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###
### Running command:
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### rm -rf epialleleR.buildbin-libdir && mkdir epialleleR.buildbin-libdir && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL --build --library=epialleleR.buildbin-libdir epialleleR_1.7.0.tar.gz
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* installing *source* package 'epialleleR' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++17
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_cx_report.cpp -o rcpp_cx_report.o
rcpp_cx_report.cpp:182:1: warning: multi-line comment [-Wcomment]
182 | // #define spit_results { \
| ^
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:32,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_cx_report.cpp:3:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of 'typename boost::container::dtl::enable_if_memtransfer_copy_assignable<I, F, F>::type boost::container::move_backward(I, I, F) [with I = dtl::pair<long long unsigned int, std::array<int, 16> >*; F = dtl::pair<long long unsigned int, std::array<int, 16> >*; typename dtl::enable_if_memtransfer_copy_assignable<I, F, F>::type = dtl::pair<long long unsigned int, std::array<int, 16> >*]':
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:2983:41: required from 'void boost::container::vector<T, Allocator, Options>::priv_insert_forward_range_expand_forward(T*, size_type, InsertionProxy, boost::move_detail::true_type) [with InsertionProxy = boost::container::dtl::insert_emplace_proxy<boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, boost::container::try_emplace_t, const long long unsigned int&, std::array<int, 16>&>; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; size_type = long long unsigned int; boost::move_detail::true_type = boost::move_detail::integral_constant<bool, true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:2827:13: required from 'boost::container::vector<T, Allocator, Options>::iterator boost::container::vector<T, Allocator, Options>::priv_insert_forward_range(const pointer&, size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_emplace_proxy<boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, boost::container::try_emplace_t, const long long unsigned int&, std::array<int, 16>&>; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, false>; pointer = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:1865:45: required from 'boost::container::vector<T, Allocator, Options>::iterator boost::container::vector<T, Allocator, Options>::emplace(const_iterator, Args&& ...) [with Args = {boost::container::try_emplace_t, const long long unsigned int&, std::array<int, 16>&}; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, false>; const_iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1020:48: required from 'std::pair<typename boost::container::dtl::select_container_type<Value, AllocatorOrContainer>::type::iterator, bool> boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::try_emplace(const_iterator, KeyType&&, Args&& ...) [with KeyType = const long long unsigned int&; Args = {std::array<int, 16>&}; Value = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; KeyOfValue = boost::container::dtl::select1st<long long unsigned int>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; typename boost::container::dtl::select_container_type<Value, AllocatorOrContainer>::type::iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, false>; typename boost::container::dtl::select_container_type<Value, AllocatorOrContainer>::type = boost::container::vector<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >, boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, void>; const_iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/flat_map.hpp:968:10: required from 'boost::container::flat_map<Key, T, Compare, Allocator>::iterator boost::container::flat_map<Key, T, Compare, Allocator>::try_emplace(const_iterator, const key_type&, Args&& ...) [with Args = {std::array<int, 16>&}; Key = long long unsigned int; T = std::array<int, 16>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = void; iterator = boost::container::vec_iterator<std::pair<long long unsigned int, std::array<int, 16> >*, false>; const_iterator = boost::container::vec_iterator<std::pair<long long unsigned int, std::array<int, 16> >*, true>; key_type = long long unsigned int]'
rcpp_cx_report.cpp:133:32: required from here
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:912:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
912 | std::memmove((boost::movelib::iterator_to_raw_pointer)(r), (boost::movelib::iterator_to_raw_pointer)(f), sizeof(value_type)*n);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} declared here
218 | struct pair
| ^~~~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of 'F boost::container::dtl::memmove(I, I, F) [with I = pair<long long unsigned int, std::array<int, 16> >*; F = pair<long long unsigned int, std::array<int, 16> >*]':
