##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SNPRelate.buildbin-libdir && mkdir SNPRelate.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SNPRelate_1.32.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SNPRelate.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SNPRelate.buildbin-libdir SNPRelate_1.32.2.tar.gz'
>>>>>>> 

* installing *source* package ‘SNPRelate’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c ConvToGDS.cpp -o ConvToGDS.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c R_SNPRelate.c -o R_SNPRelate.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c SNPRelate.cpp -o SNPRelate.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c ThreadPool.cpp -o ThreadPool.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c dGenGWAS.cpp -o dGenGWAS.o
dGenGWAS.cpp:1096:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
                        sprintf(buffer, "%.0fs", s);
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
dGenGWAS.cpp:1098:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
                        sprintf(buffer, "%.1fm", s/S_MIN);
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
dGenGWAS.cpp:1100:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
                        sprintf(buffer, "%.1fh", s/S_HOUR);
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
dGenGWAS.cpp:1102:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
                        sprintf(buffer, "%.1fd", s/S_DAY);
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
dGenGWAS.cpp:1104:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
                        sprintf(buffer, "%.1f years", s/S_YEAR);
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c dVect.cpp -o dVect.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c genBeta.cpp -o genBeta.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c genEIGMIX.cpp -o genEIGMIX.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c genFst.cpp -o genFst.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c genHWE.cpp -o genHWE.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c genIBD.cpp -o genIBD.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c genIBS.cpp -o genIBS.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c genKING.cpp -o genKING.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c genLD.cpp -o genLD.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c genPCA.cpp -o genPCA.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c genSlideWin.cpp -o genSlideWin.o
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Volumes/External/bbs-3.16-bioc-m1/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 LINKS FOR SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so
>>>>>>> 

install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so"
install_name_tool -change "/opt/R/arm64/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so"
install_name_tool -change "/opt/R/arm64/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "SNPRelate.buildbin-libdir/SNPRelate/libs/SNPRelate.so"