| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-19 12:04 -0400 (Thu, 19 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4810 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4548 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4528 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4493 |
| 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 2173/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TitanCNA 1.47.0 (landing page) Gavin Ha
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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. |
| Package: TitanCNA |
| Version: 1.47.0 |
| 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: 2025-06-18 22:40:36 -0400 (Wed, 18 Jun 2025) |
| EndedAt: 2025-06-18 22:42:20 -0400 (Wed, 18 Jun 2025) |
| EllapsedTime: 103.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
############################################################################## ############################################################################## ### ### 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 '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 F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpWyNsF8/Rinst6fbc4136bbb/TitanCNA/extdata/test_alleleCounts_chr2.txt Reading GC and mappability files Slurping: F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpWyNsF8/Rinst6fbc4136bbb/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/RtmpWyNsF8/Rinst6fbc4136bbb/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/RtmpWyNsF8/Rinst6fbc4136bbb/TitanCNA/extdata/test_tum_chr2.wig Slurping: F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpWyNsF8/Rinst6fbc4136bbb/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/RtmpWyNsF8/Rinst6fbc4136bbb/TitanCNA/extdata/test_norm_chr2.wig Slurping: F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpWyNsF8/Rinst6fbc4136bbb/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=-30474 and n=0.3977 (map), s=[0.0083,0.3766], phi=1.502 fwdBack: loglik=-34146.8614 fwdBack: priorN=0.3627 fwdBack: priorS=-2.6695 fwdBack: priorVar=-438.0550 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.0912 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 1 complete loglik=-34526.9708 fwdBack: Elapsed time for iteration 1: 0.0590m fwdBack: Iteration 2 chr: 1 Using Coordinate Descent iteration 11 with Fval=-26825 and n=0.2536 (map), s=[0.0089,0.4331], phi=1.47 fwdBack: loglik=-28950.7890 fwdBack: priorN=0.1273 fwdBack: priorS=-2.5508 fwdBack: priorVar=-751.0130 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.2480 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 2 complete loglik=-29644.1298 fwdBack: Elapsed time for iteration 2: 0.0610m fwdBack: Iteration 3 chr: 1 Using Coordinate Descent iteration 11 with Fval=-26070 and n=0.2114 (map), s=[0.0069,0.4528], phi=1.485 fwdBack: loglik=-26341.4246 fwdBack: priorN=0.0002 fwdBack: priorS=-2.7966 fwdBack: priorVar=-820.3651 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.1754 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 3 complete loglik=-27104.4178 fwdBack: Elapsed time for iteration 3: 0.0588m fwdBack: Total elapsed time: 0.2727m outputTitanResults: Correcting results... outputTitanResults: Recomputing log-likelihood. titan: Running HMM... fwdBack: Iteration 1 chr: 1