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:325:23: required from 'typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, F>::type boost::container::uninitialized_move_alloc(Allocator&, I, I, F) [with Allocator = new_allocator<dtl::pair<long long unsigned int, std::array<int, 16> > >; I = dtl::pair<long long unsigned int, std::array<int, 16> >*; F = dtl::pair<long long unsigned int, std::array<int, 16> >*; typename dtl::enable_if_memtransfer_copy_constructible<I, F, F>::type = dtl::pair<long long unsigned int, std::array<int, 16> >*]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:1205:59: required from 'void boost::container::uninitialized_move_and_insert_alloc(Allocator&, F, F, F, O, std::size_t, InsertionProxy) [with Allocator = new_allocator<dtl::pair<long long unsigned int, std::array<int, 16> > >; F = dtl::pair<long long unsigned int, std::array<int, 16> >*; O = dtl::pair<long long unsigned int, std::array<int, 16> >*; InsertionProxy = dtl::insert_range_proxy<new_allocator<dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::move_iterator<dtl::pair<long long unsigned int, std::array<int, 16> >*>, dtl::pair<long long unsigned int, std::array<int, 16> >*>; std::size_t = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:3008:10: required from 'void boost::container::vector<T, Allocator, Options>::priv_insert_forward_range_new_allocation(T*, size_type, T*, size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_range_proxy<boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:2611:10: required from 'void boost::container::vector<T, Allocator, Options>::priv_move_to_new_buffer(size_type, boost::container::version_1) [with T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; size_type = long long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:1570:39: required from 'void boost::container::vector<T, Allocator, Options>::reserve(size_type) [with T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:380:16: required from 'void boost::container::dtl::flat_tree_reserve(SequenceContainer&, typename SequenceContainer::size_type, boost::move_detail::true_) [with SequenceContainer = boost::container::vector<pair<long long unsigned int, std::array<int, 16> >, boost::container::new_allocator<pair<long long unsigned int, std::array<int, 16> > >, void>; typename SequenceContainer::size_type = long long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1393:26: required from 'void boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::reserve(size_type) [with Value = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; KeyOfValue = boost::container::dtl::select1st<long long unsigned int>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/flat_map.hpp:712:28: required from 'void boost::container::flat_map<Key, T, Compare, Allocator>::reserve(size_type) [with Key = long long unsigned int; T = std::array<int, 16>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = void; size_type = long long unsigned int]'
rcpp_cx_report.cpp:114:17: required from here
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:184:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
184 | std::memmove(dest_raw, beg_raw, sizeof(value_type)*n);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'value_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} declared here
218 | struct pair
| ^~~~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of 'I boost::container::dtl::memmove_n_source(I, std::size_t, F) [with I = boost::move_iterator<pair<long long unsigned int, std::array<int, 16> >*>; F = pair<long long unsigned int, std::array<int, 16> >*; std::size_t = long long unsigned int]':
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:553:32: required from 'typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, I>::type boost::container::uninitialized_copy_alloc_n_source(Allocator&, I, std::size_t, F) [with Allocator = new_allocator<dtl::pair<long long unsigned int, std::array<int, 16> > >; I = boost::move_iterator<dtl::pair<long long unsigned int, std::array<int, 16> >*>; F = dtl::pair<long long unsigned int, std::array<int, 16> >*; typename dtl::enable_if_memtransfer_copy_constructible<I, F, I>::type = boost::move_iterator<dtl::pair<long long unsigned int, std::array<int, 16> >*>; std::size_t = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:81:75: required from 'void boost::container::dtl::insert_range_proxy<Allocator, FwdIt, Iterator>::uninitialized_copy_n_and_update(Allocator&, Iterator, std::size_t) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; FwdIt = boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; Iterator = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; std::size_t = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:1208:54: required from 'void boost::container::uninitialized_move_and_insert_alloc(Allocator&, F, F, F, O, std::size_t, InsertionProxy) [with Allocator = new_allocator<dtl::pair<long long unsigned