Package: flowWorkspace

Version: 3.34.1

Command: rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowWorkspace_3.34.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R flowWorkspace.buildbin-libdir

StartedAt: 2020-04-15 07:30:07 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 07:33:52 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 225.6 seconds

RetCode: 0

Status:  OK

PackageFile: flowWorkspace_3.34.1.tgz

PackageFileSize: 9.941 MiB

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###
### Running command:
###
###   rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowWorkspace_3.34.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R flowWorkspace.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flowWorkspace.buildbin-libdir flowWorkspace_3.34.1.tar.gz'
>>>>>>> 

* installing *source* package ‘flowWorkspace’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c R_API.cpp -o R_API.o
In file included from R_API.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/gate.hpp:14:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
                        EVENT_DATA_TYPE thisMin=0;//input.min();
                                        ^
In file included from R_API.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/iostream:38:
In file included from /usr/local/clang7/include/c++/v1/ios:216:
In file included from /usr/local/clang7/include/c++/v1/__locale:15:
In file included from /usr/local/clang7/include/c++/v1/string:500:
In file included from /usr/local/clang7/include/c++/v1/string_view:176:
In file included from /usr/local/clang7/include/c++/v1/__string:56:
In file included from /usr/local/clang7/include/c++/v1/algorithm:644:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'trans_global' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<trans_global>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::__destroy<trans_global>' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::destroy<trans_global>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
                        ^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::clear' requested here
        clear();
        ^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::~__vector_base' requested here
    template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
                                                                         ^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                               ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from R_GatingHierarchy.cpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/gate.hpp:14:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
                        EVENT_DATA_TYPE thisMin=0;//input.min();
                                        ^
In file included from R_GatingHierarchy.cpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/iostream:38:
In file included from /usr/local/clang7/include/c++/v1/ios:216:
In file included from /usr/local/clang7/include/c++/v1/__locale:15:
In file included from /usr/local/clang7/include/c++/v1/string:500:
In file included from /usr/local/clang7/include/c++/v1/string_view:176:
In file included from /usr/local/clang7/include/c++/v1/__string:56:
In file included from /usr/local/clang7/include/c++/v1/algorithm:644:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'trans_global' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<trans_global>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::__destroy<trans_global>' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::destroy<trans_global>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
                        ^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::clear' requested here
        clear();
        ^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::~__vector_base' requested here
    template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
                                                                         ^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                               ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c R_GatingSet.cpp -o R_GatingSet.o
In file included from R_GatingSet.cpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/gate.hpp:14:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
                        EVENT_DATA_TYPE thisMin=0;//input.min();
                                        ^
In file included from R_GatingSet.cpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/iostream:38:
In file included from /usr/local/clang7/include/c++/v1/ios:216:
In file included from /usr/local/clang7/include/c++/v1/__locale:15:
In file included from /usr/local/clang7/include/c++/v1/string:500:
In file included from /usr/local/clang7/include/c++/v1/string_view:176:
In file included from /usr/local/clang7/include/c++/v1/__string:56:
In file included from /usr/local/clang7/include/c++/v1/algorithm:644:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'trans_global' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<trans_global>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::__destroy<trans_global>' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::destroy<trans_global>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
                        ^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::clear' requested here
        clear();
        ^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::~__vector_base' requested here
    template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
                                                                         ^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                               ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/flowWorkspace.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/gate.hpp:14:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
                        EVENT_DATA_TYPE thisMin=0;//input.min();
                                        ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/flowWorkspace.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/iostream:38:
In file included from /usr/local/clang7/include/c++/v1/ios:216:
In file included from /usr/local/clang7/include/c++/v1/__locale:15:
In file included from /usr/local/clang7/include/c++/v1/string:500:
In file included from /usr/local/clang7/include/c++/v1/string_view:176:
In file included from /usr/local/clang7/include/c++/v1/__string:56:
In file included from /usr/local/clang7/include/c++/v1/algorithm:644:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'trans_global' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<trans_global>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::__destroy<trans_global>' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::destroy<trans_global>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
                        ^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::clear' requested here
        clear();
        ^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::~__vector_base' requested here
    template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
                                                                         ^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                               ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c getDescendants.cpp -o getDescendants.o
