* installing *source* package ‘SimilaR’ ...
** package ‘SimilaR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 18.1.2’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/SimilaR/src'
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c CDG.cpp -o CDG.o
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c DDG.cpp -o DDG.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 /data/gannet/ripley/R/test-clang/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/scoped_ptr.hpp:13:
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<GraphPro>' is deprecated [-Wdeprecated-declarations]
75 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<GraphPro>' requested here
408 | property_ptr m_property;
| ^
/data/gannet/ripley/R/test-clang/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
61 | 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
89 | typedef boost::graph_traits<GraphType>::vertex_descriptor vertex_t;
| ^
/usr/local/clang18/bin/../include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr<GraphPro>' has been explicitly marked deprecated here
29 | class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr {
| ^
/usr/local/clang18/bin/../include/c++/v1/__config:989:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
989 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
| ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
974 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
CDG.cpp:443:10: warning: unused variable 'ifExists' [-Wunused-variable]
443 | bool ifExists = true;
| ^~~~~~~~
CDG.cpp:818:21: warning: variable 'my_uses_index' set but not used [-Wunused-but-set-variable]
818 | int my_uses_index = 0;
| ^
In file included from DDG.cpp:18:
In file included from ./common.h:33:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/scoped_ptr.hpp:13:
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<GraphPro>' is deprecated [-Wdeprecated-declarations]
75 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<GraphPro>' requested here
408 | property_ptr m_property;
| ^
/data/gannet/ripley/R/test-clang/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
61 | 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
89 | typedef boost::graph_traits<GraphType>::vertex_descriptor vertex_t;
| ^
/usr/local/clang18/bin/../include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr<GraphPro>' has been explicitly marked deprecated here
29 | class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr {
| ^
/usr/local/clang18/bin/../include/c++/v1/__config:989:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
989 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
| ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
974 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
3 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c PDG.cpp -o PDG.o
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o
1 warning generated.
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c compare-gplag.cpp -o compare-gplag.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 /data/gannet/ripley/R/test-clang/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/scoped_ptr.hpp:13:
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<GraphPro>' is deprecated [-Wdeprecated-declarations]
75 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<GraphPro>' requested here
408 | property_ptr m_property;
| ^
/data/gannet/ripley/R/test-clang/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
61 | 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
89 | typedef boost::graph_traits<GraphType>::vertex_descriptor vertex_t;
| ^
/usr/local/clang18/bin/../include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr<GraphPro>' has been explicitly marked deprecated here
29 | class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr {
| ^
/usr/local/clang18/bin/../include/c++/v1/__config:989:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
989 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
| ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
974 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
1 warning generated.
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c generateDataFrame.cpp -o generateDataFrame.o
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c pdgmykernelcomparator.cpp -o pdgmykernelcomparator.o
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c postprocessingPDG.cpp -o postprocessingPDG.o
In file included from compare-gplag.cpp:18:
In file included from ./common.h:33:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/scoped_ptr.hpp:13:
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<GraphPro>' is deprecated [-Wdeprecated-declarations]
75 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<GraphPro>' requested here
408 | property_ptr m_property;
| ^
/data/gannet/ripley/R/test-clang/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
61 | 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
89 | typedef boost::graph_traits<GraphType>::vertex_descriptor vertex_t;
| ^
/usr/local/clang18/bin/../include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr<GraphPro>' has been explicitly marked deprecated here
29 | class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr {
| ^
/usr/local/clang18/bin/../include/c++/v1/__config:989:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
989 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
| ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
974 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
1 warning generated.
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 /data/gannet/ripley/R/test-clang/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/scoped_ptr.hpp:13:
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<GraphPro>' is deprecated [-Wdeprecated-declarations]
75 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<GraphPro>' requested here
408 | property_ptr m_property;
| ^
/data/gannet/ripley/R/test-clang/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
61 | 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
89 | typedef boost::graph_traits<GraphType>::vertex_descriptor vertex_t;
| ^
/usr/local/clang18/bin/../include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr<GraphPro>' has been explicitly marked deprecated here
29 | class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr {
| ^
/usr/local/clang18/bin/../include/c++/v1/__config:989:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
989 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
| ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
974 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
pdgmykernelcomparator.cpp:382:9: warning: variable 'paired1' set but not used [-Wunused-but-set-variable]
382 | int paired1 = 0;
| ^
pdgmykernelcomparator.cpp:389:9: warning: variable 'paired2' set but not used [-Wunused-but-set-variable]
389 | int paired2 = 0;
| ^
pdgmykernelcomparator.cpp:520:17: warning: variable 'notReadyNeighbors' set but not used [-Wunused-but-set-variable]
520 | int notReadyNeighbors = 0;
| ^
4 warnings 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 /data/gannet/ripley/R/test-clang/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/scoped_ptr.hpp:13:
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<GraphPro>' is deprecated [-Wdeprecated-declarations]
75 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<GraphPro>' requested here
408 | property_ptr m_property;
| ^
/data/gannet/ripley/R/test-clang/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
61 | 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
89 | typedef boost::graph_traits<GraphType>::vertex_descriptor vertex_t;
| ^
/usr/local/clang18/bin/../include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr<GraphPro>' has been explicitly marked deprecated here
29 | class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr {
| ^
/usr/local/clang18/bin/../include/c++/v1/__config:989:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
989 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
| ^
/usr/local/clang18/bin/../include/c++/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED'
974 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
1 warning generated.
/usr/local/clang18/bin/clang++ -std=gnu++11 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o SimilaR.so CDG.o DDG.o PDG.o RcppExports.o compare-gplag.o generateDataFrame.o pdgmykernelcomparator.o postprocessingPDG.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/SimilaR/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/SimilaR/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/SimilaR/src'
installing to /data/gannet/ripley/R/packages/tests-clang/SimilaR.Rcheck/00LOCK-SimilaR/00new/SimilaR/libs
** 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)