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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/mosbi_1.0.3.tar.gz && rm -rf mosbi.buildbin-libdir && mkdir mosbi.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mosbi.buildbin-libdir mosbi_1.0.3.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL mosbi_1.0.3.zip && rm mosbi_1.0.3.tar.gz mosbi_1.0.3.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
99 76804 99 76740 0 0 345k 0 --:--:-- --:--:-- --:--:-- 345k
100 76804 100 76804 0 0 148k 0 --:--:-- --:--:-- --:--:-- 148k
install for i386
* installing *source* package 'mosbi' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c attr_graph.cpp -o attr_graph.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c attributeConnector.cpp -o attributeConnector.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c attribute_overlap.cpp -o attribute_overlap.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bicluster_methods.cpp -o bicluster_methods.o
bicluster_methods.cpp: In function 'bool validate_bicluster(Rcpp::S4, unsigned int, unsigned int)':
bicluster_methods.cpp:40:16: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'int'} and 'unsigned int' [-Wsign-compare]
if(r.length()<minRow){
~~~~~~~~~~^~~~~~~
bicluster_methods.cpp:44:16: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'int'} and 'unsigned int' [-Wsign-compare]
if(c.length()<minCol){
~~~~~~~~~~^~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_graph.cpp -o boost_graph.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:24,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> & r )
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> && r )
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/function_template.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/maybe_include.hpp:36,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/function3.hpp:11,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/dynamic_property_map.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graphviz.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graphml.hpp:20,
from boost_graph.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_write.cpp -o boost_write.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:24,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> & r )
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> && r )
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/function_template.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/maybe_include.hpp:36,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/function3.hpp:11,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/dynamic_property_map.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graphviz.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graphml.hpp:20,
from boost_write.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c distance_matrix.cpp -o distance_matrix.o
distance_matrix.cpp: In member function 'virtual void SimWorker::operator()(std::size_t, std::size_t)':
distance_matrix.cpp:244:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'unsigned int'} [-Wsign-compare]
for(int i=begin;i<end;i++){
~^~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include/RcppParallel/TinyThread.h:7,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include/RcppParallel.h:6,
from distance_matrix.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include/RcppParallel/Common.h: In instantiation of 'int RcppParallel::resolveValue(const char*, T, U) [with T = unsigned int; U = int]':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include/RcppParallel.h:57:28: required from 'void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = SimWorker; std::size_t = unsigned int]'
distance_matrix.cpp:278:43: required from here
C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
if (requestedValue != defaultValue && requestedValue > 0)
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c extractBF.cpp -o extractBF.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from extractBF.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function.hpp:30,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from extractBF.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
from extractBF.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
extractBF.cpp: In function 'Rcpp::S4 getBFCluster(Rcpp::String, int)':
extractBF.cpp:92:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
for(int i=0; i<results.size();i++){
~^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c extractQUBIC2.cpp -o extractQUBIC2.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from extractQUBIC2.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function.hpp:30,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from extractQUBIC2.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
from extractQUBIC2.cpp:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c full_graph.cpp -o full_graph.o
full_graph.cpp: In function 'Rcpp::NumericMatrix full_graph(Rcpp::List, Rcpp::NumericMatrix, double, double, double, int)':
full_graph.cpp:50:25: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for(unsigned int i=0;i<bics.length();++i){ // Loop over biclusters
~^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c misc.cpp -o misc.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c network_edge_strength.cpp -o network_edge_strength.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sample_biclusters.cpp -o sample_biclusters.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c write_matrix.cpp -o write_matrix.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o mosbi.dll tmp.def RcppExports.o attr_graph.o attributeConnector.o attribute_overlap.o bicluster_methods.o boost_graph.o boost_write.o distance_matrix.o extractBF.o extractQUBIC2.o full_graph.o misc.o network_edge_strength.o sample_biclusters.o write_matrix.o -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/mosbi.buildbin-libdir/00LOCK-mosbi/00new/mosbi/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'mosbi'
finding HTML links ... done
NoBFBiclusters html
algohistogram html
apply_threshold-bicluster_net-method html
apply_threshold-cooccurrence_net-method
html
apply_threshold html
attr_overlap html
attributeConnector html
attribute_graph html
bicluster-class html
bicluster_heatmap-bicluster-matrix-method
html
bicluster_heatmap html
bicluster_net-class html
bicluster_net_to_igraph-bicluster_net-method
html
bicluster_net_to_igraph html
bicluster_network html
bicluster_to_matrix-matrix-bicluster-method
html
bicluster_to_matrix html
check_names html
clean_bicluster_list html
colhistogram html
cooccurrence_net-class html
cooccurrence_net_to_igraph-cooccurrence_net-method
html
cooccurrence_net_to_igraph html
