0578m
fwdBack: Iteration 2 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26851 and n=0.2533 (map), s=[0.009,0.433], phi=1.47
fwdBack: loglik=-28992.1961
fwdBack: priorN=0.1266
fwdBack: priorS=-2.5393
fwdBack: priorVar=-745.8323
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.2466
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 2 complete loglik=-29680.3441
fwdBack: Elapsed time for iteration 2: 0.0562m
fwdBack: Iteration 3 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26100 and n=0.2113 (map), s=[0.0069,0.4529], phi=1.485
fwdBack: loglik=-26375.2273
fwdBack: priorN=-0.0000
fwdBack: priorS=-2.7933
fwdBack: priorVar=-814.5596
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.1747
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 3 complete loglik=-27132.4113
fwdBack: Elapsed time for iteration 3: 0.0615m
fwdBack: Total elapsed time: 0.2665m
outputTitanResults: Correcting results...
outputTitanResults: Recomputing log-likelihood.
titan: Running HMM...
fwdBack: Iteration 1 chr: 1