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###
### Running command:
###
###   rm -rf HIBAG.buildbin-libdir && mkdir HIBAG.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HIBAG_1.34.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R HIBAG.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=HIBAG.buildbin-libdir HIBAG_1.34.1.tar.gz'
>>>>>>> 

* installing *source* package ‘HIBAG’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c HIBAG.cpp -o HIBAG.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c LibHLA.cpp -o LibHLA.o
LibHLA.cpp:1241:7: warning: variable 'cpu_auto_avx2' set but not used [-Wunused-but-set-variable]
        bool cpu_auto_avx2, cpu_max;
             ^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c LibHLA_ext_avx.cpp -o LibHLA_ext_avx.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c LibHLA_ext_avx2.cpp -o LibHLA_ext_avx2.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c LibHLA_ext_avx512bw.cpp -o LibHLA_ext_avx512bw.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c LibHLA_ext_avx512f.cpp -o LibHLA_ext_avx512f.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c LibHLA_ext_avx512vpopcnt.cpp -o LibHLA_ext_avx512vpopcnt.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c LibHLA_ext_sse2.cpp -o LibHLA_ext_sse2.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c LibHLA_ext_sse4_2.cpp -o LibHLA_ext_sse4_2.o
clang++ -arch arm64 -std=gnu++11 -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 HIBAG.so HIBAG.o LibHLA.o LibHLA_ext_avx.o LibHLA_ext_avx2.o LibHLA_ext_avx512bw.o LibHLA_ext_avx512f.o LibHLA_ext_avx512vpopcnt.o LibHLA_ext_sse2.o LibHLA_ext_sse4_2.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/HIBAG.buildbin-libdir/00LOCK-HIBAG/00new/HIBAG/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 (HIBAG)


>>>>>>> 
>>>>>>> FIXING LINKS FOR HIBAG.buildbin-libdir/HIBAG/libs/HIBAG.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" "HIBAG.buildbin-libdir/HIBAG/libs/HIBAG.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" "HIBAG.buildbin-libdir/HIBAG/libs/HIBAG.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" "HIBAG.buildbin-libdir/HIBAG/libs/HIBAG.so"