* installing *source* package ‘SimilaR’ ... ** package ‘SimilaR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘Apple clang version 13.0.0 (clang-1300.0.29.30)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CDG.cpp -o CDG.o 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-arm64/Rlib/4.3/BH/include/boost/graph/adjacency_list.hpp:22: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/scoped_ptr.hpp:13: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^ /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr' requested here property_ptr m_property; ^ /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list' requested here typedef typename G::vertex_descriptor vertex_descriptor; ^ ./common.h:89:16: note: in instantiation of template class 'boost::graph_traits>' requested here typedef boost::graph_traits::vertex_descriptor vertex_t; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' 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; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DDG.cpp -o DDG.o In file included from DDG.cpp:18: In file included from ./common.h:33: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/graph/adjacency_list.hpp:22: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/scoped_ptr.hpp:13: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^ /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr' requested here property_ptr m_property; ^ /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list' requested here typedef typename G::vertex_descriptor vertex_descriptor; ^ ./common.h:89:16: note: in instantiation of template class 'boost::graph_traits>' requested here typedef boost::graph_traits::vertex_descriptor vertex_t; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' 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)) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PDG.cpp -o PDG.o 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-arm64/Rlib/4.3/BH/include/boost/graph/adjacency_list.hpp:22: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/scoped_ptr.hpp:13: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^ /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr' requested here property_ptr m_property; ^ /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list' requested here typedef typename G::vertex_descriptor vertex_descriptor; ^ ./common.h:89:16: note: in instantiation of template class 'boost::graph_traits>' requested here typedef boost::graph_traits::vertex_descriptor vertex_t; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' 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)) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c compare-gplag.cpp -o compare-gplag.o In file included from compare-gplag.cpp:18: In file included from ./common.h:33: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/graph/adjacency_list.hpp:22: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/scoped_ptr.hpp:13: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^ /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr' requested here property_ptr m_property; ^ /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list' requested here typedef typename G::vertex_descriptor vertex_descriptor; ^ ./common.h:89:16: note: in instantiation of template class 'boost::graph_traits>' requested here typedef boost::graph_traits::vertex_descriptor vertex_t; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' 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)) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c generateDataFrame.cpp -o generateDataFrame.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pdgmykernelcomparator.cpp -o pdgmykernelcomparator.o 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-arm64/Rlib/4.3/BH/include/boost/graph/adjacency_list.hpp:22: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/scoped_ptr.hpp:13: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^ /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr' requested here property_ptr m_property; ^ /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list' requested here typedef typename G::vertex_descriptor vertex_descriptor; ^ ./common.h:89:16: note: in instantiation of template class 'boost::graph_traits>' requested here typedef boost::graph_traits::vertex_descriptor vertex_t; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' 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)) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c postprocessingPDG.cpp -o postprocessingPDG.o 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-arm64/Rlib/4.3/BH/include/boost/graph/adjacency_list.hpp:22: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/scoped_ptr.hpp:13: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^ /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr' requested here property_ptr m_property; ^ /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list' requested here typedef typename G::vertex_descriptor vertex_descriptor; ^ ./common.h:89:16: note: in instantiation of template class 'boost::graph_traits>' requested here typedef boost::graph_traits::vertex_descriptor vertex_t; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' 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)) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-arm64/results/4.3/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)