* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* 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-14 (Debian 14.2.0-8) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpkWCzia/R.INSTALL23ed33573737cc/bigtabulate/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DLINUX -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bigtabulate.cpp -o bigtabulate.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/shared_ptr.hpp:17,
from bigtabulate.cpp:7:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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/include/c++/14/memory:78,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/core/checked_delete.hpp: In instantiation of ‘void boost::checked_delete(T*) [with T = BreakMapper<double>]’:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = BreakMapper<double>]’
154 | boost::checked_delete( p );
| ~~~~~~~~~~~~~~~~~~~~~^~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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>]’
280 | boost::detail::shared_count( p ).swap( pn );
| ^~~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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>]’
374 | 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 );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/core/checked_delete.hpp: In instantiation of ‘void boost::checked_delete(T*) [with T = IndexMapper<double>]’:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = IndexMapper<double>]’
154 | boost::checked_delete( p );
| ~~~~~~~~~~~~~~~~~~~~~^~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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>]’
280 | boost::detail::shared_count( p ).swap( pn );
| ^~~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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>]’
374 | 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 );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/core/checked_delete.hpp: In instantiation of ‘void boost::checked_delete(T*) [with T = BreakMapper<int>]’:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = BreakMapper<int>]’
154 | boost::checked_delete( p );
| ~~~~~~~~~~~~~~~~~~~~~^~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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>]’
280 | boost::detail::shared_count( p ).swap( pn );
| ^~~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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>]’
374 | 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 );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/core/checked_delete.hpp: In instantiation of ‘void boost::checked_delete(T*) [with T = IndexMapper<int>]’:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:154:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = IndexMapper<int>]’
154 | boost::checked_delete( p );
| ~~~~~~~~~~~~~~~~~~~~~^~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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>]’
280 | boost::detail::shared_count( p ).swap( pn );
| ^~~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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>]’
374 | 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 );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DLINUX -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bigtabulate_init.c -o bigtabulate_init.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o bigtabulate.so bigtabulate.o bigtabulate_init.o -lrt -lm -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpkWCzia/R.INSTALL23ed33573737cc/bigtabulate/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpkWCzia/R.INSTALL23ed33573737cc/bigtabulate/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpkWCzia/R.INSTALL23ed33573737cc/bigtabulate/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-bigtabulate/00new/bigtabulate/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘bigtabulate’
finding HTML links ... done
bigtabulate html
** 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)