int, std::array<int, 16> > >; F = dtl::pair<long long unsigned int, std::array<int, 16> >*; O = dtl::pair<long long unsigned int, std::array<int, 16> >*; InsertionProxy = dtl::insert_range_proxy<new_allocator<dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::move_iterator<dtl::pair<long long unsigned int, std::array<int, 16> >*>, dtl::pair<long long unsigned int, std::array<int, 16> >*>; std::size_t = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:3008:10: required from 'void boost::container::vector<T, Allocator, Options>::priv_insert_forward_range_new_allocation(T*, size_type, T*, size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_range_proxy<boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:2611:10: required from 'void boost::container::vector<T, Allocator, Options>::priv_move_to_new_buffer(size_type, boost::container::version_1) [with T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; size_type = long long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:1570:39: required from 'void boost::container::vector<T, Allocator, Options>::reserve(size_type) [with T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:380:16: required from 'void boost::container::dtl::flat_tree_reserve(SequenceContainer&, typename SequenceContainer::size_type, boost::move_detail::true_) [with SequenceContainer = boost::container::vector<pair<long long unsigned int, std::array<int, 16> >, boost::container::new_allocator<pair<long long unsigned int, std::array<int, 16> > >, void>; typename SequenceContainer::size_type = long long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1393:26: required from 'void boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::reserve(size_type) [with Value = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; KeyOfValue = boost::container::dtl::select1st<long long unsigned int>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/flat_map.hpp:712:28: required from 'void boost::container::flat_map<Key, T, Compare, Allocator>::reserve(size_type) [with Key = long long unsigned int; T = std::array<int, 16>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = void; size_type = long long unsigned int]'
rcpp_cx_report.cpp:114:17: required from here
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:214:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
214 | std::memmove(boost::movelib::iterator_to_raw_pointer(r), boost::movelib::iterator_to_raw_pointer(f), sizeof(value_type)*n);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} declared here
218 | struct pair
| ^~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_extract_patterns.cpp -o rcpp_extract_patterns.o
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:32,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_extract_patterns.cpp:2:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of 'typename boost::container::dtl::enable_if_memtransfer_copy_assignable<I, F, F>::type boost::container::move_backward(I, I, F) [with I = dtl::pair<int, int>*; F = dtl::pair<int, int>*; typename dtl::enable_if_memtransfer_copy_assignable<I, F, F>::type = dtl::pair<int, int>*]':
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:2983:41: required from 'void boost::container::vector<T, Allocator, Options>::priv_insert_forward_range_expand_forward(T*, size_type, InsertionProxy, boost::move_detail::true_type) [with InsertionProxy = boost::container::dtl::insert_emplace_proxy<boost::container::new_allocator<boost::container::dtl::pair<int, int> >, boost::container::dtl::pair<int, int>*, boost::container::try_emplace_t, int, int>; T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; size_type = long long unsigned int; boost::move_detail::true_type = boost::move_detail::integral_constant<bool, true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:2827:13: required from 'boost::container::vector<T, Allocator, Options>::iterator boost::container::vector<T, Allocator, Options>::priv_insert_forward_range(const pointer&, size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_emplace_proxy<boost::container::new_allocator<boost::container::dtl::pair<int, int> >, boost::container::dtl::pair<int, int>*, boost::container::try_emplace_t, int, int>; T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; iterator = boost::container::vec_iterator<boost::container::dtl::pair<int, int>*, false>; pointer = boost::container::dtl::pair<int, int>*; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:1865:45: required from 'boost::container::vector<T, Allocator, Options>::iterator boost::container::vector<T, Allocator, Options>::emplace(const_iterator, Args&& ...) [with Args = {boost::container::try_emplace_t, int, int}; T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; iterator = boost::container::vec_iterator<boost::container::dtl::pair<int, int>*, false>; const_iterator = boost::container::vec_iterator<boost::container::dtl::pair<int, int>*, true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1020:48: