* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘simer’ ...
** this is package ‘simer’ version ‘1.0.0’
** package ‘simer’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpxHsVjI/R.INSTALL117d0e4a83b1dd/simer/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -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/RcppProgress/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 -DARMA_64BIT_WORD=1 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -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/RcppProgress/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 -DARMA_64BIT_WORD=1 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c data_converter.cpp -o data_converter.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
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 simer.h:13,
from data_converter.cpp:17:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:38,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
from simer.h:11:
/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: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;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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;
| ^~~~~~~~
/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: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 /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/arg.hpp:25,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/placeholders.hpp:24,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/iterator_range.hpp:13,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/as_literal.hpp:18,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string.hpp:19,
from data_converter.cpp:18:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp: At global scope:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 | );
| ~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 | );
| ~
| -
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 | );
| ~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/bind/mem_fn.hpp:23,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mem_fn.hpp:22,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/function/function_template.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/function.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/split.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string.hpp:23:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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)
| ^~~~~~~~
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -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/RcppProgress/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 -DARMA_64BIT_WORD=1 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c genotype.cpp -o genotype.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
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 simer.h:13,
from genotype.cpp:1:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:38,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
from simer.h:11:
/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: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;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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;
| ^~~~~~~~
/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: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;
| ^~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -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/RcppProgress/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 -DARMA_64BIT_WORD=1 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c impute.cpp -o impute.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
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 simer.h:13,
from impute.cpp:15:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:38,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
from simer.h:11:
/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: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;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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;
| ^~~~~~~~
/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: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 /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/arg.hpp:25,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/placeholders.hpp:24,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/iterator_range.hpp:13,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/range/as_literal.hpp:18,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string.hpp:19,
from impute.cpp:16:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp: At global scope:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 | );
| ~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 | );
| ~
| -
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 | );
| ~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/bind/mem_fn.hpp:23,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mem_fn.hpp:22,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/function/function_template.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/function.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string/split.hpp:16,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/algorithm/string.hpp:23:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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)
| ^~~~~~~~
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -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/RcppProgress/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 -DARMA_64BIT_WORD=1 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c pedigree.cpp -o pedigree.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
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 simer.h:13,
from pedigree.cpp:1:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:38,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
from simer.h:11:
/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: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;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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;
| ^~~~~~~~
/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: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;
| ^~~~~~~~
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o simer.so RcppExports.o data_converter.o genotype.o impute.o pedigree.o -fopenmp -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 '/home/hornik/tmp/scratch/RtmpxHsVjI/R.INSTALL117d0e4a83b1dd/simer/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpxHsVjI/R.INSTALL117d0e4a83b1dd/simer/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpxHsVjI/R.INSTALL117d0e4a83b1dd/simer/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-simer/00new/simer/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘simer’
finding HTML links ... done
GxG.network html
IndPerGen html
annotation html
bigt html
build.cov html
cal.eff html
checkEnv html
format_time html
generate.map html
generate.pop html
geno.cvt1 html
geno.cvt2 html
genotype html
getfam html
load_if_installed html
logging.initialize html
logging.log html
logging.print html
make_line html
mate.2waycro html
mate.3waycro html
mate.4waycro html
mate html
mate.assort html
mate.backcro html
mate.clone html
mate.dh html
mate.disassort html
mate.randexself html
mate.randmate html
mate.selfpol html
mate.userped html
mkl_env html
param.annot html
param.geno html
param.global html
param.pheno html
param.reprod html
param.sel html
param.simer html
paste_label html
phenotype html
pop.geno html
pop.map html
print_accomplished html
print_bar html
print_info html
remove_bigmatrix html
reproduces html
rule_wrap html
selects html
simer.Data.Bfile2MVP html
simer.Data.Env html
simer.Data.Geno html
simer.Data.Impute html
simer.Data.Json html
simer.Data.MVP2Bfile html
simer.Data.MVP2MVP html
simer.Data.Map html
simer.Data.Ped html
simer.Data.Pheno html
simer.Data html
simer.Data.SELIND html
simer.Data.cHIBLUP html
simer html
simer.Version html
write.file 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 (simer)