* installing *source* package 'simer' ...
** this is package 'simer' version '0.9.0.6'
** package 'simer' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 13.3.0'
make[1]: Entering directory '/d/temp/2025_02_03_01_50_00_1639/RtmpEDZPxW/R.INSTALL805815724b41/simer/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/BH/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigmemory/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DARMA_64BIT_WORD=1 -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/BH/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigmemory/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DARMA_64BIT_WORD=1 -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c data_converter.cpp -o data_converter.o
In file included from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/shared_ptr.hpp:17,
from D:/RCompile/CRANpkg/lib/4.5/bigmemory/include/bigmemory/BigMatrix.h:10,
from simer.h:13,
from data_converter.cpp:17:
D:/RCompile/CRANpkg/lib/4.5/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 d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\memory:78,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/armadillo:38,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from simer.h:11:
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/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()
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/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()
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/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 )
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/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 )
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/RCompile/CRANpkg/lib/4.5/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 );
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mpl/arg.hpp:25,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mpl/placeholders.hpp:24,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/iterator/iterator_categories.hpp:16,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/iterator/iterator_facade.hpp:13,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/range/iterator_range_core.hpp:27,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/range/iterator_range.hpp:13,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/range/as_literal.hpp:18,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/algorithm/string/trim.hpp:19,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/algorithm/string.hpp:19,
from data_converter.cpp:18:
D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mpl/assert.hpp: At global scope:
D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
In file included from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/bind/mem_fn.hpp:23,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mem_fn.hpp:22,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/function/function_template.hpp:16,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/function.hpp:16,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/algorithm/string/iter_find.hpp:27,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/algorithm/string/split.hpp:16,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/algorithm/string.hpp:23:
D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/BH/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigmemory/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DARMA_64BIT_WORD=1 -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c genotype.cpp -o genotype.o
In file included from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/shared_ptr.hpp:17,
from D:/RCompile/CRANpkg/lib/4.5/bigmemory/include/bigmemory/BigMatrix.h:10,
from simer.h:13,
from genotype.cpp:1:
D:/RCompile/CRANpkg/lib/4.5/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 d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\memory:78,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/armadillo:38,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from simer.h:11:
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/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()
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/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()
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/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 )
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/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 )
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/RCompile/CRANpkg/lib/4.5/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 );
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/BH/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigmemory/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DARMA_64BIT_WORD=1 -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c impute.cpp -o impute.o
In file included from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/shared_ptr.hpp:17,
from D:/RCompile/CRANpkg/lib/4.5/bigmemory/include/bigmemory/BigMatrix.h:10,
from simer.h:13,
from impute.cpp:15:
D:/RCompile/CRANpkg/lib/4.5/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 d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\memory:78,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/armadillo:38,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from simer.h:11:
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/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()
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/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()
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/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 )
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/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 )
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/RCompile/CRANpkg/lib/4.5/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 );
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mpl/arg.hpp:25,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mpl/placeholders.hpp:24,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/iterator/iterator_categories.hpp:16,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/iterator/iterator_facade.hpp:13,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/range/iterator_range_core.hpp:27,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/range/iterator_range.hpp:13,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/range/as_literal.hpp:18,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/algorithm/string/trim.hpp:19,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/algorithm/string.hpp:19,
from impute.cpp:16:
D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mpl/assert.hpp: At global scope:
D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
In file included from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/bind/mem_fn.hpp:23,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/mem_fn.hpp:22,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/function/function_template.hpp:16,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/function.hpp:16,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/algorithm/string/iter_find.hpp:27,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/algorithm/string/split.hpp:16,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/algorithm/string.hpp:23:
D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/BH/include' -I'D:/RCompile/CRANpkg/lib/4.5/bigmemory/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -DARMA_64BIT_WORD=1 -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -c pedigree.cpp -o pedigree.o
In file included from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/shared_ptr.hpp:17,
from D:/RCompile/CRANpkg/lib/4.5/bigmemory/include/bigmemory/BigMatrix.h:10,
from simer.h:13,
from pedigree.cpp:1:
D:/RCompile/CRANpkg/lib/4.5/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 d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\memory:78,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/armadillo:38,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from simer.h:11:
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/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()
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/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()
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/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 )
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/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 )
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/RCompile/CRANpkg/lib/4.5/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 );
| ^~~~~~~~
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o simer.dll tmp.def RcppExports.o data_converter.o genotype.o impute.o pedigree.o -fopenmp -LD:/RCompile/recent/R/bin/x64 -lRlapack -LD:/RCompile/recent/R/bin/x64 -lRblas -lgfortran -lquadmath -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2025_02_03_01_50_00_1639/RtmpEDZPxW/R.INSTALL805815724b41/simer/src'
make[1]: Entering directory '/d/temp/2025_02_03_01_50_00_1639/RtmpEDZPxW/R.INSTALL805815724b41/simer/src'
make[1]: Leaving directory '/d/temp/2025_02_03_01_50_00_1639/RtmpEDZPxW/R.INSTALL805815724b41/simer/src'
installing to d:/Rcompile/CRANpkg/lib/4.5/00LOCK-simer/00new/simer/libs/x64
** R
** data
** inst
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'simer' as simer_0.9.0.6.zip
* DONE (simer)