################################################################################################################################################################## Running command:###### rm -rf GGPA.buildbin-libdir && mkdir GGPA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GGPA_1.22.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GGPA.buildbin-libdir###############################################################################################################################################################>>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GGPA.buildbin-libdir GGPA_1.22.0.tar.gz'>>>>>>> * installing *source* package ‘GGPA’ ...** this is package ‘GGPA’ version ‘1.22.0’** using staged installation** libsusing C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’using SDK: ‘MacOSX11.3.1.sdk’clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c 1_Main.cpp -o 1_Main.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c 3_Param.cpp -o 3_Param.o3_Param.cpp:74:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if ( ( Data.Y(i,i_SNP) > 0 ) & ( Data.Y(i,i_SNP) <= Data.threshold_on ) ){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &&3_Param.cpp:74:12: note: cast one or both operands to int to silence this warning1 warning generated.clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Gibbs_e_it_no_ann.cpp -o Gibbs_e_it_no_ann.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.oclang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o GGPA.so 1_Main.o 3_Param.o Gibbs_e_it_no_ann.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework Rinstalling to /Users/biocbuild/bbs-3.22-bioc/meat/GGPA.buildbin-libdir/00LOCK-GGPA/00new/GGPA/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 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 (GGPA)>>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR GGPA.buildbin-libdir/GGPA/libs/GGPA.so>>>>>>> >>>>>>> Paths before fix:GGPA.buildbin-libdir/GGPA/libs/GGPA.so:GGPA.so (compatibility version 0.0.0, current version 0.0.0)/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.5.0, current version 4.5.2)/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.2)/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)/System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0)>>>>>>> Fix with install_name_tool:install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "GGPA.buildbin-libdir/GGPA/libs/GGPA.so"install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "GGPA.buildbin-libdir/GGPA/libs/GGPA.so"install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "GGPA.buildbin-libdir/GGPA/libs/GGPA.so"install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "GGPA.buildbin-libdir/GGPA/libs/GGPA.so"install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "GGPA.buildbin-libdir/GGPA/libs/GGPA.so">>>>>>> Paths after fix:GGPA.buildbin-libdir/GGPA/libs/GGPA.so:GGPA.so (compatibility version 0.0.0, current version 0.0.0)/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.5.0, current version 4.5.2)/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.2)/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)/System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0)