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This page was generated on 2025-02-06 11:41 -0500 (Thu, 06 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4719
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4480
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4491
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4444
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 2159/2295HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TitanCNA 1.45.0  (landing page)
Gavin Ha
Snapshot Date: 2025-02-05 13:48 -0500 (Wed, 05 Feb 2025)
git_url: https://git.bioconductor.org/packages/TitanCNA
git_branch: devel
git_last_commit: 19f37d4
git_last_commit_date: 2024-10-29 09:51:45 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped

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: 1.45.0
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: 2025-02-05 22:13:32 -0500 (Wed, 05 Feb 2025)
EndedAt: 2025-02-05 22:15:09 -0500 (Wed, 05 Feb 2025)
EllapsedTime: 97.9 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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###
### 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
###
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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/RtmpkvxPyL/Rinst3554109ed57/TitanCNA/extdata/test_alleleCounts_chr2.txt
Reading GC and mappability files
Slurping: E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpkvxPyL/Rinst3554109ed57/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/RtmpkvxPyL/Rinst3554109ed57/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/RtmpkvxPyL/Rinst3554109ed57/TitanCNA/extdata/test_tum_chr2.wig
Slurping: E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpkvxPyL/Rinst3554109ed57/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/RtmpkvxPyL/Rinst3554109ed57/TitanCNA/extdata/test_norm_chr2.wig
Slurping: E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpkvxPyL/Rinst3554109ed57/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=-30449 and n=0.3972 (map), s=[0.0082,0.3761], phi=1.499
fwdBack: loglik=-34143.8558
fwdBack: priorN=0.3623
fwdBack: priorS=-2.6736
fwdBack: priorVar=-439.9563
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.1050
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 1 complete loglik=-34525.8848
fwdBack: Elapsed time for iteration 1: 0.0557m
fwdBack: Iteration 2 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26799 and n=0.2537 (map), s=[0.0086,0.4331], phi=1.47
fwdBack: loglik=-28902.5162
fwdBack: priorN=0.1275
fwdBack: priorS=-2.5818
fwdBack: priorVar=-756.2848
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.2507
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 2 complete loglik=-29601.1623
fwdBack: Elapsed time for iteration 2: 0.0597m
fwdBack: Iteration 3 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26045 and n=0.2103 (map), s=[0.0068,0.4534], phi=1.484
fwdBack: loglik=-26310.0345
fwdBack: priorN=-0.0036
fwdBack: priorS=-2.8055
fwdBack: priorVar=-826.5523
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.1761
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 3 complete loglik=-27079.2284
fwdBack: Elapsed time for iteration 3: 0.0565m
fwdBack: Total elapsed time: 0.2615m
outputTitanResults: Correcting results...
outputTitanResults: Recomputing log-likelihood.
titan: Running HMM...
fwdBack: Iteration 1 chr: 1