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INSTALL report for SNPRelate on tokay2

This page was generated on 2019-10-16 12:31:00 -0400 (Wed, 16 Oct 2019).

Package 1552/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPRelate 1.18.1
Xiuwen Zheng
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/SNPRelate
Branch: RELEASE_3_9
Last Commit: 81c581b
Last Changed Date: 2019-07-03 14:00:19 -0400 (Wed, 03 Jul 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SNPRelate
Version: 1.18.1
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SNPRelate_1.18.1.tar.gz && rm -rf SNPRelate.buildbin-libdir && mkdir SNPRelate.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SNPRelate.buildbin-libdir SNPRelate_1.18.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SNPRelate_1.18.1.zip && rm SNPRelate_1.18.1.tar.gz SNPRelate_1.18.1.zip
StartedAt: 2019-10-15 18:49:05 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 18:51:39 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 153.8 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SNPRelate_1.18.1.tar.gz && rm -rf SNPRelate.buildbin-libdir && mkdir SNPRelate.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SNPRelate.buildbin-libdir SNPRelate_1.18.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SNPRelate_1.18.1.zip && rm SNPRelate_1.18.1.tar.gz SNPRelate_1.18.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1252k  100 1252k    0     0  11.9M      0 --:--:-- --:--:-- --:--:-- 12.7M

install for i386

* installing *source* package 'SNPRelate' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ConvToGDS.cpp -o ConvToGDS.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_SNPRelate.c -o R_SNPRelate.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c SNPRelate.cpp -o SNPRelate.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ThreadPool.cpp -o ThreadPool.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dGenGWAS.cpp -o dGenGWAS.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dVect.cpp -o dVect.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genBeta.cpp -o genBeta.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genEIGMIX.cpp -o genEIGMIX.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genFst.cpp -o genFst.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genHWE.cpp -o genHWE.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genIBD.cpp -o genIBD.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genIBS.cpp -o genIBS.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genKING.cpp -o genKING.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genLD.cpp -o genLD.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genPCA.cpp -o genPCA.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genSlideWin.cpp -o genSlideWin.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o SNPRelate.dll tmp.def ConvToGDS.o R_SNPRelate.o SNPRelate.o ThreadPool.o dGenGWAS.o dVect.o genBeta.o genEIGMIX.o genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genSlideWin.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/SNPRelate.buildbin-libdir/00LOCK-SNPRelate/00new/SNPRelate/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SNPRelate'
    finding HTML links ... done
    SNPGDSFileClass-class                   html  
    SNPRelate-package                       html  
    hapmap_geno                             html  
    snpgdsAdmixPlot                         html  
    snpgdsAdmixProp                         html  
    snpgdsAlleleSwitch                      html  
    snpgdsApartSelection                    html  
    snpgdsBED2GDS                           html  
    finding level-2 HTML links ... done

    snpgdsClose                             html  
    snpgdsCombineGeno                       html  
    snpgdsCreateGeno                        html  
    snpgdsCreateGenoSet                     html  
    snpgdsCutTree                           html  
    snpgdsDiss                              html  
    snpgdsDrawTree                          html  
    snpgdsEIGMIX                            html  
    snpgdsErrMsg                            html  
    snpgdsExampleFileName                   html  
    snpgdsFst                               html  
    snpgdsGDS2BED                           html  
    snpgdsGDS2Eigen                         html  
    snpgdsGDS2PED                           html  
    snpgdsGEN2GDS                           html  
    snpgdsGRM                               html  
    snpgdsGetGeno                           html  
    snpgdsHCluster                          html  
    snpgdsHWE                               html  
    snpgdsIBDKING                           html  
    snpgdsIBDMLE                            html  
    snpgdsIBDMLELogLik                      html  
    snpgdsIBDMoM                            html  
    snpgdsIBDSelection                      html  
    snpgdsIBS                               html  
    snpgdsIBSNum                            html  
    snpgdsIndInb                            html  
    snpgdsIndInbCoef                        html  
    snpgdsIndivBeta                         html  
    snpgdsLDMat                             html  
    snpgdsLDpair                            html  
    snpgdsLDpruning                         html  
    snpgdsMergeGRM                          html  
    snpgdsOpen                              html  
    snpgdsOption                            html  
    snpgdsPCA                               html  
    snpgdsPCACorr                           html  
    snpgdsPCASNPLoading                     html  
    snpgdsPCASampLoading                    html  
    snpgdsPED2GDS                           html  
    snpgdsPairIBD                           html  
    snpgdsPairIBDMLELogLik                  html  
    snpgdsPairScore                         html  
    snpgdsSNPList                           html  
    snpgdsSNPListClass                      html  
    snpgdsSNPListIntersect                  html  
    snpgdsSNPRateFreq                       html  
    snpgdsSampMissRate                      html  
    snpgdsSelectSNP                         html  
    snpgdsSlidingWindow                     html  
    snpgdsSummary                           html  
    snpgdsTranspose                         html  
    snpgdsVCF2GDS                           html  
    snpgdsVCF2GDS_R                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'SNPRelate' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ConvToGDS.cpp -o ConvToGDS.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_SNPRelate.c -o R_SNPRelate.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c SNPRelate.cpp -o SNPRelate.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ThreadPool.cpp -o ThreadPool.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dGenGWAS.cpp -o dGenGWAS.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dVect.cpp -o dVect.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genBeta.cpp -o genBeta.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genEIGMIX.cpp -o genEIGMIX.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genFst.cpp -o genFst.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genHWE.cpp -o genHWE.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genIBD.cpp -o genIBD.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genIBS.cpp -o genIBS.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genKING.cpp -o genKING.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genLD.cpp -o genLD.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genPCA.cpp -o genPCA.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DUSING_R -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c genSlideWin.cpp -o genSlideWin.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o SNPRelate.dll tmp.def ConvToGDS.o R_SNPRelate.o SNPRelate.o ThreadPool.o dGenGWAS.o dVect.o genBeta.o genEIGMIX.o genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genSlideWin.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/SNPRelate.buildbin-libdir/SNPRelate/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SNPRelate' as SNPRelate_1.18.1.zip
* DONE (SNPRelate)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SNPRelate' successfully unpacked and MD5 sums checked