############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL epialleleR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'epialleleR' ... ** using staged installation ** libs g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-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-3.15-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:32, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:29, from rcpp_cx_report.cpp:3: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of 'typename boost::container::dtl::enable_if_memtransfer_copy_assignable::type boost::container::move_backward(I, I, F) [with I = boost::container::dtl::pair >*; F = boost::container::dtl::pair >*; typename boost::container::dtl::enable_if_memtransfer_copy_assignable::type = boost::container::dtl::pair >*]': F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:2983:41: required from 'void boost::container::vector::priv_insert_forward_range_expand_forward(T*, boost::container::vector::size_type, InsertionProxy, boost::move_detail::true_type) [with InsertionProxy = boost::container::dtl::insert_emplace_proxy > >, boost::container::dtl::pair >*, boost::container::try_emplace_t, const long long unsigned int&, std::array&>; T = boost::container::dtl::pair >; A = boost::container::new_allocator > >; Options = void; boost::container::vector::size_type = long long unsigned int; boost::move_detail::true_type = boost::move_detail::integral_constant]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:2827:13: required from 'boost::container::vector::iterator boost::container::vector::priv_insert_forward_range(const pointer&, boost::container::vector::size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_emplace_proxy > >, boost::container::dtl::pair >*, boost::container::try_emplace_t, const long long unsigned int&, std::array&>; T = boost::container::dtl::pair >; A = boost::container::new_allocator > >; Options = void; boost::container::vector::iterator = boost::container::vec_iterator >*, false>; boost::container::vector::pointer = boost::container::dtl::pair >*; boost::container::vector::size_type = long long unsigned int]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:1865:45: required from 'boost::container::vector::iterator boost::container::vector::emplace(boost::container::vector::const_iterator, Args&& ...) [with Args = {boost::container::try_emplace_t, const long long unsigned int&, std::array&}; T = boost::container::dtl::pair >; A = boost::container::new_allocator > >; Options = void; boost::container::vector::iterator = boost::container::vec_iterator >*, false>; boost::container::vector::const_iterator = boost::container::vec_iterator >*, true>]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1020:48: required from 'std::pair::type::iterator, bool> boost::container::dtl::flat_tree::try_emplace(boost::container::dtl::flat_tree::const_iterator, KeyType&&, Args&& ...) [with KeyType = const long long unsigned int&; Args = {std::array&}; Value = boost::container::dtl::pair >; KeyOfValue = boost::container::dtl::select1st; Compare = std::less; AllocatorOrContainer = boost::container::new_allocator > >; typename boost::container::dtl::select_container_type::type::iterator = boost::container::vec_iterator >*, false>; boost::container::dtl::flat_tree::const_iterator = boost::container::vec_iterator >*, true>]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:968:10: required from 'boost::container::flat_map::iterator boost::container::flat_map::try_emplace(boost::container::flat_map::const_iterator, const key_type&, Args&& ...) [with Args = {std::array&}; Key = long long unsigned int; T = std::array; Compare = std::less; AllocatorOrContainer = void; boost::container::flat_map::iterator = boost::container::vec_iterator >*, false>; boost::container::flat_map::const_iterator = boost::container::vec_iterator >*, true>; boost::container::flat_map::key_type = long long unsigned int]' rcpp_cx_report.cpp:133:55: required from here F:/biocbuild/bbs-3.15-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 >*>::element_type' {aka 'struct boost::container::dtl::pair >'} 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-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:29, from rcpp_cx_report.cpp:3: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'boost::movelib::detail::iterator_to_element_ptr >*>::element_type' {aka 'struct boost::container::dtl::pair >'} declared here 218 | struct pair | ^~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:32, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:29, from rcpp_cx_report.cpp:3: F:/biocbuild/bbs-3.15-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 = boost::container::dtl::pair >*; F = boost::container::dtl::pair >*]': F:/biocbuild/bbs-3.15-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::type