##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf motifmatchr.buildbin-libdir && mkdir motifmatchr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh motifmatchr_1.10.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R motifmatchr.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=motifmatchr.buildbin-libdir motifmatchr_1.10.0.tar.gz'
>>>>>>> 

* 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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:26:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/4.0/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<MOODS::scan::Motif>::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<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >::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<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >::~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<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >::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<std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::__destroy<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::destroy<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >' 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::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::__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::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::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::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::~__vector_base' requested here
    template <class _Tp, class _Alloc> 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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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<MOODS::scan::Motif>::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<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >::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<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >::~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<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >::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<std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::__destroy<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::destroy<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >' 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::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::__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::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::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::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::~__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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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<MOODS::scan::Motif>::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<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >::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<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >::~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<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >::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<std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::__destroy<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::destroy<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >' 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::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::__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::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::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::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::~__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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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 /Users/biocbuild/bbs-3.11-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 LINKS FOR motifmatchr.buildbin-libdir/motifmatchr/libs/motifmatchr.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "motifmatchr.buildbin-libdir/motifmatchr/libs/motifmatchr.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/lib/libquadmath.0.dylib" "motifmatchr.buildbin-libdir/motifmatchr/libs/motifmatchr.so"