* installing *source* package ‘bigtabulate’ ...
** this is package ‘bigtabulate’ version ‘1.1.9’
** 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 (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
using C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/bigtabulate/src'
g++ -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:17,
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:326:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
326 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from /usr/include/c++/14/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:23:
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
354 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
365 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
423 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
430 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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:432:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
432 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | 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:150:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = BreakMapper<double>]’
150 | boost::checked_delete( p );
| ~~~~~~~~~~~~~~~~~~~~~^~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:205:20: required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, shared_count&) [with T = Mapper<double>; Y = BreakMapper<double>]’
205 | boost::detail::shared_count( p ).swap( pn );
| ^~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:283:44: required from ‘boost::shared_ptr<T>::shared_ptr(Y*) [with Y = BreakMapper<double>; T = Mapper<double>]’
283 | boost::detail::sp_pointer_construct( this, p, pn );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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*]’
438 | mappers.push_back( MapperPtr(
| ^~~~~~~~~~
439 | new BreakMapper<RType>( breaks[i][0], breaks[i][1],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
440 | breaks[i][2], INTEGER(useNA)[0] > 0 ) ) );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigtabulate.cpp:772:24: required from here
772 | return TAPPLY<double>( MatrixAccessor<double>( REAL(numericMatrix),
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
773 | static_cast<index_type>(Rf_nrows(numericMatrix)) ),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
774 | columns, breaks, returnTable, useNA,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
775 | returnSummary, processColumns, summaryNARM, splitcol, splitlist );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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:150:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = IndexMapper<double>]’
150 | boost::checked_delete( p );
| ~~~~~~~~~~~~~~~~~~~~~^~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:205:20: required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, shared_count&) [with T = Mapper<double>; Y = IndexMapper<double>]’
205 | boost::detail::shared_count( p ).swap( pn );
| ^~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:283:44: required from ‘boost::shared_ptr<T>::shared_ptr(Y*) [with Y = IndexMapper<double>; T = Mapper<double>]’
283 | boost::detail::sp_pointer_construct( this, p, pn );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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*]’
445 | mappers.push_back( MapperPtr(
| ^~~~~~~~~~
446 | new IndexMapper<RType>( RData(vec),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
447 | RData(vec) + vecLen, INTEGER(useNA)[0] > 0 ) ) );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigtabulate.cpp:772:24: required from here
772 | return TAPPLY<double>( MatrixAccessor<double>( REAL(numericMatrix),
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
773 | static_cast<index_type>(Rf_nrows(numericMatrix)) ),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
774 | columns, breaks, returnTable, useNA,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
775 | returnSummary, processColumns, summaryNARM, splitcol, splitlist );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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]
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 = BreakMapper<int>]’:
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = BreakMapper<int>]’
150 | boost::checked_delete( p );
| ~~~~~~~~~~~~~~~~~~~~~^~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:205:20: required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, shared_count&) [with T = Mapper<int>; Y = BreakMapper<int>]’
205 | boost::detail::shared_count( p ).swap( pn );
| ^~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:283:44: required from ‘boost::shared_ptr<T>::shared_ptr(Y*) [with Y = BreakMapper<int>; T = Mapper<int>]’
283 | boost::detail::sp_pointer_construct( this, p, pn );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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*]’
438 | mappers.push_back( MapperPtr(
| ^~~~~~~~~~
439 | new BreakMapper<RType>( breaks[i][0], breaks[i][1],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
440 | breaks[i][2], INTEGER(useNA)[0] > 0 ) ) );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigtabulate.cpp:782:21: required from here
782 | return TAPPLY<int>( MatrixAccessor<int>( INTEGER(numericMatrix),
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
783 | static_cast<index_type>(Rf_nrows(numericMatrix)) ),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
784 | columns, breaks, returnTable, useNA,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
785 | returnSummary, processColumns, summaryNARM, splitcol, splitlist );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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]
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<int>]’:
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = IndexMapper<int>]’
150 | boost::checked_delete( p );
| ~~~~~~~~~~~~~~~~~~~~~^~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:205:20: required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, shared_count&) [with T = Mapper<int>; Y = IndexMapper<int>]’
205 | boost::detail::shared_count( p ).swap( pn );
| ^~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:283:44: required from ‘boost::shared_ptr<T>::shared_ptr(Y*) [with Y = IndexMapper<int>; T = Mapper<int>]’
283 | boost::detail::sp_pointer_construct( this, p, pn );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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*]’
445 | mappers.push_back( MapperPtr(
| ^~~~~~~~~~
446 | new IndexMapper<RType>( RData(vec),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
447 | RData(vec) + vecLen, INTEGER(useNA)[0] > 0 ) ) );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigtabulate.cpp:782:21: required from here
782 | return TAPPLY<int>( MatrixAccessor<int>( INTEGER(numericMatrix),
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
783 | static_cast<index_type>(Rf_nrows(numericMatrix)) ),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
784 | columns, breaks, returnTable, useNA,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
785 | returnSummary, processColumns, summaryNARM, splitcol, splitlist );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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]
44 | delete x;
| ^~~~~~~~
gcc -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++ -std=gnu++17 -shared -L/usr/local/lib64 -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)