############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf normr.buildbin-libdir && mkdir normr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh normr_1.31.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R normr.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=normr.buildbin-libdir normr_1.31.0.tar.gz' >>>>>>> * installing *source* package ‘normr’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_GLIBCXX_USE_C99 -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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_GLIBCXX_USE_C99 -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 em.cpp -o em.o em.cpp:255:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] if ((r.size() <= 0) | (s.size() <= 0)) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ || em.cpp:255:9: note: cast one or both operands to int to silence this warning 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_GLIBCXX_USE_C99 -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 normr_init.c -o normr_init.o 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 normr.so RcppExports.o em.o normr_init.o -D_GLIBCXX_USE_C99 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/normr.buildbin-libdir/00LOCK-normr/00new/normr/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘getClasses’ in package ‘normr’ ** 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 (normr) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR normr.buildbin-libdir/normr/libs/normr.so >>>>>>> >>>>>>> Paths before fix: normr.buildbin-libdir/normr/libs/normr.so: normr.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" "normr.buildbin-libdir/normr/libs/normr.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "normr.buildbin-libdir/normr/libs/normr.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "normr.buildbin-libdir/normr/libs/normr.so" >>>>>>> Paths after fix: normr.buildbin-libdir/normr/libs/normr.so: normr.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)