* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’ * installing *source* package ‘LOMAR’ ... ** package ‘LOMAR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘Debian clang version 18.1.4 (1)’ make[1]: Entering directory '/tmp/RtmpBzFSdr/R.INSTALL1ac4581982de62/LOMAR/src' clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DBOOST_DISABLE_THREADS -fpic -g -O3 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DBOOST_DISABLE_THREADS -fpic -g -O3 -Wall -pedantic -c diag.cpp -o diag.o In file included from diag.cpp:9: In file included from ./tdautils/ripsL2.h:5: In file included from ./topology/rips.h:6: In file included from ./topology/simplex.h:221: ./topology/simplex.hpp:12:1: warning: 'BoundaryIterator' defined as a struct here but previously declared as a class; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 12 | struct Simplex::BoundaryIterator: public boost::iterator_adaptor::ComparePair: | ^ ./topology/rips.h:34:9: note: did you mean struct here? 34 | class ComparePair; | ^~~~~ | struct In file included from diag.cpp:9: In file included from ./tdautils/ripsL2.h:9: In file included from ./topology/persistence-diagram.h:176: In file included from ./topology/persistence-diagram.hpp:143: 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; | ^ ./topology/persistence-diagram.hpp:163:40: note: in instantiation of template class 'boost::graph_traits>' requested here 163 | typedef std::vector::vertex_descriptor> MatchingVector; | ^ /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"))) | ^ In file included from diag.cpp:9: In file included from ./tdautils/ripsL2.h:9: In file included from ./topology/persistence-diagram.h:176: In file included from ./topology/persistence-diagram.hpp:143: 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/archive/detail/basic_oarchive.hpp:49:44: note: in instantiation of template class 'boost::scoped_ptr' requested here 49 | boost::scoped_ptr pimpl; | ^ /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"))) | ^ In file included from diag.cpp:9: In file included from ./tdautils/ripsL2.h:9: In file included from ./topology/persistence-diagram.h:176: In file included from ./topology/persistence-diagram.hpp:143: 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/archive/detail/basic_iarchive.hpp:51:44: note: in instantiation of template class 'boost::scoped_ptr' requested here 51 | boost::scoped_ptr pimpl; | ^ /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"))) | ^ In file included from diag.cpp:13: ./tdautils/gridUtils.h:183:13: warning: unused variable 'value' [-Wunused-variable] 183 | double value, value2; // max of value and value 2 is the fcn value. | ^~~~~ ./tdautils/gridUtils.h:183:20: warning: unused variable 'value2' [-Wunused-variable] 183 | double value, value2; // max of value and value 2 is the fcn value. | ^~~~~~ In file included from diag.cpp:26: ./kde.h:21:16: warning: unused variable 'pi' [-Wunused-variable] 21 | const double pi = 3.141592653589793; | ^~ In file included from diag.cpp:9: In file included from ./tdautils/ripsL2.h:8: In file included from ./topology/dynamic-persistence.h:332: ./topology/dynamic-persistence.hpp:60:73: warning: unused typedef 'TrailIterator' [-Wunused-local-typedef] 60 | typedef typename Element::Trail::iterator TrailIterator; | ^ 9 warnings generated. clang++-18 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o LOMAR.so RcppExports.o diag.o -lgmp -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR make[1]: Leaving directory '/tmp/RtmpBzFSdr/R.INSTALL1ac4581982de62/LOMAR/src' make[1]: Entering directory '/tmp/RtmpBzFSdr/R.INSTALL1ac4581982de62/LOMAR/src' make[1]: Leaving directory '/tmp/RtmpBzFSdr/R.INSTALL1ac4581982de62/LOMAR/src' installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-LOMAR/00new/LOMAR/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 (LOMAR)