* installing *source* package ‘bigtabulate’ ... ** package ‘bigtabulate’ successfully unpacked and MD5 sums checked ** using staged installation checking for Sun Studio compiler... no checking for OS... Linux ** libs using C compiler: ‘gcc-13 (GCC) 13.2.0’ using C++ compiler: ‘g++-13 (GCC) 13.2.0’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/bigtabulate/src' g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLINUX -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -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 bigtabulate.cpp -o bigtabulate.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/shared_ptr.hpp:17, from bigtabulate.cpp:7: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( 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<typename> class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> 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<typename> class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template<typename> class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template<typename> class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template<typename> class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template<typename> class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)': /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27: /data/gannet/ripley/R/test-dev/BH/include/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = BreakMapper<double>]': /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:34: required from 'boost::detail::shared_count::shared_count(Y*) [with Y = BreakMapper<double>]' /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:280:20: required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, shared_count&) [with T = Mapper<double>; Y = BreakMapper<double>]' /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:374:44: required from 'boost::shared_ptr<T>::shared_ptr(Y*) [with Y = BreakMapper<double>; T = Mapper<double>]' bigtabulate.cpp:438:26: required from 'SEXPREC* TAPPLY(MatrixAccessorType, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) [with RType = double; MatrixAccessorType = MatrixAccessor<double>; SEXP = SEXPREC*]' bigtabulate.cpp:772:24: required from here /data/gannet/ripley/R/test-dev/BH/include/boost/core/checked_delete.hpp:44:5: warning: deleting object of polymorphic class type 'BreakMapper<double>' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 44 | delete x; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = IndexMapper<double>]': /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:34: required from 'boost::detail::shared_count::shared_count(Y*) [with Y = IndexMapper<double>]' /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:280:20: required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, shared_count&) [with T = Mapper<double>; Y = IndexMapper<double>]' /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:374:44: required from 'boost::shared_ptr<T>::shared_ptr(Y*) [with Y = IndexMapper<double>; T = Mapper<double>]' bigtabulate.cpp:445:26: required from 'SEXPREC* TAPPLY(MatrixAccessorType, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) [with RType = double; MatrixAccessorType = MatrixAccessor<double>; SEXP = SEXPREC*]' bigtabulate.cpp:772:24: required from here /data/gannet/ripley/R/test-dev/BH/include/boost/core/checked_delete.hpp:44:5: warning: deleting object of polymorphic class type 'IndexMapper<double>' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] /data/gannet/ripley/R/test-dev/BH/include/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = BreakMapper<int>]': /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:34: required from 'boost::detail::shared_count::shared_count(Y*) [with Y = BreakMapper<int>]' /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:280:20: required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, shared_count&) [with T = Mapper<int>; Y = BreakMapper<int>]' /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:374:44: required from 'boost::shared_ptr<T>::shared_ptr(Y*) [with Y = BreakMapper<int>; T = Mapper<int>]' bigtabulate.cpp:438:26: required from 'SEXPREC* TAPPLY(MatrixAccessorType, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) [with RType = int; MatrixAccessorType = MatrixAccessor<int>; SEXP = SEXPREC*]' bigtabulate.cpp:782:21: required from here /data/gannet/ripley/R/test-dev/BH/include/boost/core/checked_delete.hpp:44:5: warning: deleting object of polymorphic class type 'BreakMapper<int>' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] /data/gannet/ripley/R/test-dev/BH/include/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = IndexMapper<int>]': /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:34: required from 'boost::detail::shared_count::shared_count(Y*) [with Y = IndexMapper<int>]' /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:280:20: required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, shared_count&) [with T = Mapper<int>; Y = IndexMapper<int>]' /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:374:44: required from 'boost::shared_ptr<T>::shared_ptr(Y*) [with Y = IndexMapper<int>; T = Mapper<int>]' bigtabulate.cpp:445:26: required from 'SEXPREC* TAPPLY(MatrixAccessorType, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) [with RType = int; MatrixAccessorType = MatrixAccessor<int>; SEXP = SEXPREC*]' bigtabulate.cpp:782:21: required from here /data/gannet/ripley/R/test-dev/BH/include/boost/core/checked_delete.hpp:44:5: warning: deleting object of polymorphic class type 'IndexMapper<int>' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLINUX -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c bigtabulate_init.c -o bigtabulate_init.o g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o bigtabulate.so bigtabulate.o bigtabulate_init.o -lrt -lm make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/bigtabulate/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/bigtabulate/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/bigtabulate/src' installing to /data/gannet/ripley/R/packages/tests-devel/bigtabulate.Rcheck/00LOCK-bigtabulate/00new/bigtabulate/libs ** R ** 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 (bigtabulate)