############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf SMAD.buildbin-libdir && mkdir SMAD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SMAD_1.22.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SMAD.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SMAD.buildbin-libdir SMAD_1.22.0.tar.gz' >>>>>>> * installing *source* package ‘SMAD’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GetDICE.cpp -o GetDICE.o GetDICE.cpp:16:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if((mat(r, c1) == 1) & (mat(r, c2) == 1)){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && GetDICE.cpp:16:12: note: cast one or both operands to int to silence this warning GetDICE.cpp:18:19: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] } else if((mat(r, c1) == 1) & (mat(r, c2) == 0)){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && GetDICE.cpp:18:19: note: cast one or both operands to int to silence this warning GetDICE.cpp:20:19: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] } else if((mat(r, c1) == 0) & (mat(r, c2) == 1)){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && GetDICE.cpp:20:19: note: cast one or both operands to int to silence this warning 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GetPPN.cpp -o GetPPN.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -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 SMAD.so GetDICE.o GetPPN.o RcppExports.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/SMAD.buildbin-libdir/00LOCK-SMAD/00new/SMAD/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 (SMAD) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR SMAD.buildbin-libdir/SMAD/libs/SMAD.so >>>>>>> >>>>>>> Paths before fix: SMAD.buildbin-libdir/SMAD/libs/SMAD.so: SMAD.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /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) /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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "SMAD.buildbin-libdir/SMAD/libs/SMAD.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "SMAD.buildbin-libdir/SMAD/libs/SMAD.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "SMAD.buildbin-libdir/SMAD/libs/SMAD.so" >>>>>>> Paths after fix: SMAD.buildbin-libdir/SMAD/libs/SMAD.so: SMAD.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /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) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)