############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf motifmatchr.buildbin-libdir && mkdir motifmatchr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh motifmatchr_1.24.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R motifmatchr.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=motifmatchr.buildbin-libdir motifmatchr_1.24.0.tar.gz' >>>>>>> * installing *source* package ‘motifmatchr’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c r_interface.cpp -o r_interface.o In file included from r_interface.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include/RcppCommon.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/unordered_map:411: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__hash_table:15: /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2084:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor] delete __ptr; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2345:7: note: in instantiation of member function 'std::default_delete::operator()' requested here __ptr_.second()(__tmp); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2299:19: note: in instantiation of member function 'std::unique_ptr::reset' requested here ~unique_ptr() { reset(); } ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1686:92: note: in instantiation of member function 'std::unique_ptr::~unique_ptr' requested here _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1578:21: note: in instantiation of member function 'std::allocator>::destroy' requested here __a.destroy(__p); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1419:14: note: in instantiation of function template specialization 'std::allocator_traits>>::__destroy>' requested here {__destroy(__has_destroy(), __a, __p);} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:428:25: note: in instantiation of function template specialization 'std::allocator_traits>>::destroy>' requested here __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end)); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:371:29: note: in instantiation of member function 'std::__vector_base, std::allocator>>::__destruct_at_end' requested here void clear() _NOEXCEPT {__destruct_at_end(__begin_);} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:465:9: note: in instantiation of member function 'std::__vector_base, std::allocator>>::clear' requested here clear(); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:551:5: note: in instantiation of member function 'std::__vector_base, std::allocator>>::~__vector_base' requested here ~vector() ^ ./MOODS/scanner.h:31:11: note: in instantiation of member function 'std::vector>::~vector' requested here class Scanner { ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MOODS/scanner.cpp -o MOODS/scanner.o In file included from MOODS/scanner.cpp:12: /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2084:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor] delete __ptr; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2345:7: note: in instantiation of member function 'std::default_delete::operator()' requested here __ptr_.second()(__tmp); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2299:19: note: in instantiation of member function 'std::unique_ptr::reset' requested here ~unique_ptr() { reset(); } ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1686:92: note: in instantiation of member function 'std::unique_ptr::~unique_ptr' requested here _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1578:21: note: in instantiation of member function 'std::allocator>::destroy' requested here __a.destroy(__p); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1419:14: note: in instantiation of function template specialization 'std::allocator_traits>>::__destroy>' requested here {__destroy(__has_destroy(), __a, __p);} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:428:25: note: in instantiation of function template specialization 'std::allocator_traits>>::destroy>' requested here __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end)); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:371:29: note: in instantiation of member function 'std::__vector_base, std::allocator>>::__destruct_at_end' requested here void clear() _NOEXCEPT {__destruct_at_end(__begin_);} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:465:9: note: in instantiation of member function 'std::__vector_base, std::allocator>>::clear' requested here clear(); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:497:5: note: in instantiation of member function 'std::__vector_base, std::allocator>>::~__vector_base' requested here vector() _NOEXCEPT_(is_nothrow_default_constructible::value) ^ MOODS/scanner.cpp:28:14: note: in instantiation of member function 'std::vector>::vector' requested here Scanner::Scanner(unsigned int window_size){ ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MOODS/motif_h.cpp -o MOODS/motif_h.o MOODS/motif_h.cpp:256:25: warning: '&' within '^' [-Wbitwise-op-parentheses] CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]]; ~~~~~^~~~~~~~~~~~~~~~~ ~ MOODS/motif_h.cpp:256:25: note: place parentheses around the '&' expression to silence this warning CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]]; ^ ( ) 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MOODS/motif_0.cpp -o MOODS/motif_0.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MOODS/moods_tools.cpp -o MOODS/moods_tools.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MOODS/moods_scan.cpp -o MOODS/moods_scan.o MOODS/moods_scan.cpp:97:14: warning: unused variable 'done' [-Wunused-variable] bool done = 0; ^ MOODS/moods_scan.cpp:252:33: warning: '&' within '|' [-Wbitwise-op-parentheses] CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]]; ~~~~~^~~~~~~~~~~~~~~~~ ~ MOODS/moods_scan.cpp:252:33: note: place parentheses around the '&' expression to silence this warning CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]]; ^ ( ) In file included from MOODS/moods_scan.cpp:3: In file included from ./MOODS/moods.h:5: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:276: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__bit_reference:15: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/algorithm:643: /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2084:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor] delete __ptr; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2345:7: note: in instantiation of member function 'std::default_delete::operator()' requested here __ptr_.second()(__tmp); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2299:19: note: in instantiation of member function 'std::unique_ptr::reset' requested here ~unique_ptr() { reset(); } ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1686:92: note: in instantiation of member function 'std::unique_ptr::~unique_ptr' requested here _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1578:21: note: in instantiation of member function 'std::allocator>::destroy' requested here __a.destroy(__p); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1419:14: note: in instantiation of function template specialization 'std::allocator_traits>>::__destroy>' requested here {__destroy(__has_destroy(), __a, __p);} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:428:25: note: in instantiation of function template specialization 'std::allocator_traits>>::destroy>' requested here __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end)); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:371:29: note: in instantiation of member function 'std::__vector_base, std::allocator>>::__destruct_at_end' requested here void clear() _NOEXCEPT {__destruct_at_end(__begin_);} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:465:9: note: in instantiation of member function 'std::__vector_base, std::allocator>>::clear' requested here clear(); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:551:5: note: in instantiation of member function 'std::__vector_base, std::allocator>>::~__vector_base' requested here ~vector() ^ ./MOODS/scanner.h:31:11: note: in instantiation of member function 'std::vector>::~vector' requested here class Scanner { ^ 3 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MOODS/match_types.cpp -o MOODS/match_types.o clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o motifmatchr.so ./RcppExports.o ./r_interface.o ./MOODS/scanner.o ./MOODS/motif_h.o ./MOODS/motif_0.o ./MOODS/moods_tools.o ./MOODS/moods_scan.o ./MOODS/moods_parsers.o ./MOODS/moods_misc.o ./MOODS/match_types.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.18-bioc/meat/motifmatchr.buildbin-libdir/00LOCK-motifmatchr/00new/motifmatchr/libs ** R ** data ** 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 (motifmatchr) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR motifmatchr.buildbin-libdir/motifmatchr/libs/motifmatchr.so >>>>>>> >>>>>>> Paths before fix: motifmatchr.buildbin-libdir/motifmatchr/libs/motifmatchr.so: motifmatchr.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3) /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/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "motifmatchr.buildbin-libdir/motifmatchr/libs/motifmatchr.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "motifmatchr.buildbin-libdir/motifmatchr/libs/motifmatchr.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "motifmatchr.buildbin-libdir/motifmatchr/libs/motifmatchr.so" >>>>>>> Paths after fix: motifmatchr.buildbin-libdir/motifmatchr/libs/motifmatchr.so: motifmatchr.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3) /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)