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###
### Running command:
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### rm -rf epialleleR.buildbin-libdir && mkdir epialleleR.buildbin-libdir && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL --build --library=epialleleR.buildbin-libdir epialleleR_1.15.3.tar.gz
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* installing *source* package 'epialleleR' ...
** this is package 'epialleleR' version '1.15.3'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
using C++17
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_call_methylation.cpp -o rcpp_call_methylation.o
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_check_bam.cpp -o rcpp_check_bam.o
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_cx_report.cpp -o rcpp_cx_report.o
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/vector.hpp:32,
from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29,
from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_cx_report.cpp:3:
E:/biocbuild/bbs-3.21-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 = std::pair<long long unsigned int, std::array<int, 32> >*; F = std::pair<long long unsigned int, std::array<int, 32> >*]':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:377:23: 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<std::pair<long long unsigned int, std::array<int, 32> > >; I = std::pair<long long unsigned int, std::array<int, 32> >*; F = std::pair<long long unsigned int, std::array<int, 32> >*; typename dtl::enable_if_memtransfer_copy_constructible<I, F, F>::type = std::pair<long long unsigned int, std::array<int, 32> >*]'
377 | { return dtl::memmove(f, l, r); }
| ~~~~~~~~~~~~^~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:1306:59: required from 'void boost::container::uninitialized_move_and_insert_alloc(Allocator&, F, F, F, O, std::size_t, InsertionProxy) [with Allocator = new_allocator<std::pair<long long unsigned int, std::array<int, 32> > >; F = std::pair<long long unsigned int, std::array<int, 32> >*; O = std::pair<long long unsigned int, std::array<int, 32> >*; InsertionProxy = dtl::insert_range_proxy<new_allocator<std::pair<long long unsigned int, std::array<int, 32> > >, boost::move_iterator<std::pair<long long unsigned int, std::array<int, 32> >*> >; std::size_t = long long unsigned int]'
1306 | O d_last = ::boost::container::uninitialized_move_alloc(a, first, pos, d_first);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/vector.hpp:3277:10: 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<std::pair<long long unsigned int, std::array<int, 32> > >, boost::move_iterator<std::pair<long long unsigned int, std::array<int, 32> >*> >; T = std::pair<long long unsigned int, std::array<int, 32> >; A = void; Options = void; size_type = long long unsigned int]'
3276 | boost::container::uninitialized_move_and_insert_alloc
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3277 | (a, raw_old_buffer, pos, this->priv_raw_end(), new_start, n, insert_range_proxy);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/vector.hpp:2837:10: required from 'void boost::container::vector<T, Allocator, Options>::priv_move_to_new_buffer(size_type, boost::container::version_1) [with T = std::pair<long long unsigned int, std::array<int, 32> >; A = void; Options = void; size_type = long long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]'
2836 | this->priv_insert_forward_range_new_allocation
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2837 | ( boost::movelib::to_raw_pointer(p), new_cap, this->priv_raw_end(), 0, this->priv_dummy_empty_proxy());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/vector.hpp:1657:39: required from 'void boost::container::vector<T, Allocator, Options>::reserve(size_type) [with T = std::pair<long long unsigned int, std::array<int, 32> >; A = void; Options = void; size_type = long long unsigned int]'
1657 | this->priv_move_to_new_buffer(new_cap, alloc_version());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:410:16: required from 'void boost::container::dtl::flat_tree_reserve(SequenceContainer&, typename SequenceContainer::size_type, boost::move_detail::true_) [with SequenceContainer = boost::container::vector<std::pair<long long unsigned int, std::array<int, 32> >, void, void>; typename SequenceContainer::size_type = long long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]'
410 | tseq.reserve(cap);
| ~~~~~~~~~~~~^~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1462:26: required from 'void boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::reserve(size_type) [with Value = std::pair<long long unsigned int, std::array<int, 32> >; KeyOfValue = boost::container::dtl::select1st<long long unsigned int>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = void; size_type = long long unsigned int]'
1462 | (flat_tree_reserve)(this->m_data.m_seq, cnt, dtl::bool_<value>());
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/flat_map.hpp:756:28: required from 'void boost::container::flat_map<Key, T, Compare, Allocator>::reserve(size_type) [with Key = long long unsigned int; T = std::array<int, 32>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = void; size_type = long long unsigned int]'
756 | { m_flat_tree.reserve(cnt); }
| ~~~~~~~~~~~~~~~~~~~^~~~~
rcpp_cx_report.cpp:107:17: required from here
107 | cx_map.reserve(100000); // reserving helps?
