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BUILD BIN report for SNPRelate on merida2

This page was generated on 2018-10-17 08:53:30 -0400 (Wed, 17 Oct 2018).

Package 1398/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPRelate 1.14.0
Xiuwen Zheng
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/SNPRelate
Branch: RELEASE_3_7
Last Commit: 9501cbf
Last Changed Date: 2018-04-30 10:35:34 -0400 (Mon, 30 Apr 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: SNPRelate
Version: 1.14.0
Command: rm -rf SNPRelate.buildbin-libdir && mkdir SNPRelate.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SNPRelate_1.14.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SNPRelate.buildbin-libdir
StartedAt: 2018-10-17 02:10:20 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:11:29 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 69.6 seconds
RetCode: 0
Status:  OK 
PackageFile: SNPRelate_1.14.0.tgz
PackageFileSize: 3.621 MiB

Command output

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###
### Running command:
###
###   rm -rf SNPRelate.buildbin-libdir && mkdir SNPRelate.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SNPRelate_1.14.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SNPRelate.buildbin-libdir
###
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##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SNPRelate.buildbin-libdir SNPRelate_1.14.0.tar.gz'
>>>>>>> 

* installing *source* package ‘SNPRelate’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c ConvToGDS.cpp -o ConvToGDS.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_SNPRelate.c -o R_SNPRelate.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SNPRelate.cpp -o SNPRelate.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c ThreadPool.cpp -o ThreadPool.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c dGenGWAS.cpp -o dGenGWAS.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c dVect.cpp -o dVect.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genBeta.cpp -o genBeta.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genEIGMIX.cpp -o genEIGMIX.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genFst.cpp -o genFst.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genHWE.cpp -o genHWE.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genIBD.cpp -o genIBD.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genIBS.cpp -o genIBS.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genKING.cpp -o genKING.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genLD.cpp -o genLD.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genPCA.cpp -o genPCA.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genSlideWin.cpp -o genSlideWin.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o SNPRelate.so 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 -lpthread -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.7-bioc/meat/SNPRelate.buildbin-libdir/SNPRelate/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SNPRelate)


>>>>>>> 
>>>>>>> FIXING LINKS FOR SNPRelate.buildbin-libdir/SNPRelate/libs//SNPRelate.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs//SNPRelate.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs//SNPRelate.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs//SNPRelate.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs//SNPRelate.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs//SNPRelate.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs//SNPRelate.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs//SNPRelate.so"