* installing to library ‘/home/hornik/tmp/R.check/r-patched-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 13.2.0-13) 13.2.0’
using C++14
make[1]: Entering directory '/tmp/Rtmp2ckTtx/R.INSTALL2c60cc288c9027/bigMap/src'
g++-13 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include/ -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/RcppArmadillo/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 RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include/ -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/RcppArmadillo/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 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-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include/ -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/RcppArmadillo/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 wtt.cpp -o wtt.o
g++-13 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include/ -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/RcppArmadillo/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 zBeta.cpp -o zBeta.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 /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigmemory/include/bigmemory/BigMatrix.h:10,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from zBeta.cpp:16:
/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | 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++/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-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include/ -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/RcppArmadillo/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 zTSNE.cpp -o zTSNE.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 /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigmemory/include/bigmemory/BigMatrix.h:10,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from zTSNE.cpp:16:
/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++/13/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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | 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++/13/bits/unique_ptr.h:65:28: note: declared here
65 | 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++/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-patched-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-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp2ckTtx/R.INSTALL2c60cc288c9027/bigMap/src'
make[1]: Entering directory '/tmp/Rtmp2ckTtx/R.INSTALL2c60cc288c9027/bigMap/src'
make[1]: Leaving directory '/tmp/Rtmp2ckTtx/R.INSTALL2c60cc288c9027/bigMap/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-bigMap/00new/bigMap/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘bigMap’
finding HTML links ... done
bdm.boxp html
bdm.cost html
bdm.dMap html
bdm.dMap.plot html
bdm.example html
bdm.fName html
bdm.init html
bdm.labels html
bdm.local html
bdm.merge.s2nr html
bdm.mybdm html
bdm.optk.plot html
bdm.optk.s2nr html
bdm.pakde html
bdm.pakde.plot html
bdm.ptsne html
bdm.ptsne.plot html
bdm.qMap html
bdm.save html
bdm.scp html
bdm.wtt html
bdm.wtt.plot html
** 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)