| ~~~~~~~~~~~~~~^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:231:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct std::pair<long long unsigned int, std::array<int, 32> >'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
231 | std::memmove(dest_raw, beg_raw, sizeof(value_type)*n);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/stl_algobase.h:64,
from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/specfun.h:43,
from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/cmath:3898,
from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:100,
from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:66,
from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/RcppCommon.h:30,
from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/Rcpp.h:27,
from rcpp_cx_report.cpp:1:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/stl_pair.h:284:12: note: 'value_type' {aka 'struct std::pair<long long unsigned int, std::array<int, 32> >'} declared here
284 | struct pair
| ^~~~
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools45/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 E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/vector.hpp:32,
from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29,
from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_extract_patterns.cpp:5:
E:/biocbuild/bbs-3.21-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 = std::pair<int, int>*; F = std::pair<int, int>*]':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:377:23: 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<std::pair<int, int> >; I = std::pair<int, int>*; F = std::pair<int, int>*; typename dtl::enable_if_memtransfer_copy_constructible<I, F, F>::type = std::pair<int, int>*]'
377 | { return dtl::memmove(f, l, r); }
| ~~~~~~~~~~~~^~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:1306:59: required from 'void boost::container::uninitialized_move_and_insert_alloc(Allocator&, F, F, F, O, std::size_t, InsertionProxy) [with Allocator = new_allocator<std::pair<int, int> >; F = std::pair<int, int>*; O = std::pair<int, int>*; InsertionProxy = dtl::insert_range_proxy<new_allocator<std::pair<int, int> >, boost::move_iterator<std::pair<int, int>*> >; std::size_t = long long unsigned int]'
1306 | O d_last = ::boost::container::uninitialized_move_alloc(a, first, pos, d_first);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/vector.hpp:3277:10: 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<std::pair<int, int> >, boost::move_iterator<std::pair<int, int>*> >; T = std::pair<int, int>; A = void; Options = void; size_type = long long unsigned int]'
3276 | boost::container::uninitialized_move_and_insert_alloc
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3277 | (a, raw_old_buffer, pos, this->priv_raw_end(), new_start, n, insert_range_proxy);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/vector.hpp:2837:10: required from 'void boost::container::vector<T, Allocator, Options>::priv_move_to_new_buffer(size_type, boost::container::version_1) [with T = std::pair<int, int>; A = void; Options = void; size_type = long long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]'
2836 | this->priv_insert_forward_range_new_allocation
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2837 | ( boost::movelib::to_raw_pointer(p), new_cap, this->priv_raw_end(), 0, this->priv_dummy_empty_proxy());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/vector.hpp:1657:39: required from 'void boost::container::vector<T, Allocator, Options>::reserve(size_type) [with T = std::pair<int, int>; A = void; Options = void; size_type = long long unsigned int]'
1657 | this->priv_move_to_new_buffer(new_cap, alloc_version());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:410:16: required from 'void boost::container::dtl::flat_tree_reserve(SequenceContainer&, typename SequenceContainer::size_type, boost::move_detail::true_) [with SequenceContainer = boost::container::vector<std::pair<int, int>, void, void>; typename SequenceContainer::size_type = long long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]'
410 | tseq.reserve(cap);
| ~~~~~~~~~~~~^~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1462:26: required from 'void boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::reserve(size_type) [with Value = std::pair<int, int>; KeyOfValue = boost::container::dtl::select1st<int>; Compare = std::less<int>; AllocatorOrContainer = void; size_type = long long unsigned int]'
1462 | (flat_tree_reserve)(this->m_data.m_seq, cnt, dtl::bool_<value>());
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/flat_map.hpp:756:28: 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]'
756 | { m_flat_tree.reserve(cnt); }
| ~~~~~~~~~~~~~~~~~~~^~~~~
rcpp_extract_patterns.cpp:58:18: required from here