boost::container::uninitialized_move_alloc(Allocator&, I, I, F) [with Allocator = boost::container::new_allocator > >; I = boost::container::dtl::pair >*; F = boost::container::dtl::pair >*; typename boost::container::dtl::enable_if_memtransfer_copy_constructible::type = boost::container::dtl::pair >*]' F:/biocbuild/bbs-3.15-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 = boost::container::new_allocator > >; F = boost::container::dtl::pair >*; O = boost::container::dtl::pair >*; InsertionProxy = boost::container::dtl::insert_range_proxy > >, boost::move_iterator >*>, boost::container::dtl::pair >*>; std::size_t = long long unsigned int]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:3008:10: required from 'void boost::container::vector::priv_insert_forward_range_new_allocation(T*, boost::container::vector::size_type, T*, boost::container::vector::size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_range_proxy > >, boost::move_iterator >*>, boost::container::dtl::pair >*>; T = boost::container::dtl::pair >; A = boost::container::new_allocator > >; Options = void; boost::container::vector::size_type = long long unsigned int]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:2611:10: required from 'void boost::container::vector::priv_move_to_new_buffer(boost::container::vector::size_type, boost::container::version_1) [with T = boost::container::dtl::pair >; A = boost::container::new_allocator > >; Options = void; boost::container::vector::size_type = long long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:1570:39: required from 'void boost::container::vector::reserve(boost::container::vector::size_type) [with T = boost::container::dtl::pair >; A = boost::container::new_allocator > >; Options = void; boost::container::vector::size_type = long long unsigned int]' F:/biocbuild/bbs-3.15-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 >, boost::container::new_allocator > >, void>; typename SequenceContainer::size_type = long long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1393:26: required from 'void boost::container::dtl::flat_tree::reserve(boost::container::dtl::flat_tree::size_type) [with Value = boost::container::dtl::pair >; KeyOfValue = boost::container::dtl::select1st; Compare = std::less; AllocatorOrContainer = boost::container::new_allocator > >; boost::container::dtl::flat_tree::size_type = long long unsigned int]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:712:28: required from 'void boost::container::flat_map::reserve(boost::container::flat_map::size_type) [with Key = long long unsigned int; T = std::array; Compare = std::less; AllocatorOrContainer = void; boost::container::flat_map::size_type = long long unsigned int]' rcpp_cx_report.cpp:114:24: required from here F:/biocbuild/bbs-3.15-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 >'} 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); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:29, from rcpp_cx_report.cpp:3: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'value_type' {aka 'struct boost::container::dtl::pair >'} declared here 218 | struct pair | ^~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:32, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:29, from rcpp_cx_report.cpp:3: F:/biocbuild/bbs-3.15-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 >*>; F = boost::container::dtl::pair >*; std::size_t = long long unsigned int]': F:/biocbuild/bbs-3.15-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::type boost::container::uninitialized_copy_alloc_n_source(Allocator&, I, std::size_t, F) [with Allocator = boost::container::new_allocator > >; I = boost::move_iterator >*>; F = boost::container::dtl::pair >*; typename boost::container::dtl::enable_if_memtransfer_copy_constructible::type = boost::move_iterator >*>; std::size_t = long long unsigned int]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:81:75: required from 'void boost::container::dtl::insert_range_proxy::uninitialized_copy_n_and_update(Allocator&, Iterator, std::size_t) [with Allocator = boost::container::new_allocator > >; FwdIt = boost::move_iterator >*>; Iterator = boost::container::dtl::pair >*; std::size_t = long long unsigned int]' F:/biocbuild/bbs-3.15-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 = boost::container::new_allocator > >; F = boost::container::dtl::pair >*; O = boost::container::dtl::pair >*; InsertionProxy = boost::container::dtl::insert_range_proxy > >, boost::move_iterator >*>, boost::container::dtl::pair >*>; std::size_t = long long unsigned int]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:3008:10: required from 'void boost::container::vector::priv_insert_forward_range_new_allocation(T*, boost::container::vector::size_type, T*, boost::container::vector::size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_range_proxy > >, boost::move_iterator >*>, boost::container::dtl::pair >*>; T = boost::container::dtl::pair >; A = boost::container::new_allocator > >; Options = void; boost::container::vector::size_type = long long unsigned int]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:2611:10: required from 'void boost::container::vector::priv_move_to_new_buffer(boost::container::vector::size_type, boost::container::version_1) [with T = boost::container::dtl::pair >; A = boost::container::new_allocator > >; Options = void; boost::container::vector::size_type = long long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:1570:39: required from 'void boost::container::vector::reserve(boost::container::vector::size_type) [with T = boost::container::dtl::pair >; A = boost::container::new_allocator > >; Options = void; boost::container::vector::size_type = long long unsigned int]' F:/biocbuild/bbs-3.15-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 >, boost::container::new_allocator > >, void>; typename SequenceContainer::size_type = long long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1393:26: required from 'void boost::container::dtl::flat_tree::reserve(boost::container::dtl::flat_tree::size_type) [with Value = boost::container::dtl::pair >; KeyOfValue = boost::container::dtl::select1st; Compare = std::less; AllocatorOrContainer = boost::container::new_allocator > >; boost::container::dtl::flat_tree::size_type = long long unsigned int]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:712:28: required from 'void boost::container::flat_map::reserve(boost::container::flat_map::size_type) [with Key = long long unsigned int; T = std::array; Compare = std::less; AllocatorOrContainer = void; boost::container::flat_map::size_type = long long unsigned int]' rcpp_cx_report.cpp:114:24: required from here F:/biocbuild/bbs-3.15-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 >*>::element_type' {aka 'struct boost::container::dtl::pair >'} 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); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:29, from rcpp_cx_report.cpp:3: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'boost::movelib::detail::iterator_to_element_ptr >*>::element_type' {aka 'struct boost::container::dtl::pair >'} declared here 218 | struct pair | ^~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-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-3.15-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:32, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:29, from rcpp_extract_patterns.cpp:2: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of 'typename boost::container::dtl::enable_if_memtransfer_copy_assignable::type boost::container::move_backward(I, I, F) [with I = boost::container::dtl::pair*; F = boost::container::dtl::pair*; typename boost::container::dtl::enable_if_memtransfer_copy_assignable::type = boost::container::dtl::pair*]': F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:2983:41: required from 'void boost::container::vector::priv_insert_forward_range_expand_forward(T*, boost::container::vector::size_type, InsertionProxy, boost::move_detail::true_type) [with InsertionProxy = boost::container::dtl::insert_emplace_proxy >, boost::container::dtl::pair*, boost::container::try_emplace_t, int, int>; T = boost::container::dtl::pair; A = boost::container::new_allocator >; Options = void; boost::container::vector::size_type = long long unsigned int; boost::move_detail::true_type = boost::move_detail::integral_constant]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:2827:13: required from 'boost::container::vector::iterator boost::container::vector::priv_insert_forward_range(const pointer&, boost::container::vector::size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_emplace_proxy >, boost::container::dtl::pair*, boost::container::try_emplace_t, int, int>; T = boost::container::dtl::pair; A = boost::container::new_allocator >; Options = void; boost::container::vector::iterator = boost::container::vec_iterator*, false>; boost::container::vector::pointer = boost::container::dtl::pair*; boost::container::vector::size_type = long long unsigned int]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:1865:45: required from 'boost::container::vector::iterator boost::container::vector::emplace(boost::container::vector::const_iterator, Args&& ...) [with Args = {boost::container::try_emplace_t, int, int}; T = boost::container::dtl::pair; A = boost::container::new_allocator >; Options = void; boost::container::vector::iterator = boost::container::vec_iterator*, false>; boost::container::vector::const_iterator = boost::container::vec_iterator*, true>]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1020:48: