* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’ * installing *source* package ‘pcalg’ ... ** package ‘pcalg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘Debian clang version 18.1.4 (1)’ using C++ compiler: ‘Debian clang version 18.1.4 (1)’ make[1]: Entering directory '/tmp/RtmpZYZhMY/R.INSTALL14d7ae1469e05f/pcalg/src' clang++-18 -std=gnu++17 -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I"../inst/include" -fpic -g -O3 -Wall -pedantic -c constraint.cpp -o constraint.o In file included from constraint.cpp:8: In file included from ../inst/include/pcalg/constraint.hpp:8: ../inst/include/pcalg/armaLapack.hpp:17:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 17 | #define NDEBUG | ^ :1:9: note: previous definition is here 1 | #define NDEBUG 1 | ^ In file included from constraint.cpp:8: In file included from ../inst/include/pcalg/constraint.hpp:10: 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; | ^ ../inst/include/pcalg/constraint.hpp:14:16: note: in instantiation of template class 'boost::graph_traits>' requested here 14 | typedef boost::graph_traits::out_edge_iterator UndirOutEdgeIter; | ^ /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"))) | ^ 2 warnings generated. clang++-18 -std=gnu++17 -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I"../inst/include" -fpic -g -O3 -Wall -pedantic -c gies.cpp -o gies.o In file included from gies.cpp:21: In file included from ../inst/include/pcalg/constraint.hpp:8: ../inst/include/pcalg/armaLapack.hpp:17:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 17 | #define NDEBUG | ^ :1:9: note: previous definition is here 1 | #define NDEBUG 1 | ^ In file included from gies.cpp:12: 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; | ^ ../inst/include/pcalg/constraint.hpp:14:16: note: in instantiation of template class 'boost::graph_traits>' requested here 14 | typedef boost::graph_traits::out_edge_iterator UndirOutEdgeIter; | ^ /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"))) | ^ 2 warnings generated. clang++-18 -std=gnu++17 -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I"../inst/include" -fpic -g -O3 -Wall -pedantic -c greedy.cpp -o greedy.o In file included from greedy.cpp:8: In file included from ../inst/include/pcalg/greedy.hpp:11: In file included from ../inst/include/pcalg/score.hpp:12: ../inst/include/pcalg/armaLapack.hpp:17:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 17 | #define NDEBUG | ^ :1:9: note: previous definition is here 1 | #define NDEBUG 1 | ^ In file included from greedy.cpp:8: In file included from ../inst/include/pcalg/greedy.hpp:18: 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; | ^ ../inst/include/pcalg/greedy.hpp:57:16: note: in instantiation of template class 'boost::graph_traits>' requested here 57 | 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"))) | ^ greedy.cpp:862:30: warning: unused variable 'vi' [-Wunused-variable] 862 | std::vector::iterator vi; | ^~ 3 warnings generated. clang-18 -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/RcppArmadillo/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 -c init.c -o init.o clang++-18 -std=gnu++17 -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I"../inst/include" -fpic -g -O3 -Wall -pedantic -c score.cpp -o score.o In file included from score.cpp:6: In file included from ../inst/include/pcalg/score.hpp:12: ../inst/include/pcalg/armaLapack.hpp:17:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 17 | #define NDEBUG | ^ :1:9: note: previous definition is here 1 | #define NDEBUG 1 | ^ In file included from score.cpp:7: In file included from ../inst/include/pcalg/greedy.hpp:18: 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; | ^ ../inst/include/pcalg/greedy.hpp:57:16: note: in instantiation of template class 'boost::graph_traits>' requested here 57 | 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"))) | ^ score.cpp:170:29: warning: unused variable 'vi' [-Wunused-variable] 170 | std::vector::iterator vi; | ^~ 3 warnings generated. clang++-18 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o pcalg.so constraint.o gies.o greedy.o init.o score.o -llapack -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lRblas -L/usr/lib/llvm-18/lib -lFortran_main -lFortranRuntime -lFortranDecimal -lm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR make[1]: Leaving directory '/tmp/RtmpZYZhMY/R.INSTALL14d7ae1469e05f/pcalg/src' make[1]: Entering directory '/tmp/RtmpZYZhMY/R.INSTALL14d7ae1469e05f/pcalg/src' make[1]: Leaving directory '/tmp/RtmpZYZhMY/R.INSTALL14d7ae1469e05f/pcalg/src' installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-pcalg/00new/pcalg/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** 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 (pcalg)