Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4554
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2181/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TitanCNA 1.47.1  (landing page)
Gavin Ha
Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 Aug 2025)
git_url: https://git.bioconductor.org/packages/TitanCNA
git_branch: devel
git_last_commit: eed2321
git_last_commit_date: 2025-07-24 08:31:07 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for TitanCNA on palomino8

To the developers/maintainers of the TitanCNA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TitanCNA.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: TitanCNA
Version: 1.47.1
Command: chmod a+r TitanCNA -R && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data TitanCNA
StartedAt: 2025-08-14 23:47:06 -0400 (Thu, 14 Aug 2025)
EndedAt: 2025-08-14 23:48:52 -0400 (Thu, 14 Aug 2025)
EllapsedTime: 105.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r TitanCNA -R && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data TitanCNA
###
##############################################################################
##############################################################################


* 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