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This page was generated on 2022-12-06 11:06:49 -0500 (Tue, 06 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4277
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4193
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
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

BUILD results for TitanCNA on nebbiolo1


To the developers/maintainers of the TitanCNA package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2031/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TitanCNA 1.37.0  (landing page)
Gavin Ha
Snapshot Date: 2022-12-05 14:00:11 -0500 (Mon, 05 Dec 2022)
git_url: https://git.bioconductor.org/packages/TitanCNA
git_branch: master
git_last_commit: 5c82ab3
git_last_commit_date: 2022-11-01 11:09:35 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: TitanCNA
Version: 1.37.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data TitanCNA
StartedAt: 2022-12-05 18:09:26 -0500 (Mon, 05 Dec 2022)
EndedAt: 2022-12-05 18:10:47 -0500 (Mon, 05 Dec 2022)
EllapsedTime: 80.4 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R 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 ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::desc’ by ‘dplyr::desc’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::slice’ by ‘dplyr::slice’ when loading ‘TitanCNA’
Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomeInfoDb::intersect’ by ‘dplyr::intersect’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘TitanCNA’
Warning: replacing previous import ‘dplyr::select’ by ‘VariantAnnotation::select’ when loading ‘TitanCNA’
titan: Loading data /tmp/Rtmpp7oHfu/Rinst21e3f338f11794/TitanCNA/extdata/test_alleleCounts_chr2.txt
Reading GC and mappability files
Slurping: /tmp/Rtmpp7oHfu/Rinst21e3f338f11794/TitanCNA/extdata/gc_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Slurping: /tmp/Rtmpp7oHfu/Rinst21e3f338f11794/TitanCNA/extdata/map_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Loading tumour file:/tmp/Rtmpp7oHfu/Rinst21e3f338f11794/TitanCNA/extdata/test_tum_chr2.wig
Slurping: /tmp/Rtmpp7oHfu/Rinst21e3f338f11794/TitanCNA/extdata/test_tum_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Loading normal file:/tmp/Rtmpp7oHfu/Rinst21e3f338f11794/TitanCNA/extdata/test_norm_chr2.wig
Slurping: /tmp/Rtmpp7oHfu/Rinst21e3f338f11794/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=-30334 and n=0.393 (map), s=[0.008,0.370], phi=1.485
fwdBack: loglik=-34140.2879
fwdBack: priorN=0.3586
fwdBack: priorS=-2.7050
fwdBack: priorVar=-436.1621
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.1754
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 1 complete loglik=-34518.6282
fwdBack: Elapsed time for iteration 1: 0.0413m
fwdBack: Iteration 2 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26816 and n=0.2548 (map), s=[0.0074,0.4321], phi=1.472
fwdBack: loglik=-28718.2262
fwdBack: priorN=0.1304
fwdBack: priorS=-2.7372
fwdBack: priorVar=-752.7694
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.2406
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 2 complete loglik=-29413.4994
fwdBack: Elapsed time for iteration 2: 0.0447m
fwdBack: Iteration 3 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26057 and n=0.2114 (map), s=[0.0068,0.4529], phi=1.487
fwdBack: loglik=-26328.3888
fwdBack: priorN=0.0001
fwdBack: priorS=-2.8107
fwdBack: priorVar=-823.3308
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.1642
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 3 complete loglik=-27094.3508
fwdBack: Elapsed time for iteration 3: 0.0408m
fwdBack: Total elapsed time: 0.2064m
outputTitanResults: Correcting results...
outputTitanResults: Recomputing log-likelihood.
titan: Running HMM...
fwdBack: Iteration 1 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-22759 and n=0.2167 (fixed), s=[0.00,0.45], phi=1.487
fwdBack: loglik=-35781.5022
fwdBack: priorN=0.0000
fwdBack: priorS=0.0000
fwdBack: priorVar=-669.7531
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=0.0000
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 1 complete loglik=-36389.9117
fwdBack: Elapsed time for iteration 1: 0.0378m
fwdBack: Total elapsed time: 0.0647m
Error: processing vignette 'TitanCNA.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'TitanCNA.tex' failed.
LaTeX errors:
! Missing $ inserted.
<inserted text> 
                $
l.718   \item Time zone America/New_
                                    York
! Emergency stop.
<inserted text> 
                $
l.718   \item Time zone America/New_
                                    York
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘TitanCNA.Rnw’

SUMMARY: processing the following file failed:
  ‘TitanCNA.Rnw’

Error: Vignette re-building failed.
Execution halted