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This page was generated on 2022-01-17 11:08:34 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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

INSTALL results for TitanCNA on riesling1


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? here 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 1954/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TitanCNA 1.33.0  (landing page)
Gavin Ha
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/TitanCNA
git_branch: master
git_last_commit: c6f65f7
git_last_commit_date: 2021-10-26 12:13:15 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'BiocGenerics' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: TitanCNA
Version: 1.33.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL TitanCNA
StartedAt: 2022-01-16 16:09:58 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 16:10:47 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 48.6 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL TitanCNA
###
##############################################################################
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'TitanCNA' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c fwd_backC_clonalCN.c -o fwd_backC_clonalCN.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c getPositionOverlapC.c -o getPositionOverlapC.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c register.c -o register.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c viterbiC_clonalCN.c -o viterbiC_clonalCN.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o TitanCNA.dll tmp.def fwd_backC_clonalCN.o getPositionOverlapC.o register.o viterbiC_clonalCN.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-TitanCNA/00new/TitanCNA/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::collapse' by 'dplyr::collapse' 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 'IRanges::slice' by 'dplyr::slice' when loading 'TitanCNA'
Warning: replacing previous import 'GenomeInfoDb::intersect' by 'dplyr::intersect' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' 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::combine' by 'dplyr::combine' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'TitanCNA'
Warning: replacing previous import 'dplyr::select' by 'VariantAnnotation::select' when loading 'TitanCNA'
** help
*** installing help indices
  converting help for package 'TitanCNA'
    finding HTML links ... done
    TitanCNA-dataset                        html  
    TitanCNA-output                         html  
    TitanCNA-package                        html  
    TitanCNA-plotting                       html  
    computeSDbwIndex                        html  
    correctCN                               html  
    correctReadDepth                        html  
    filterData                              html  
    getPositionOverlap                      html  
    haplotype                               html  
    loadAlleleCounts                        html  
    loadDefaultParameters                   html  
    runEMclonalCN                           html  
    finding level-2 HTML links ... done

    viterbiClonalCN                         html  
    wigImport                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::collapse' by 'dplyr::collapse' 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 'IRanges::slice' by 'dplyr::slice' when loading 'TitanCNA'
Warning: replacing previous import 'GenomeInfoDb::intersect' by 'dplyr::intersect' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' 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::combine' by 'dplyr::combine' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'TitanCNA'
Warning: replacing previous import 'dplyr::select' by 'VariantAnnotation::select' when loading 'TitanCNA'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::collapse' by 'dplyr::collapse' 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 'IRanges::slice' by 'dplyr::slice' when loading 'TitanCNA'
Warning: replacing previous import 'GenomeInfoDb::intersect' by 'dplyr::intersect' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' 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::combine' by 'dplyr::combine' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'TitanCNA'
Warning: replacing previous import 'dplyr::select' by 'VariantAnnotation::select' when loading 'TitanCNA'
** testing if installed package keeps a record of temporary installation path
* DONE (TitanCNA)
Making 'packages.html' ... done