required from 'std::pair::type::iterator, bool> boost::container::dtl::flat_tree::try_emplace(boost::container::dtl::flat_tree::const_iterator, KeyType&&, Args&& ...) [with KeyType = int; Args = {int}; Value = boost::container::dtl::pair; KeyOfValue = boost::container::dtl::select1st; Compare = std::less; AllocatorOrContainer = boost::container::new_allocator >; typename boost::container::dtl::select_container_type::type::iterator = boost::container::vec_iterator*, false>; boost::container::dtl::flat_tree::const_iterator = boost::container::vec_iterator*, true>]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:1004:34: required from 'boost::container::flat_map::iterator boost::container::flat_map::try_emplace(boost::container::flat_map::const_iterator, boost::container::flat_map::key_type&&, Args&& ...) [with Args = {int}; Key = int; T = int; Compare = std::less; AllocatorOrContainer = void; boost::container::flat_map::iterator = boost::container::vec_iterator*, false>; boost::container::flat_map::const_iterator = boost::container::vec_iterator*, true>; boost::container::flat_map::key_type = int]' rcpp_extract_patterns.cpp:103:60: required from here F:/biocbuild/bbs-3.15-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*>::element_type' {aka 'struct boost::container::dtl::pair'} 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-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:29, from rcpp_extract_patterns.cpp:2: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'boost::movelib::detail::iterator_to_element_ptr*>::element_type' {aka 'struct boost::container::dtl::pair'} declared here 218 | struct pair | ^~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:32, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:29, from rcpp_extract_patterns.cpp:2: F:/biocbuild/bbs-3.15-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 = boost::container::dtl::pair*; F = boost::container::dtl::pair*]': F:/biocbuild/bbs-3.15-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::type boost::container::uninitialized_move_alloc(Allocator&, I, I, F) [with Allocator = boost::container::new_allocator >; I = boost::container::dtl::pair*; F = boost::container::dtl::pair*; typename boost::container::dtl::enable_if_memtransfer_copy_constructible::type = boost::container::dtl::pair*]' F:/biocbuild/bbs-3.15-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 = boost::container::new_allocator >; F = boost::container::dtl::pair*; O = boost::container::dtl::pair*; InsertionProxy = boost::container::dtl::insert_range_proxy >, boost::move_iterator*>, boost::container::dtl::pair*>; std::size_t = long long unsigned int]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:3008:10: required from 'void boost::container::vector::priv_insert_forward_range_new_allocation(T*, boost::container::vector::size_type, T*, boost::container::vector::size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_range_proxy >, boost::move_iterator*>, boost::container::dtl::pair*>; T = boost::container::dtl::pair; A = boost::container::new_allocator >; Options = void; boost::container::vector::size_type = long long unsigned int]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:2611:10: required from 'void boost::container::vector::priv_move_to_new_buffer(boost::container::vector::size_type, boost::container::version_1) [with T = boost::container::dtl::pair; A = boost::container::new_allocator >; Options = void; boost::container::vector::size_type = long long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:1570:39: required from 'void boost::container::vector::reserve(boost::container::vector::size_type) [with T = boost::container::dtl::pair; A = boost::container::new_allocator >; Options = void; boost::container::vector::size_type = long long unsigned int]' F:/biocbuild/bbs-3.15-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, boost::container::new_allocator >, void>; typename SequenceContainer::size_type = long long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1393:26: required from 'void boost::container::dtl::flat_tree::reserve(boost::container::dtl::flat_tree::size_type) [with Value = boost::container::dtl::pair; KeyOfValue = boost::container::dtl::select1st; Compare = std::less; AllocatorOrContainer = boost::container::new_allocator >; boost::container::dtl::flat_tree::size_type = long long unsigned int]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:712:28: required from 'void boost::container::flat_map::reserve(boost::container::flat_map::size_type) [with Key = int; T = int; Compare = std::less; AllocatorOrContainer = void; boost::container::flat_map::size_type = long long unsigned int]' rcpp_extract_patterns.cpp:68:67: required from here F:/biocbuild/bbs-3.15-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'} 