* installing *source* package ‘SimilaR’ ...
** package ‘SimilaR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CDG.cpp -o CDG.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DDG.cpp -o DDG.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PDG.cpp -o PDG.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c compare-gplag.cpp -o compare-gplag.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c generateDataFrame.cpp -o generateDataFrame.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pdgmykernelcomparator.cpp -o pdgmykernelcomparator.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c postprocessingPDG.cpp -o postprocessingPDG.o
In file included from DDG.cpp:18:
In file included from ./common.h:33:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/scoped_ptr.hpp:13:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<GraphPro>' is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<GraphPro>' requested here
property_ptr m_property;
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, Vertex, Edge, GraphPro>' requested here
typedef typename G::vertex_descriptor vertex_descriptor;
^
./common.h:89:16: note: in instantiation of template class 'boost::graph_traits<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, Vertex, Edge, GraphPro>>' requested here
typedef boost::graph_traits<GraphType>::vertex_descriptor vertex_t;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<GraphPro>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
^
In file included from CDG.cpp:18:
In file included from ./CDG.h:18:
In file included from ./common.h:33:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/scoped_ptr.hpp:13:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<GraphPro>' is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<GraphPro>' requested here
property_ptr m_property;
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, Vertex, Edge, GraphPro>' requested here
typedef typename G::vertex_descriptor vertex_descriptor;
^
./common.h:89:16: note: in instantiation of template class 'boost::graph_traits<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, Vertex, Edge, GraphPro>>' requested here
typedef boost::graph_traits<GraphType>::vertex_descriptor vertex_t;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<GraphPro>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
^
In file included from PDG.cpp:18:
In file included from ./PDG.h:18:
In file included from ./common.h:33:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/scoped_ptr.hpp:13:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<GraphPro>' is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<GraphPro>' requested here
property_ptr m_property;
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, Vertex, Edge, GraphPro>' requested here
typedef typename G::vertex_descriptor vertex_descriptor;
^
./common.h:89:16: note: in instantiation of template class 'boost::graph_traits<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, Vertex, Edge, GraphPro>>' requested here
typedef boost::graph_traits<GraphType>::vertex_descriptor vertex_t;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<GraphPro>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
^
In file included from compare-gplag.cpp:18:
In file included from ./common.h:33:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/scoped_ptr.hpp:13:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<GraphPro>' is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<GraphPro>' requested here
property_ptr m_property;
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, Vertex, Edge, GraphPro>' requested here
typedef typename G::vertex_descriptor vertex_descriptor;
^
./common.h:89:16: note: in instantiation of template class 'boost::graph_traits<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, Vertex, Edge, GraphPro>>' requested here
typedef boost::graph_traits<GraphType>::vertex_descriptor vertex_t;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<GraphPro>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
^
CDG.cpp:443:10: warning: unused variable 'ifExists' [-Wunused-variable]
bool ifExists = true;
^
CDG.cpp:818:21: warning: variable 'my_uses_index' set but not used [-Wunused-but-set-variable]
int my_uses_index = 0;
^
1 warning generated.
1 warning generated.
1 warning generated.
In file included from postprocessingPDG.cpp:18:
In file included from ./postprocessingPDG.h:19:
In file included from ./common.h:33:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/scoped_ptr.hpp:13:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<GraphPro>' is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<GraphPro>' requested here
property_ptr m_property;
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, Vertex, Edge, GraphPro>' requested here
typedef typename G::vertex_descriptor vertex_descriptor;
^
./common.h:89:16: note: in instantiation of template class 'boost::graph_traits<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, Vertex, Edge, GraphPro>>' requested here
typedef boost::graph_traits<GraphType>::vertex_descriptor vertex_t;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<GraphPro>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
^
In file included from pdgmykernelcomparator.cpp:18:
In file included from ./pdgmykernelcomparator.h:18:
In file included from ./pdgkernelcomparator.h:19:
In file included from ./pdgcomparator.h:19:
In file included from ./common.h:33:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/scoped_ptr.hpp:13:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<GraphPro>' is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<GraphPro>' requested here
property_ptr m_property;
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, Vertex, Edge, GraphPro>' requested here
typedef typename G::vertex_descriptor vertex_descriptor;
^
./common.h:89:16: note: in instantiation of template class 'boost::graph_traits<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, Vertex, Edge, GraphPro>>' requested here
typedef boost::graph_traits<GraphType>::vertex_descriptor vertex_t;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<GraphPro>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
^
pdgmykernelcomparator.cpp:382:9: warning: variable 'paired1' set but not used [-Wunused-but-set-variable]
int paired1 = 0;
^
pdgmykernelcomparator.cpp:389:9: warning: variable 'paired2' set but not used [-Wunused-but-set-variable]
int paired2 = 0;
^
pdgmykernelcomparator.cpp:520:17: warning: variable 'notReadyNeighbors' set but not used [-Wunused-but-set-variable]
int notReadyNeighbors = 0;
^
4 warnings generated.
3 warnings generated.
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o SimilaR.so CDG.o DDG.o PDG.o RcppExports.o compare-gplag.o generateDataFrame.o pdgmykernelcomparator.o postprocessingPDG.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.4/SimilaR.Rcheck/00LOCK-SimilaR/00new/SimilaR/libs
** generating debug symbols (dSYM)
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (SimilaR)