* installing *source* package ‘LOMAR’ ... ** package ‘LOMAR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-13 (GCC) 13.2.0’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/LOMAR/src' g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DBOOST_DISABLE_THREADS -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DBOOST_DISABLE_THREADS -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c diag.cpp -o diag.o In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /data/gannet/ripley/R/test-dev/BH/include/boost/property_map/vector_property_map.hpp:14, from /data/gannet/ripley/R/test-dev/BH/include/boost/property_map/property_map.hpp:598, from ./utilities/property-maps.h:6, from ./topology/complex-traits.h:6, from ./topology/filtration.h:7, from ./tdautils/ripsL2.h:6, from diag.cpp:9: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/local/gcc13/include/c++/13.2.0/memory:78, from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:27: /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/bind/mem_fn.hpp:25, from /data/gannet/ripley/R/test-dev/BH/include/boost/bind/bind.hpp:26, from /data/gannet/ripley/R/test-dev/BH/include/boost/multi_index/detail/ord_index_impl.hpp:82, from /data/gannet/ripley/R/test-dev/BH/include/boost/multi_index/ordered_index.hpp:17, from ./topology/filtration.h:14: /data/gannet/ripley/R/test-dev/BH/include/boost/get_pointer.hpp: At global scope: /data/gannet/ripley/R/test-dev/BH/include/boost/get_pointer.hpp:48:40: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 48 | template T * get_pointer(std::auto_ptr const& p) | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from ./topology/dynamic-persistence.h:332, from ./tdautils/ripsL2.h:8: ./topology/dynamic-persistence.hpp: In member function 'bool DynamicPersistenceTrails::transpose(iterator, const DimensionFunctor&, Visitor)': ./topology/dynamic-persistence.hpp:60:73: warning: typedef 'TrailIterator' locally defined but not used [-Wunused-local-typedefs] 60 | typedef typename Element::Trail::iterator TrailIterator; | ^~~~~~~~~~~~~ In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/scoped_ptr.hpp:13, from /data/gannet/ripley/R/test-dev/BH/include/boost/graph/adjacency_list.hpp:22, from ./topology/persistence-diagram.hpp:143, from ./topology/persistence-diagram.h:176, from ./tdautils/ripsL2.h:9: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'template class std::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() ) | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from diag.cpp:26: ./kde.h: In instantiation of 'RealVector kde(const RealMatrix&, const RealMatrix&, unsigned int, unsigned int, unsigned int, double, const std::string&, const RealVector&, bool, const Print&) [with RealVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; RealMatrix = Rcpp::Matrix<14>; Print = void(const char*, ...); std::string = std::__cxx11::basic_string]': diag.cpp:166:13: required from here ./kde.h:21:16: warning: unused variable 'pi' [-Wunused-variable] 21 | const double pi = 3.141592653589793; | ^~ In file included from diag.cpp:13: ./tdautils/gridUtils.h: In instantiation of 'void addOddTets(int, int, int, int, int, VectorList&) [with VectorList = std::vector >]': ./tdautils/gridUtils.h:315:14: required from 'void addAllTetrahedra(int, int, int, int, int, VectorList&) [with VectorList = std::vector >]' ./tdautils/gridUtils.h:363:20: required from 'void simplicesFromGrid(const DimensionVector&, int, VectorList&) [with DimensionVector = Rcpp::Vector<13>; VectorList = std::vector >]' ./grid.h:90:22: required from 'void gridFiltration(const RealVector&, const DimensionVector&, int, const std::string&, bool, const Print&, std::vector&, std::vector&) [with RealVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; DimensionVector = Rcpp::Vector<13>; Print = void(const char*, ...); VertexVector = std::vector; std::string = std::__cxx11::basic_string]' diag.cpp:68:17: required from here ./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. | ^~~~~~ g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o LOMAR.so RcppExports.o diag.o -lgmp make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/LOMAR/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/LOMAR/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/LOMAR/src' installing to /data/gannet/ripley/R/packages/tests-devel/LOMAR.Rcheck/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)