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); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:29, from rcpp_extract_patterns.cpp:2: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'value_type' {aka 'struct boost::container::dtl::pair'} declared here 218 | struct pair | ^~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:32, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:29, from rcpp_extract_patterns.cpp:2: F:/biocbuild/bbs-3.15-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*>; F = boost::container::dtl::pair*; std::size_t = long long unsigned int]': F:/biocbuild/bbs-3.15-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::type boost::container::uninitialized_copy_alloc_n_source(Allocator&, I, std::size_t, F) [with Allocator = boost::container::new_allocator >; I = boost::move_iterator*>; F = boost::container::dtl::pair*; typename boost::container::dtl::enable_if_memtransfer_copy_constructible::type = boost::move_iterator*>; std::size_t = long long unsigned int]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:81:75: required from 'void boost::container::dtl::insert_range_proxy::uninitialized_copy_n_and_update(Allocator&, Iterator, std::size_t) [with Allocator = boost::container::new_allocator >; FwdIt = boost::move_iterator*>; Iterator = boost::container::dtl::pair*; std::size_t = long long unsigned int]' F:/biocbuild/bbs-3.15-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 = boost::container::new_allocator >; F = boost::container::dtl::pair*; O = boost::container::dtl::pair*; InsertionProxy = boost::container::dtl::insert_range_proxy >, boost::move_iterator*>, boost::container::dtl::pair*>; std::size_t = long long unsigned int]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:3008:10: required from 'void boost::container::vector::priv_insert_forward_range_new_allocation(T*, boost::container::vector::size_type, T*, boost::container::vector::size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_range_proxy >, boost::move_iterator*>, boost::container::dtl::pair*>; T = boost::container::dtl::pair; A = boost::container::new_allocator >; Options = void; boost::container::vector::size_type = long long unsigned int]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:2611:10: required from 'void boost::container::vector::priv_move_to_new_buffer(boost::container::vector::size_type, boost::container::version_1) [with T = boost::container::dtl::pair; A = boost::container::new_allocator >; Options = void; boost::container::vector::size_type = long long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/vector.hpp:1570:39: required from 'void boost::container::vector::reserve(boost::container::vector::size_type) [with T = boost::container::dtl::pair; A = boost::container::new_allocator >; Options = void; boost::container::vector::size_type = long long unsigned int]' F:/biocbuild/bbs-3.15-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, boost::container::new_allocator >, void>; typename SequenceContainer::size_type = long long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1393:26: required from 'void boost::container::dtl::flat_tree::reserve(boost::container::dtl::flat_tree::size_type) [with Value = boost::container::dtl::pair; KeyOfValue = boost::container::dtl::select1st; Compare = std::less; AllocatorOrContainer = boost::container::new_allocator >; boost::container::dtl::flat_tree::size_type = long long unsigned int]' F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:712:28: required from 'void boost::container::flat_map::reserve(boost::container::flat_map::size_type) [with Key = int; T = int; Compare = std::less; AllocatorOrContainer = void; boost::container::flat_map::size_type = long long unsigned int]' rcpp_extract_patterns.cpp:68:67: required from here F:/biocbuild/bbs-3.15-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*>::element_type' {aka 'struct boost::container::dtl::pair'} 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); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/flat_map.hpp:29, from rcpp_extract_patterns.cpp:2: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'boost::movelib::detail::iterator_to_element_ptr*>::element_type' {aka 'struct boost::container::dtl::pair'} declared here 218 | struct pair | ^~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.15-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-3.15-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -lsbml-static -lwinmm -lwldap32 -lgdi32 -lbz2 -lcurl -lrtmp -lssl -lssh2 -lidn2 -lunistring -lcharset -lintl -liconv -lgcrypt -lcrypto -lgpg-error -lws2_32 -llzma -lz -lzstd -lmincore -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.15-bioc/R/library/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 * DONE (epialleleR)