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INSTALL report for contiBAIT on tokay2

This page was generated on 2020-10-17 11:56:22 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE contiBAIT PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 366/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
contiBAIT 1.16.0
Kieran O'Neill
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/contiBAIT
Branch: RELEASE_3_11
Last Commit: 43200c3
Last Changed Date: 2020-05-15 13:49:58 -0400 (Fri, 15 May 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: contiBAIT
Version: 1.16.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/contiBAIT_1.16.0.tar.gz && rm -rf contiBAIT.buildbin-libdir && mkdir contiBAIT.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=contiBAIT.buildbin-libdir contiBAIT_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL contiBAIT_1.16.0.zip && rm contiBAIT_1.16.0.tar.gz contiBAIT_1.16.0.zip
StartedAt: 2020-10-16 19:13:27 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 19:16:04 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 156.8 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/contiBAIT_1.16.0.tar.gz && rm -rf contiBAIT.buildbin-libdir && mkdir contiBAIT.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=contiBAIT.buildbin-libdir contiBAIT_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL contiBAIT_1.16.0.zip && rm contiBAIT_1.16.0.tar.gz contiBAIT_1.16.0.zip
###
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install for i386

* installing *source* package 'contiBAIT' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c buildLinkageGroups.cpp -o buildLinkageGroups.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c computeSim.cpp -o computeSim.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c orderContigsGreedy.cpp -o orderContigsGreedy.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o contiBAIT.dll tmp.def buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/contiBAIT.buildbin-libdir/00LOCK-contiBAIT/00new/contiBAIT/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** help
*** installing help indices
  converting help for package 'contiBAIT'
    finding HTML links ... done
    BAIT                                    html  
    ChrTable                                html  
    ContigOrdering                          html  
    LibraryGroupList                        html  
    LinkageGroupList                        html  
    StrandFreqMatrix                        html  
    StrandReadMatrix                        html  
    StrandStateList                         html  
    StrandStateMatrix                       html  
    barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method
                                            html  
    clusterContigs-StrandStateMatrix-method
                                            html  
    contiBAIT                               html  
    exampleChrTable                         html  
    exampleContigOrder                      html  
    exampleCrickFreq                        html  
    exampleDividedChr                       html  
    exampleLGList                           html  
    exampleLibList                          html  
    exampleReadCounts                       html  
    exampleStrandFreq                       html  
    exampleWCMatrix                         html  
    exampleWatsonFreq                       html  
    findSexGroups-LinkageGroupList-StrandStateMatrix-method
                                            html  
    findSimilarLibraries                    html  
    fixLinkageGroups                        html  
    flipOrderedLinkageGroups                html  
    highlightAssemblyErrors                 html  
    ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method
                                            html  
    locateMisorients                        html  
    makeBoxPlot                             html  
    makeChrTable                            html  
    mapGapFromOverlap                       html  
    mergeFlankedLGs                         html  
    orderAllLinkageGroups                   html  
    orderContigsGreedy                      html  
    orderContigsTSP                         html  
    plotContigOrder                         html  
    plotLGDistances-LinkageGroupList-StrandStateMatrix-method
                                            html  
    plotWCdistribution-StrandFreqMatrix-method
                                            html  
    preprocessStrandTable-StrandFreqMatrix-method
                                            html  
    reorientAndMergeLGs                     html  
    show-ContigOrdering-method              html  
    show-LibraryGroupList-method            html  
    show-LinkageGroupList-method            html  
    show-OrientationFrame-method            html  
    show-StrandFreqMatrix-method            html  
    show-StrandReadMatrix-method            html  
    show-StrandStateList-method             html  
    show-StrandStateMatrix-method           html  
    strandSeqFreqTable                      html  
    thoroughBed                             html  
    writeBed                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'contiBAIT' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c buildLinkageGroups.cpp -o buildLinkageGroups.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c computeSim.cpp -o computeSim.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c orderContigsGreedy.cpp -o orderContigsGreedy.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o contiBAIT.dll tmp.def buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/contiBAIT.buildbin-libdir/contiBAIT/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
* MD5 sums
packaged installation of 'contiBAIT' as contiBAIT_1.16.0.zip
* DONE (contiBAIT)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'contiBAIT' successfully unpacked and MD5 sums checked