* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘bigMap’ ...
** package ‘bigMap’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
using C++14
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpeITH4h/R.INSTALL1533d0672c401d/bigMap/src'
g++-13 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tsne.cpp -o tsne.o
tsne.cpp: In member function ‘void TSNE::D2P(double*, int, double*, double*)’:
tsne.cpp:270:29: warning: unused variable ‘ij’ [-Wunused-variable]
270 | int ij = tIdx(n, i, j);
| ^~
g++-13 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c wtt.cpp -o wtt.o
g++-13 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c zBeta.cpp -o zBeta.o
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/shared_ptr.hpp:17,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include/bigmemory/BigMatrix.h:10,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from zBeta.cpp:16:
/home/hornik/tmp/R.check/r-devel-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++/13/memory:78,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-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-devel-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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
g++-13 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c zTSNE.cpp -o zTSNE.o
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/shared_ptr.hpp:17,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include/bigmemory/BigMatrix.h:10,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from zTSNE.cpp:16:
/home/hornik/tmp/R.check/r-devel-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++/13/memory:78,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-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-devel-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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
zTSNE.cpp: In function ‘void zChnks(Rcpp::List&, const arma::Mat<double>&, const arma::Col<int>&, const Rcpp::List&)’:
zTSNE.cpp:168:55: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
168 | for (size_t i = brks(l, 0); i < brks(l, 1); i++) {
| ~~^~~~~~~~~~~~
g++-13 -std=gnu++14 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o bigMap.so RcppExports.o tsne.o wtt.o zBeta.o zTSNE.o -llapack -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpeITH4h/R.INSTALL1533d0672c401d/bigMap/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpeITH4h/R.INSTALL1533d0672c401d/bigMap/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpeITH4h/R.INSTALL1533d0672c401d/bigMap/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-bigMap/00new/bigMap/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (bigMap)