##############################################################################
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###
### Running command:
###
###   rm -rf SNPRelate.buildbin-libdir && mkdir SNPRelate.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SNPRelate_1.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SNPRelate.buildbin-libdir
###
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##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SNPRelate.buildbin-libdir SNPRelate_1.40.0.tar.gz'
>>>>>>> 

* installing *source* package ‘SNPRelate’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ConvToGDS.cpp -o ConvToGDS.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_SNPRelate.c -o R_SNPRelate.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c SNPRelate.cpp -o SNPRelate.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ThreadPool.cpp -o ThreadPool.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c dGenGWAS.cpp -o dGenGWAS.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c dVect.cpp -o dVect.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c genBeta.cpp -o genBeta.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c genEIGMIX.cpp -o genEIGMIX.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c genFst.cpp -o genFst.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c genHWE.cpp -o genHWE.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c genIBD.cpp -o genIBD.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c genIBS.cpp -o genIBS.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c genKING.cpp -o genKING.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c genLD.cpp -o genLD.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c genPCA.cpp -o genPCA.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gdsfmt/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c genSlideWin.cpp -o genSlideWin.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/SNPRelate.buildbin-libdir/00LOCK-SNPRelate/00new/SNPRelate/libs
** R
** data
*** moving datasets to lazyload DB
** 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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SNPRelate)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so
>>>>>>> 

>>>>>>> Paths before fix:
SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so:
	SNPRelate.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.2)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so"

>>>>>>> Paths after fix:
SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so:
	SNPRelate.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.2)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)