Install log for 'SimilaR'

* 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<GraphPro>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> 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<GraphPro>' 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<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;
         ^
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<GraphPro>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> 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<GraphPro>' 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<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))
                                               ^
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<GraphPro>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> 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<GraphPro>' 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<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))
                                               ^
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<GraphPro>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> 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<GraphPro>' 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<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))
                                               ^
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<GraphPro>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> 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<GraphPro>' 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<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))
                                               ^
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<GraphPro>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> 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<GraphPro>' 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<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))
                                               ^
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)