Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

BUILD BIN report for TitanCNA on tokay1

This page was generated on 2019-04-13 11:23:48 -0400 (Sat, 13 Apr 2019).

Package 1566/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TitanCNA 1.20.1
Gavin Ha , Sohrab P Shah
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/TitanCNA
Branch: RELEASE_3_8
Last Commit: 3636b53
Last Changed Date: 2019-01-04 13:07:37 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: TitanCNA
Version: 1.20.1
Command: rm -rf TitanCNA.buildbin-libdir && mkdir TitanCNA.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TitanCNA.buildbin-libdir TitanCNA_1.20.1.tar.gz
StartedAt: 2019-04-13 08:01:45 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 08:02:31 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 45.6 seconds
RetCode: 0
Status:  OK  
PackageFile: TitanCNA_1.20.1.zip
PackageFileSize: 3.887 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf TitanCNA.buildbin-libdir && mkdir TitanCNA.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TitanCNA.buildbin-libdir TitanCNA_1.20.1.tar.gz
###
##############################################################################
##############################################################################



install for i386

* installing *source* package 'TitanCNA' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c fwd_backC_clonalCN.c -o fwd_backC_clonalCN.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c getPositionOverlapC.c -o getPositionOverlapC.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c register.c -o register.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c viterbiC_clonalCN.c -o viterbiC_clonalCN.o
C:/Rtools/mingw_32/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/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/TitanCNA.buildbin-libdir/TitanCNA/libs/i386
** 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 'data.table::between' by 'dplyr::between' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::collapse' by 'dplyr::collapse' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::desc' by 'dplyr::desc' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'TitanCNA'
Warning: replacing previous import 'GenomeInfoDb::intersect' by 'dplyr::intersect' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::slice' by 'dplyr::slice' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::last' by 'dplyr::last' 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  
    correctReadDepth                        html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpE3wGUT/R.INSTALL408825523746/TitanCNA/man/correctReadDepth.Rd:17: file link 'wigToRangedData' in package 'HMMcopy' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpE3wGUT/R.INSTALL408825523746/TitanCNA/man/correctReadDepth.Rd:58: file link 'wigToRangedData' in package 'HMMcopy' does not exist and so has been treated as a topic
    extractAlleleReadCounts                 html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpE3wGUT/R.INSTALL408825523746/TitanCNA/man/extractAlleleReadCounts.Rd:31: file link 'PileupParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpE3wGUT/R.INSTALL408825523746/TitanCNA/man/extractAlleleReadCounts.Rd:59: file link 'PileupParam' in package 'Rsamtools' does not exist and so has been treated as a topic
    filterData                              html  
    getPositionOverlap                      html  
    haplotype                               html  
    loadAlleleCounts                        html  
    loadDefaultParameters                   html  
    runEMclonalCN                           html  
    finding level-2 HTML links ... done

    viterbiClonalCN                         html  
    wigToRangedData                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::collapse' by 'dplyr::collapse' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::desc' by 'dplyr::desc' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'TitanCNA'
Warning: replacing previous import 'GenomeInfoDb::intersect' by 'dplyr::intersect' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::slice' by 'dplyr::slice' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'TitanCNA'
Warning: replacing previous import 'dplyr::select' by 'VariantAnnotation::select' when loading 'TitanCNA'
In R CMD INSTALL

install for x64

* installing *source* package 'TitanCNA' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c fwd_backC_clonalCN.c -o fwd_backC_clonalCN.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c getPositionOverlapC.c -o getPositionOverlapC.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c register.c -o register.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c viterbiC_clonalCN.c -o viterbiC_clonalCN.o
C:/Rtools/mingw_64/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 -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/TitanCNA.buildbin-libdir/TitanCNA/libs/x64
** testing if installed package can be loaded
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 'data.table::between' by 'dplyr::between' when loading 'TitanCNA'
Warning: replacing previous import 'dplyr::select' by 'VariantAnnotation::select' when loading 'TitanCNA'
* MD5 sums
packaged installation of 'TitanCNA' as TitanCNA_1.20.1.zip
* DONE (TitanCNA)
In R CMD INSTALL
In R CMD INSTALL