################################################################################################################################################################## Running command:###### rm -rf sRACIPE.buildbin-libdir && mkdir sRACIPE.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh sRACIPE_2.2.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R sRACIPE.buildbin-libdir###############################################################################################################################################################>>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=sRACIPE.buildbin-libdir sRACIPE_2.2.0.tar.gz'>>>>>>> * installing *source* package ‘sRACIPE’ ...** this is package ‘sRACIPE’ version ‘2.2.0’** using staged installation** libsusing C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’using C++11using SDK: ‘MacOSX11.3.1.sdk’clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c generateThresholds.cpp -o generateThresholds.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c header.cpp -o header.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c limitcycle.cpp -o limitcycle.olimitcycle.cpp:327:9: warning: variable 'countSameMinDist' set but not used [-Wunused-but-set-variable] int countSameMinDist=0; ^1 warning generated.clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c simulateGRC.cpp -o simulateGRC.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c steppers.cpp -o steppers.oclang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c steppersConv.cpp -o steppersConv.osteppersConv.cpp:37:10: warning: variable 'i' set but not used [-Wunused-but-set-variable] double i=0.0; ^steppersConv.cpp:170:8: warning: variable 'i' set but not used [-Wunused-but-set-variable]double i=0.0; ^steppersConv.cpp:422:10: warning: variable 'i' set but not used [-Wunused-but-set-variable] double i=0.0; ^3 warnings generated.clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o sRACIPE.so RcppExports.o generateThresholds.o header.o limitcycle.o simulateGRC.o steppers.o steppersConv.o -F/Library/Frameworks/R.framework/.. -framework Rinstalling to /Users/biocbuild/bbs-3.22-bioc/meat/sRACIPE.buildbin-libdir/00LOCK-sRACIPE/00new/sRACIPE/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 (sRACIPE)>>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR sRACIPE.buildbin-libdir/sRACIPE/libs/sRACIPE.so>>>>>>> >>>>>>> Paths before fix:sRACIPE.buildbin-libdir/sRACIPE/libs/sRACIPE.so:sRACIPE.so (compatibility version 0.0.0, current version 0.0.0)/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)>>>>>>> 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" "sRACIPE.buildbin-libdir/sRACIPE/libs/sRACIPE.so"install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "sRACIPE.buildbin-libdir/sRACIPE/libs/sRACIPE.so"install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "sRACIPE.buildbin-libdir/sRACIPE/libs/sRACIPE.so">>>>>>> Paths after fix:sRACIPE.buildbin-libdir/sRACIPE/libs/sRACIPE.so:sRACIPE.so (compatibility version 0.0.0, current version 0.0.0)/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)
