############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf bcSeq.buildbin-libdir && mkdir bcSeq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bcSeq_1.28.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R bcSeq.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=bcSeq.buildbin-libdir bcSeq_1.28.0.tar.gz' >>>>>>> * installing *source* package ‘bcSeq’ ... ** 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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c CRISPR_matching.cpp -o CRISPR_matching.o In file included from CRISPR_matching.cpp:3: In file included from ./helper/count.h:6: ./helper/fastqCheck.h:54:26: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] sequence.push_back(move(line)); ^ std:: ./helper/fastqCheck.h:55:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] sequence_ids.push_back(move(id)); ^ std:: ./helper/fastqCheck.h:56:28: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] phredScore.push_back(move(phred)); ^ std:: In file included from CRISPR_matching.cpp:3: ./helper/count.h:37:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] library.push_back(move(line)); ^ std:: ./helper/count.h:38:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] library_ids.push_back(move(id)); ^ std:: ./helper/count.h:72:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] library.push_back(move(line)); ^ std:: ./helper/count.h:73:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] library_ids.push_back(move(id)); ^ std:: 7 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include -pthread -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 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Trie_edit.cpp -o Trie_edit.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Trie_hamming.cpp -o Trie_hamming.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c Trie_util.cpp -o Trie_util.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c alignment.cpp -o alignment.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c trimRead.cpp -o trimRead.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix/include' -I/opt/R/arm64/include -pthread -fPIC -falign-functions=64 -Wall -g -O2 -c uniqueBar.cpp -o uniqueBar.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 bcSeq.so CRISPR_matching.o RcppExports.o Trie_edit.o Trie_hamming.o Trie_util.o alignment.o init.o trimRead.o uniqueBar.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/bcSeq.buildbin-libdir/00LOCK-bcSeq/00new/bcSeq/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 (bcSeq) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR bcSeq.buildbin-libdir/bcSeq/libs/bcSeq.so >>>>>>> >>>>>>> Paths before fix: bcSeq.buildbin-libdir/bcSeq/libs/bcSeq.so: bcSeq.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" "bcSeq.buildbin-libdir/bcSeq/libs/bcSeq.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "bcSeq.buildbin-libdir/bcSeq/libs/bcSeq.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "bcSeq.buildbin-libdir/bcSeq/libs/bcSeq.so" >>>>>>> Paths after fix: bcSeq.buildbin-libdir/bcSeq/libs/bcSeq.so: bcSeq.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)