############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf levi.buildbin-libdir && mkdir levi.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh levi_1.24.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R levi.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=levi.buildbin-libdir levi_1.24.0.tar.gz' >>>>>>> * installing *source* package ‘levi’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ 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 RcppExports.cpp -o RcppExports.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 SigCoordPiso.cpp -o SigCoordPiso.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 matrix_entrada.cpp -o matrix_entrada.o matrix_entrada.cpp:22:21: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if ((coord(m,0) < q) & (bandcoord(m,0) == 0)) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && matrix_entrada.cpp:22:21: note: cast one or both operands to int to silence this warning matrix_entrada.cpp:31:25: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if ((coord(m,0) == q) & (coord(m,1) < p) & ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && matrix_entrada.cpp:31:25: note: cast one or both operands to int to silence this warning matrix_entrada.cpp:31:25: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if ((coord(m,0) == q) & (coord(m,1) < p) & ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && matrix_entrada.cpp:31:25: 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 matrix_saida.cpp -o matrix_saida.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 levi.so RcppExports.o SigCoordPiso.o matrix_entrada.o matrix_saida.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/levi.buildbin-libdir/00LOCK-levi/00new/levi/libs ** R ** 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 (levi) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR levi.buildbin-libdir/levi/libs/levi.so >>>>>>> >>>>>>> Paths before fix: levi.buildbin-libdir/levi/libs/levi.so: levi.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 4.4.2) /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" "levi.buildbin-libdir/levi/libs/levi.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "levi.buildbin-libdir/levi/libs/levi.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "levi.buildbin-libdir/levi/libs/levi.so" >>>>>>> Paths after fix: levi.buildbin-libdir/levi/libs/levi.so: levi.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 4.4.2) /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)