required from 'std::pair<typename boost::container::dtl::select_container_type<Value, AllocatorOrContainer>::type::iterator, bool> boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::try_emplace(const_iterator, KeyType&&, Args&& ...) [with KeyType = int; Args = {int}; Value = boost::container::dtl::pair<int, int>; KeyOfValue = boost::container::dtl::select1st<int>; Compare = std::less<int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; typename boost::container::dtl::select_container_type<Value, AllocatorOrContainer>::type::iterator = boost::container::vec_iterator<boost::container::dtl::pair<int, int>*, false>; typename boost::container::dtl::select_container_type<Value, AllocatorOrContainer>::type = boost::container::vector<boost::container::dtl::pair<int, int>, boost::container::new_allocator<boost::container::dtl::pair<int, int> >, void>; const_iterator = boost::container::vec_iterator<boost::container::dtl::pair<int, int>*, true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/flat_map.hpp:1004:34: required from 'boost::container::flat_map<Key, T, Compare, Allocator>::iterator boost::container::flat_map<Key, T, Compare, Allocator>::try_emplace(const_iterator, key_type&&, Args&& ...) [with Args = {int}; Key = int; T = int; Compare = std::less<int>; AllocatorOrContainer = void; iterator = boost::container::vec_iterator<std::pair<int, int>*, false>; const_iterator = boost::container::vec_iterator<std::pair<int, int>*, true>; key_type = int]'
rcpp_extract_patterns.cpp:103:43: required from here
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:912:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
912 | std::memmove((boost::movelib::iterator_to_raw_pointer)(r), (boost::movelib::iterator_to_raw_pointer)(f), sizeof(value_type)*n);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} declared here
218 | struct pair
| ^~~~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of 'F boost::container::dtl::memmove(I, I, F) [with I = pair<int, int>*; F = pair<int, int>*]':
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:325:23: required from 'typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, F>::type boost::container::uninitialized_move_alloc(Allocator&, I, I, F) [with Allocator = new_allocator<dtl::pair<int, int> >; I = dtl::pair<int, int>*; F = dtl::pair<int, int>*; typename dtl::enable_if_memtransfer_copy_constructible<I, F, F>::type = dtl::pair<int, int>*]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:1205:59: required from 'void boost::container::uninitialized_move_and_insert_alloc(Allocator&, F, F, F, O, std::size_t, InsertionProxy) [with Allocator = new_allocator<dtl::pair<int, int> >; F = dtl::pair<int, int>*; O = dtl::pair<int, int>*; InsertionProxy = dtl::insert_range_proxy<new_allocator<dtl::pair<int, int> >, boost::move_iterator<dtl::pair<int, int>*>, dtl::pair<int, int>*>; std::size_t = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:3008:10: required from 'void boost::container::vector<T, Allocator, Options>::priv_insert_forward_range_new_allocation(T*, size_type, T*, size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_range_proxy<boost::container::new_allocator<boost::container::dtl::pair<int, int> >, boost::move_iterator<boost::container::dtl::pair<int, int>*>, boost::container::dtl::pair<int, int>*>; T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:2611:10: required from 'void boost::container::vector<T, Allocator, Options>::priv_move_to_new_buffer(size_type, boost::container::version_1) [with T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; size_type = long long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:1570:39: required from 'void boost::container::vector<T, Allocator, Options>::reserve(size_type) [with T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:380:16: required from 'void boost::container::dtl::flat_tree_reserve(SequenceContainer&, typename SequenceContainer::size_type, boost::move_detail::true_) [with SequenceContainer = boost::container::vector<pair<int, int>, boost::container::new_allocator<pair<int, int> >, void>; typename SequenceContainer::size_type = long long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1393:26: required from 'void boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::reserve(size_type) [with Value = boost::container::dtl::pair<int, int>; KeyOfValue = boost::container::dtl::select1st<int>; Compare = std::less<int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/flat_map.hpp:712:28: required from 'void boost::container::flat_map<Key, T, Compare, Allocator>::reserve(size_type) [with Key = int; T = int; Compare = std::less<int>; AllocatorOrContainer = void; size_type = long long unsigned int]'
rcpp_extract_patterns.cpp:68:18: required from here
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:184:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
