############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL motifmatchr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘motifmatchr’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -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/4.1/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/RcppCommon.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp/r/headers.h:62: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153: In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/unordered_map:384: In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/__hash_table:16: /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2335:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor] delete __ptr; ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2648:7: note: in instantiation of member function 'std::__1::default_delete::operator()' requested here __ptr_.second()(__tmp); ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2602:19: note: in instantiation of member function 'std::__1::unique_ptr >::reset' requested here ~unique_ptr() { reset(); } ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1880:64: note: in instantiation of member function 'std::__1::unique_ptr >::~unique_ptr' requested here _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();} ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1742:18: note: in instantiation of member function 'std::__1::allocator > >::destroy' requested here {__a.destroy(__p);} ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1595:14: note: in instantiation of function template specialization 'std::__1::allocator_traits > > >::__destroy > >' requested here {__destroy(__has_destroy(), __a, __p);} ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits > > >::destroy > >' requested here __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end)); ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base >, std::__1::allocator > > >::__destruct_at_end' requested here void clear() _NOEXCEPT {__destruct_at_end(__begin_);} ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base >, std::__1::allocator > > >::clear' requested here clear(); ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base >, std::__1::allocator > > >::~__vector_base' requested here template friend class _LIBCPP_TEMPLATE_VIS vector; ^ 1 warning generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c MOODS/scanner.cpp -o MOODS/scanner.o In file included from MOODS/scanner.cpp:12: /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2335:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor] delete __ptr; ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2648:7: note: in instantiation of member function 'std::__1::default_delete::operator()' requested here __ptr_.second()(__tmp); ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2602:19: note: in instantiation of member function 'std::__1::unique_ptr >::reset' requested here ~unique_ptr() { reset(); } ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1880:64: note: in instantiation of member function 'std::__1::unique_ptr >::~unique_ptr' requested here _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();} ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1742:18: note: in instantiation of member function 'std::__1::allocator > >::destroy' requested here {__a.destroy(__p);} ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1595:14: note: in instantiation of function template specialization 'std::__1::allocator_traits > > >::__destroy > >' requested here {__destroy(__has_destroy(), __a, __p);} ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits > > >::destroy > >' requested here __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end)); ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base >, std::__1::allocator > > >::__destruct_at_end' requested here void clear() _NOEXCEPT {__destruct_at_end(__begin_);} ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base >, std::__1::allocator > > >::clear' requested here clear(); ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/vector:464:28: note: in instantiation of member function 'std::__1::__vector_base >, std::__1::allocator > > >::~__vector_base' requested here class _LIBCPP_TEMPLATE_VIS vector ^ 1 warning generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c MOODS/motif_0.cpp -o MOODS/motif_0.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c MOODS/moods_tools.cpp -o MOODS/moods_tools.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -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/usr/include/c++/v1/vector:270: In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/__bit_reference:15: In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/algorithm:644: /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2335:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor] delete __ptr; ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2648:7: note: in instantiation of member function 'std::__1::default_delete::operator()' requested here __ptr_.second()(__tmp); ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2602:19: note: in instantiation of member function 'std::__1::unique_ptr >::reset' requested here ~unique_ptr() { reset(); } ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1880:64: note: in instantiation of member function 'std::__1::unique_ptr >::~unique_ptr' requested here _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();} ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1742:18: note: in instantiation of member function 'std::__1::allocator > >::destroy' requested here {__a.destroy(__p);} ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1595:14: note: in instantiation of function template specialization 'std::__1::allocator_traits > > >::__destroy > >' requested here {__destroy(__has_destroy(), __a, __p);} ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits > > >::destroy > >' requested here __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end)); ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base >, std::__1::allocator > > >::__destruct_at_end' requested here void clear() _NOEXCEPT {__destruct_at_end(__begin_);} ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base >, std::__1::allocator > > >::clear' requested here clear(); ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/vector:464:28: note: in instantiation of member function 'std::__1::__vector_base >, std::__1::allocator > > >::~__vector_base' requested here class _LIBCPP_TEMPLATE_VIS vector ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c MOODS/match_types.cpp -o MOODS/match_types.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/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)