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### Running command:
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###   chmod a+r TitanCNA -R && F:\biocbuild\bbs-3.22-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 'GenomicRanges::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'
Warning in fun(libname, pkgname) :
  Package 'TitanCNA' is deprecated and will be removed from Bioconductor
  version 3.23
titan: Loading data F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpaKesl9/Rinst20d8825ec5cac/TitanCNA/extdata/test_alleleCounts_chr2.txt
Reading GC and mappability files
Slurping: F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpaKesl9/Rinst20d8825ec5cac/TitanCNA/extdata/gc_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Slurping: F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpaKesl9/Rinst20d8825ec5cac/TitanCNA/extdata/map_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Loading tumour file:F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpaKesl9/Rinst20d8825ec5cac/TitanCNA/extdata/test_tum_chr2.wig
Slurping: F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpaKesl9/Rinst20d8825ec5cac/TitanCNA/extdata/test_tum_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Loading normal file:F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpaKesl9/Rinst20d8825ec5cac/TitanCNA/extdata/test_norm_chr2.wig
Slurping: F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpaKesl9/Rinst20d8825ec5cac/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=-30480 and n=0.398 (map), s=[0.0083,0.3765], phi=1.503
fwdBack: loglik=-34146.0015
fwdBack: priorN=0.3630
fwdBack: priorS=-2.6681
fwdBack: priorVar=-437.5219
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.0896
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 1 complete loglik=-34525.5745
fwdBack: Elapsed time for iteration 1: 0.0622m
fwdBack: Iteration 2 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26833 and n=0.2538 (map), s=[0.009,0.433], phi=1.47
fwdBack: loglik=-28964.5593
fwdBack: priorN=0.1277
fwdBack: priorS=-2.5422
fwdBack: priorVar=-749.4067
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.2498
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 2 complete loglik=-29656.2866
fwdBack: Elapsed time for iteration 2: 0.0593m
fwdBack: Iteration 3 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26079 and n=0.2113 (map), s=[0.0069,0.4528], phi=1.484
fwdBack: loglik=-26351.3730
fwdBack: priorN=-0.0002
fwdBack: priorS=-2.7979
fwdBack: priorVar=-818.3951
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.1764
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 3 complete loglik=-27112.3989
fwdBack: Elapsed time for iteration 3: 0.0583m
fwdBack: Total elapsed time: 0.2792m
outputTitanResults: Correcting results...
outputTitanResults: Recomputing log-likelihood.
titan: Running HMM...
fwdBack: Iteration 1 chr: 1