184 | std::memmove(dest_raw, beg_raw, sizeof(value_type)*n);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'value_type' {aka 'struct boost::container::dtl::pair<int, int>'} declared here
218 | struct pair
| ^~~~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of 'I boost::container::dtl::memmove_n_source(I, std::size_t, F) [with I = boost::move_iterator<pair<int, int>*>; F = pair<int, int>*; std::size_t = long long unsigned int]':
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:553:32: required from 'typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, I>::type boost::container::uninitialized_copy_alloc_n_source(Allocator&, I, std::size_t, F) [with Allocator = new_allocator<dtl::pair<int, int> >; I = boost::move_iterator<dtl::pair<int, int>*>; F = dtl::pair<int, int>*; typename dtl::enable_if_memtransfer_copy_constructible<I, F, I>::type = boost::move_iterator<dtl::pair<int, int>*>; std::size_t = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:81:75: required from 'void boost::container::dtl::insert_range_proxy<Allocator, FwdIt, Iterator>::uninitialized_copy_n_and_update(Allocator&, Iterator, std::size_t) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; FwdIt = boost::move_iterator<boost::container::dtl::pair<int, int>*>; Iterator = boost::container::dtl::pair<int, int>*; std::size_t = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:1208:54: required from 'void boost::container::uninitialized_move_and_insert_alloc(Allocator&, F, F, F, O, std::size_t, InsertionProxy) [with Allocator = new_allocator<dtl::pair<int, int> >; F = dtl::pair<int, int>*; O = dtl::pair<int, int>*; InsertionProxy = dtl::insert_range_proxy<new_allocator<dtl::pair<int, int> >, boost::move_iterator<dtl::pair<int, int>*>, dtl::pair<int, int>*>; std::size_t = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:3008:10: required from 'void boost::container::vector<T, Allocator, Options>::priv_insert_forward_range_new_allocation(T*, size_type, T*, size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_range_proxy<boost::container::new_allocator<boost::container::dtl::pair<int, int> >, boost::move_iterator<boost::container::dtl::pair<int, int>*>, boost::container::dtl::pair<int, int>*>; T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:2611:10: required from 'void boost::container::vector<T, Allocator, Options>::priv_move_to_new_buffer(size_type, boost::container::version_1) [with T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; size_type = long long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:1570:39: required from 'void boost::container::vector<T, Allocator, Options>::reserve(size_type) [with T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:380:16: required from 'void boost::container::dtl::flat_tree_reserve(SequenceContainer&, typename SequenceContainer::size_type, boost::move_detail::true_) [with SequenceContainer = boost::container::vector<pair<int, int>, boost::container::new_allocator<pair<int, int> >, void>; typename SequenceContainer::size_type = long long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1393:26: required from 'void boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::reserve(size_type) [with Value = boost::container::dtl::pair<int, int>; KeyOfValue = boost::container::dtl::select1st<int>; Compare = std::less<int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/flat_map.hpp:712:28: required from 'void boost::container::flat_map<Key, T, Compare, Allocator>::reserve(size_type) [with Key = int; T = int; Compare = std::less<int>; AllocatorOrContainer = void; size_type = long long unsigned int]'
rcpp_extract_patterns.cpp:68:18: required from here
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:214:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
214 | std::memmove(boost::movelib::iterator_to_raw_pointer(r), boost::movelib::iterator_to_raw_pointer(f), sizeof(value_type)*n);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} declared here
218 | struct pair
| ^~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_fep.cpp -o rcpp_fep.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_get_base_freqs.cpp -o rcpp_get_base_freqs.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_get_xm_beta.cpp -o rcpp_get_xm_beta.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_match_target.cpp -o rcpp_match_target.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_read_bam.cpp -o rcpp_read_bam.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_threshold_reads.cpp -o rcpp_threshold_reads.o
g++ -shared -s -static-libgcc -o epialleleR.dll tmp.def RcppExports.o rcpp_cx_report.o rcpp_extract_patterns.o rcpp_fep.o rcpp_get_base_freqs.o rcpp_get_xm_beta.o rcpp_match_target.o rcpp_read_bam.o rcpp_threshold_reads.o F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc-rtools43/meat/epialleleR.buildbin-libdir/00LOCK-epialleleR/00new/epialleleR/libs/x64
** 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
** 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 'epialleleR' as epialleleR_1.7.0.zip
* DONE (epialleleR)