In file included from getDescendants.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/gate.hpp:14:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
                        EVENT_DATA_TYPE thisMin=0;//input.min();
                                        ^
In file included from getDescendants.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/iostream:38:
In file included from /usr/local/clang7/include/c++/v1/ios:216:
In file included from /usr/local/clang7/include/c++/v1/__locale:15:
In file included from /usr/local/clang7/include/c++/v1/string:500:
In file included from /usr/local/clang7/include/c++/v1/string_view:176:
In file included from /usr/local/clang7/include/c++/v1/__string:56:
In file included from /usr/local/clang7/include/c++/v1/algorithm:644:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'trans_global' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<trans_global>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::__destroy<trans_global>' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::destroy<trans_global>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
                        ^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::clear' requested here
        clear();
        ^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::~__vector_base' requested here
    template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
                                                                         ^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                               ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c getPopStats.cpp -o getPopStats.o
In file included from getPopStats.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/gate.hpp:14:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
                        EVENT_DATA_TYPE thisMin=0;//input.min();
                                        ^
In file included from getPopStats.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/iostream:38:
In file included from /usr/local/clang7/include/c++/v1/ios:216:
In file included from /usr/local/clang7/include/c++/v1/__locale:15:
In file included from /usr/local/clang7/include/c++/v1/string:500:
In file included from /usr/local/clang7/include/c++/v1/string_view:176:
In file included from /usr/local/clang7/include/c++/v1/__string:56:
In file included from /usr/local/clang7/include/c++/v1/algorithm:644:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'trans_global' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<trans_global>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::__destroy<trans_global>' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::destroy<trans_global>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
                        ^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::clear' requested here
        clear();
        ^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::~__vector_base' requested here
    template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
                                                                         ^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                               ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from getSingleCellExpression.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/gate.hpp:14:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
                        EVENT_DATA_TYPE thisMin=0;//input.min();
                                        ^
In file included from getSingleCellExpression.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/iostream:38:
In file included from /usr/local/clang7/include/c++/v1/ios:216:
In file included from /usr/local/clang7/include/c++/v1/__locale:15:
In file included from /usr/local/clang7/include/c++/v1/string:500:
In file included from /usr/local/clang7/include/c++/v1/string_view:176:
In file included from /usr/local/clang7/include/c++/v1/__string:56:
In file included from /usr/local/clang7/include/c++/v1/algorithm:644:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'trans_global' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<trans_global>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::__destroy<trans_global>' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::destroy<trans_global>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
                        ^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::clear' requested here
        clear();
        ^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::~__vector_base' requested here
    template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
                                                                         ^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                               ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c setCounts.cpp -o setCounts.o
In file included from setCounts.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/gate.hpp:14:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
                        EVENT_DATA_TYPE thisMin=0;//input.min();
                                        ^
In file included from setCounts.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/iostream:38:
In file included from /usr/local/clang7/include/c++/v1/ios:216:
In file included from /usr/local/clang7/include/c++/v1/__locale:15:
In file included from /usr/local/clang7/include/c++/v1/string:500:
In file included from /usr/local/clang7/include/c++/v1/string_view:176:
In file included from /usr/local/clang7/include/c++/v1/__string:56:
In file included from /usr/local/clang7/include/c++/v1/algorithm:644:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'trans_global' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<trans_global>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::__destroy<trans_global>' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::destroy<trans_global>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
                        ^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::clear' requested here
        clear();
        ^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::~__vector_base' requested here
    template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
                                                                         ^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                               ^
2 warnings generated.
mkdir -p "/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib"
ar rs "/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o
ar: creating archive /Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/libflowWorkspace.a
clang++ -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 flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/lib/GatingSet.pb.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/lib/libprotobuf.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowWorkspace.so; fi
installing to /Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/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 (flowWorkspace)


>>>>>>> 
>>>>>>> FIXING LINKS FOR flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"