cpp_matrix_subsetting html
detect_elements html
dim-bicluster-method html
distance_matrix html
ensemble_biclusters html
feature_louvain_overlap html
feature_network html
filter_bicluster_size html
filter_biclusters html
filter_matrix html
filter_subsets html
full_graph html
getAkmbiclustClusters html
getBFCluster html
getBicAREbiclusters html
getBiclustClusters html
getBiclustpyClusters html
getFabiaClusters html
getIsaClusters html
getQUBIC2biclusters html
get_adjacency-bicluster_net-method html
get_adjacency html
get_algorithms html
get_bic_net_algorithms-bicluster_net-method
html
get_bic_net_algorithms html
get_biclusters html
get_louvain_communities-bicluster_net-method
html
get_louvain_communities-cooccurrence_net-method
html
get_louvain_communities html
getallBFClusters html
has_names html
is_subset_or_identical html
network_edge_strength html
network_edge_strength_float html
node_size html
occurance_matrix html
occurance_table html
p_overlap html
p_overlap_2d html
p_overlap_2d_higher html
p_overlap_higher html
plot-bicluster_net-missing-method html
plot-cooccurrence_net-missing-method html
plot_algo_network html
plot_piechart_bicluster_network html
randomize_matrix html
replace_threshold html
replace_values html
replace_values_float html
rowhistogram html
run_akmbiclust html
run_bimax html
run_cc html
run_fabia html
run_isa html
run_plaid html
run_qubic html
run_quest html
run_spectral html
run_unibic html
run_xmotifs html
sample_biclusters html
select_biclusters_from_bicluster_network-bicluster_net-list-method
html
select_biclusters_from_bicluster_network
html
set_bicluster_names-bicluster-matrix-method
html
set_bicluster_names html
similarity_matrix html
transpose_bicluster html
validate_bicluster html
write_graphml html
write_matrix html
zero_subsetting html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'mosbi' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c attr_graph.cpp -o attr_graph.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c attributeConnector.cpp -o attributeConnector.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c attribute_overlap.cpp -o attribute_overlap.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bicluster_methods.cpp -o bicluster_methods.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_graph.cpp -o boost_graph.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:24,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> & r )
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> && r )
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/function_template.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/maybe_include.hpp:36,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/function3.hpp:11,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/dynamic_property_map.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graphviz.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graphml.hpp:20,
from boost_graph.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_write.cpp -o boost_write.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:24,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> & r )
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> && r )
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/function_template.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/maybe_include.hpp:36,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/function3.hpp:11,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/dynamic_property_map.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graphviz.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graphml.hpp:20,
from boost_write.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c distance_matrix.cpp -o distance_matrix.o
distance_matrix.cpp: In member function 'virtual void SimWorker::operator()(std::size_t, std::size_t)':
distance_matrix.cpp:244:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i=begin;i<end;i++){
~^~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include/RcppParallel/TinyThread.h:7,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include/RcppParallel.h:6,
from distance_matrix.cpp:2:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include/RcppParallel/Common.h: In instantiation of 'int RcppParallel::resolveValue(const char*, T, U) [with T = long long unsigned int; U = int]':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include/RcppParallel.h:57:28: required from 'void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = SimWorker; std::size_t = long long unsigned int]'
distance_matrix.cpp:278:43: required from here
C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: 'long long unsigned int' and 'int' [-Wsign-compare]
if (requestedValue != defaultValue && requestedValue > 0)
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c extractBF.cpp -o extractBF.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from extractBF.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function.hpp:30,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from extractBF.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
from extractBF.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
extractBF.cpp: In function 'Rcpp::S4 getBFCluster(Rcpp::String, int)':
extractBF.cpp:92:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i=0; i<results.size();i++){
~^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c extractQUBIC2.cpp -o extractQUBIC2.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from extractQUBIC2.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function.hpp:30,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from extractQUBIC2.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27,
from extractQUBIC2.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c full_graph.cpp -o full_graph.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c misc.cpp -o misc.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c network_edge_strength.cpp -o network_edge_strength.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sample_biclusters.cpp -o sample_biclusters.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c write_matrix.cpp -o write_matrix.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o mosbi.dll tmp.def RcppExports.o attr_graph.o attributeConnector.o attribute_overlap.o bicluster_methods.o boost_graph.o boost_write.o distance_matrix.o extractBF.o extractQUBIC2.o full_graph.o misc.o network_edge_strength.o sample_biclusters.o write_matrix.o -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/mosbi.buildbin-libdir/mosbi/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mosbi' as mosbi_1.0.3.zip
* DONE (mosbi)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'mosbi' successfully unpacked and MD5 sums checked
