* installing *source* package ‘SimilaR’ ... ** package ‘SimilaR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘clang version 18.1.4’ 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 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' is deprecated [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr 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' 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' requested here 61 | typedef typename G::vertex_descriptor vertex_descriptor; | ^ ./common.h:89:16: note: in instantiation of template class 'boost::graph_traits>' requested here 89 | typedef boost::graph_traits::vertex_descriptor vertex_t; | ^ /usr/local/clang18/bin/../include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr' 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; | ^ 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 DDG.cpp -o DDG.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 PDG.cpp -o PDG.o 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' is deprecated [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr 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' 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' requested here 61 | typedef typename G::vertex_descriptor vertex_descriptor; | ^ ./common.h:89:16: note: in instantiation of template class 'boost::graph_traits>' requested here 89 | typedef boost::graph_traits::vertex_descriptor vertex_t; | ^ /usr/local/clang18/bin/../include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr' 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__)) | ^ 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' is deprecated [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr 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' 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' requested here 61 | typedef typename G::vertex_descriptor vertex_descriptor; | ^ ./common.h:89:16: note: in instantiation of template class 'boost::graph_traits>' requested here 89 | typedef boost::graph_traits::vertex_descriptor vertex_t; | ^ /usr/local/clang18/bin/../include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr' 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 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 /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' is deprecated [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr 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' 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' requested here 61 | typedef typename G::vertex_descriptor vertex_descriptor; | ^ ./common.h:89:16: note: in instantiation of template class 'boost::graph_traits>' requested here 89 | typedef boost::graph_traits::vertex_descriptor vertex_t; | ^ /usr/local/clang18/bin/../include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr' 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' is deprecated [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr 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' 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' requested here 61 | typedef typename G::vertex_descriptor vertex_descriptor; | ^ ./common.h:89:16: note: in instantiation of template class 'boost::graph_traits>' requested here 89 | typedef boost::graph_traits::vertex_descriptor vertex_t; | ^ /usr/local/clang18/bin/../include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr' 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; | ^ 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' is deprecated [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr 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' 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' requested here 61 | typedef typename G::vertex_descriptor vertex_descriptor; | ^ ./common.h:89:16: note: in instantiation of template class 'boost::graph_traits>' requested here 89 | typedef boost::graph_traits::vertex_descriptor vertex_t; | ^ /usr/local/clang18/bin/../include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr' 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__)) | ^ 4 warnings generated. 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)