Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

This page was generated on 2025-08-18 11:42 -0400 (Mon, 18 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4566
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 2202/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TitanCNA 1.46.0  (landing page)
Gavin Ha
Snapshot Date: 2025-08-14 13:40 -0400 (Thu, 14 Aug 2025)
git_url: https://git.bioconductor.org/packages/TitanCNA
git_branch: RELEASE_3_21
git_last_commit: 29d317a
git_last_commit_date: 2025-04-15 10:30:47 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for TitanCNA on palomino7

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: 1.46.0
Command: chmod a+r TitanCNA -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data TitanCNA
StartedAt: 2025-08-14 22:44:33 -0400 (Thu, 14 Aug 2025)
EndedAt: 2025-08-14 22:46:19 -0400 (Thu, 14 Aug 2025)
EllapsedTime: 106.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r TitanCNA -R && E:\biocbuild\bbs-3.21-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 '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/RtmpKM3wXQ/Rinst15054562479f1/TitanCNA/extdata/test_alleleCounts_chr2.txt
Reading GC and mappability files
Slurping: E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpKM3wXQ/Rinst15054562479f1/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/RtmpKM3wXQ/Rinst15054562479f1/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/RtmpKM3wXQ/Rinst15054562479f1/TitanCNA/extdata/test_tum_chr2.wig
Slurping: E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpKM3wXQ/Rinst15054562479f1/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/RtmpKM3wXQ/Rinst15054562479f1/TitanCNA/extdata/test_norm_chr2.wig
Slurping: E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpKM3wXQ/Rinst15054562479f1/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=-30487 and n=0.3975 (map), s=[0.0083,0.3762], phi=1.503
fwdBack: loglik=-34151.5515
fwdBack: priorN=0.3625
fwdBack: priorS=-2.6697
fwdBack: priorVar=-434.8236
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.0865
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 1 complete loglik=-34528.4252
fwdBack: Elapsed time for iteration 1: 0.0583m
fwdBack: Iteration 2 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26856 and n=0.2537 (map), s=[0.0089,0.4330], phi=1.471
fwdBack: loglik=-28971.8464
fwdBack: priorN=0.1276
fwdBack: priorS=-2.5537
fwdBack: priorVar=-744.7865
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.2428
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 2 complete loglik=-29658.9582
fwdBack: Elapsed time for iteration 2: 0.0625m
fwdBack: Iteration 3 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26106 and n=0.2112 (map), s=[0.0069,0.4529], phi=1.486
fwdBack: loglik=-26380.5559
fwdBack: priorN=-0.0004
fwdBack: priorS=-2.7957
fwdBack: priorVar=-813.2946
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.1704
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 3 complete loglik=-27136.4733
fwdBack: Elapsed time for iteration 3: 0.0650m
fwdBack: Total elapsed time: 0.2785m
outputTitanResults: Correcting results...
outputTitanResults: Recomputing log-likelihood.
titan: Running HMM...
fwdBack: Iteration 1 chr: 1