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BUILD BIN report for SeqArray on tokay2

This page was generated on 2018-10-17 08:37:04 -0400 (Wed, 17 Oct 2018).

Package 1343/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqArray 1.20.2
Xiuwen Zheng
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/SeqArray
Branch: RELEASE_3_7
Last Commit: 7277e82
Last Changed Date: 2018-09-10 03:37:41 -0400 (Mon, 10 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SeqArray
Version: 1.20.2
Command: rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SeqArray.buildbin-libdir SeqArray_1.20.2.tar.gz
StartedAt: 2018-10-17 06:58:40 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 06:59:44 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 64.2 seconds
RetCode: 0
Status:  OK  
PackageFile: SeqArray_1.20.2.zip
PackageFileSize: 3.675 MiB

Command output

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###
### Running command:
###
###   rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SeqArray.buildbin-libdir SeqArray_1.20.2.tar.gz
###
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install for i386

* installing *source* package 'SeqArray' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ConvToGDS.cpp -o ConvToGDS.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c FileMerge.cpp -o FileMerge.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c GetData.cpp -o GetData.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Index.cpp -o Index.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c LinkSNPRelate.cpp -o LinkSNPRelate.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Methods.cpp -o Methods.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_SeqArray.c -o R_SeqArray.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ReadBySample.cpp -o ReadBySample.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ReadByVariant.cpp -o ReadByVariant.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c SeqArray.cpp -o SeqArray.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pkg_test.cpp -o pkg_test.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c samtools_ext.c -o samtools_ext.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c vectorization.c -o vectorization.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o SeqArray.dll tmp.def ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/SeqArray.buildbin-libdir/SeqArray/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SeqArray'
    finding HTML links ... done
    KG_P1_SampData                          html  
    SeqArray-package                        html  
    SeqVarGDSClass-class                    html  
    finding level-2 HTML links ... done

    seqAlleleFreq                           html  
    seqApply                                html  
    seqAsVCF                                html  
    seqBED2GDS                              html  
    seqBlockApply                           html  
    seqClose                                html  
    seqDelete                               html  
    seqDigest                               html  
    seqExampleFileName                      html  
    seqExport                               html  
    seqGDS2SNP                              html  
    seqGDS2VCF                              html  
    seqGetData                              html  
    seqGetFilter                            html  
    seqMerge                                html  
    seqMissing                              html  
    seqNumAllele                            html  
    seqOpen                                 html  
    seqOptimize                             html  
    seqParallel                             html  
    seqParallelSetup                        html  
    seqSNP2GDS                              html  
    seqSetFilter                            html  
    seqSetFilterCond                        html  
    seqStorageOption                        html  
    seqSummary                              html  
    seqSystem                               html  
    seqTranspose                            html  
    seqVCF2GDS                              html  
    seqVCF_Header                           html  
    seqVCF_SampID                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SeqArray' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ConvToGDS.cpp -o ConvToGDS.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c FileMerge.cpp -o FileMerge.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c GetData.cpp -o GetData.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Index.cpp -o Index.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c LinkSNPRelate.cpp -o LinkSNPRelate.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Methods.cpp -o Methods.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_SeqArray.c -o R_SeqArray.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ReadBySample.cpp -o ReadBySample.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ReadByVariant.cpp -o ReadByVariant.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c SeqArray.cpp -o SeqArray.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pkg_test.cpp -o pkg_test.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c samtools_ext.c -o samtools_ext.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c vectorization.c -o vectorization.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o SeqArray.dll tmp.def ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/SeqArray.buildbin-libdir/SeqArray/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SeqArray' as SeqArray_1.20.2.zip
* DONE (SeqArray)
In R CMD INSTALL
In R CMD INSTALL