* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’ * installing *source* package ‘SimilaR’ ... ** package ‘SimilaR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘Debian clang version 18.1.4 (1)’ using C++11 make[1]: Entering directory '/tmp/RtmpANBY4P/R.INSTALL388467116a8a02/SimilaR/src' clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:22: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/scoped_ptr.hpp:13: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^ /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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; | ^ /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/backward/auto_ptr.h:291:7: note: 'auto_ptr' has been explicitly marked deprecated here 291 | } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr"); | ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:108:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST' 108 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT) | ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:100:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST' 100 | __attribute__ ((__deprecated__ ("use '" ALT "' instead"))) | ^ 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. clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c DDG.cpp -o DDG.o In file included from DDG.cpp:18: In file included from ./common.h:33: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:22: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/scoped_ptr.hpp:13: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^ /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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; | ^ /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/backward/auto_ptr.h:291:7: note: 'auto_ptr' has been explicitly marked deprecated here 291 | } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr"); | ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:108:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST' 108 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT) | ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:100:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST' 100 | __attribute__ ((__deprecated__ ("use '" ALT "' instead"))) | ^ DDG.cpp:85:56: warning: unused variable 'e_data_end3' [-Wunused-variable] 85 | vector< edge_t>::iterator e_data3, e_data_end3; | ^~~~~~~~~~~ DDG.cpp:78:52: warning: unused variable 'e_data_end2' [-Wunused-variable] 78 | vector< edge_t>::iterator e_data2, e_data_end2; | ^~~~~~~~~~~ DDG.cpp:69:47: warning: unused variable 'e_data_end' [-Wunused-variable] 69 | vector< edge_t>::iterator e_data, e_data_end; | ^~~~~~~~~~ 4 warnings generated. clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:22: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/scoped_ptr.hpp:13: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^ /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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; | ^ /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/backward/auto_ptr.h:291:7: note: 'auto_ptr' has been explicitly marked deprecated here 291 | } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr"); | ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:108:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST' 108 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT) | ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:100:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST' 100 | __attribute__ ((__deprecated__ ("use '" ALT "' instead"))) | ^ 1 warning generated. clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c RcppExports.cpp -o RcppExports.o clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:22: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/scoped_ptr.hpp:13: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^ /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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; | ^ /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/backward/auto_ptr.h:291:7: note: 'auto_ptr' has been explicitly marked deprecated here 291 | } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr"); | ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:108:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST' 108 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT) | ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:100:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST' 100 | __attribute__ ((__deprecated__ ("use '" ALT "' instead"))) | ^ 1 warning generated. clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c generateDataFrame.cpp -o generateDataFrame.o clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:22: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/scoped_ptr.hpp:13: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^ /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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; | ^ /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/backward/auto_ptr.h:291:7: note: 'auto_ptr' has been explicitly marked deprecated here 291 | } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr"); | ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:108:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST' 108 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT) | ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:100:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST' 100 | __attribute__ ((__deprecated__ ("use '" ALT "' instead"))) | ^ 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. clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -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 /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:22: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/scoped_ptr.hpp:13: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 75 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^ /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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; | ^ /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/backward/auto_ptr.h:291:7: note: 'auto_ptr' has been explicitly marked deprecated here 291 | } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr"); | ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:108:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST' 108 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT) | ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:100:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST' 100 | __attribute__ ((__deprecated__ ("use '" ALT "' instead"))) | ^ 1 warning generated. clang++-18 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o SimilaR.so CDG.o DDG.o PDG.o RcppExports.o compare-gplag.o generateDataFrame.o pdgmykernelcomparator.o postprocessingPDG.o -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR make[1]: Leaving directory '/tmp/RtmpANBY4P/R.INSTALL388467116a8a02/SimilaR/src' make[1]: Entering directory '/tmp/RtmpANBY4P/R.INSTALL388467116a8a02/SimilaR/src' make[1]: Leaving directory '/tmp/RtmpANBY4P/R.INSTALL388467116a8a02/SimilaR/src' installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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 * creating tarball packaged installation of ‘SimilaR’ as ‘SimilaR_1.0.8_R_x86_64-pc-linux-gnu.tar.gz’ * DONE (SimilaR)