58 | pos_map.reserve(std::max((int)(target_end-target_start), 0xFFFF));
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:231:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct std::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
231 | std::memmove(dest_raw, beg_raw, sizeof(value_type)*n);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/stl_algobase.h:64,
from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/specfun.h:43,
from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/cmath:3898,
from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:100,
from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:66,
from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/RcppCommon.h:30,
from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/Rcpp.h:27,
from rcpp_extract_patterns.cpp:4:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/stl_pair.h:284:12: note: 'value_type' {aka 'struct std::pair<int, int>'} declared here
284 | struct pair
| ^~~~
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools45/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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools45/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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools45/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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools45/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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_mhl_report.cpp -o rcpp_mhl_report.o
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/vector.hpp:32,
from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29,
from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_mhl_report.cpp:3:
E:/biocbuild/bbs-3.21-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 = std::pair<long long unsigned int, std::array<long long unsigned int, 32> >*; F = std::pair<long long unsigned int, std::array<long long unsigned int, 32> >*]':
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:377:23: 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<std::pair<long long unsigned int, std::array<long long unsigned int, 32> > >; I = std::pair<long long unsigned int, std::array<long long unsigned int, 32> >*; F = std::pair<long long unsigned int, std::array<long long unsigned int, 32> >*; typename dtl::enable_if_memtransfer_copy_constructible<I, F, F>::type = std::pair<long long unsigned int, std::array<long long unsigned int, 32> >*]'
377 | { return dtl::memmove(f, l, r); }
| ~~~~~~~~~~~~^~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:1306:59: required from 'void boost::container::uninitialized_move_and_insert_alloc(Allocator&, F, F, F, O, std::size_t, InsertionProxy) [with Allocator = new_allocator<std::pair<long long unsigned int, std::array<long long unsigned int, 32> > >; F = std::pair<long long unsigned int, std::array<long long unsigned int, 32> >*; O = std::pair<long long unsigned int, std::array<long long unsigned int, 32> >*; InsertionProxy = dtl::insert_range_proxy<new_allocator<std::pair<long long unsigned int, std::array<long long unsigned int, 32> > >, boost::move_iterator<std::pair<long long unsigned int, std::array<long long unsigned int, 32> >*> >; std::size_t = long long unsigned int]'
1306 | O d_last = ::boost::container::uninitialized_move_alloc(a, first, pos, d_first);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/vector.hpp:3277:10: 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<std::pair<long long unsigned int, std::array<long long unsigned int, 32> > >, boost::move_iterator<std::pair<long long unsigned int, std::array<long long unsigned int, 32> >*> >; T = std::pair<long long unsigned int, std::array<long long unsigned int, 32> >; A = void; Options = void; size_type = long long unsigned int]'
3276 | boost::container::uninitialized_move_and_insert_alloc
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3277 | (a, raw_old_buffer, pos, this->priv_raw_end(), new_start, n, insert_range_proxy);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/vector.hpp:2837:10: required from 'void boost::container::vector<T, Allocator, Options>::priv_move_to_new_buffer(size_type, boost::container::version_1) [with T = std::pair<long long unsigned int, std::array<long long unsigned int, 32> >; A = void; Options = void; size_type = long long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]'
2836 | this->priv_insert_forward_range_new_allocation
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2837 | ( boost::movelib::to_raw_pointer(p), new_cap, this->priv_raw_end(), 0, this->priv_dummy_empty_proxy());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/vector.hpp:1657:39: required from 'void boost::container::vector<T, Allocator, Options>::reserve(size_type) [with T = std::pair<long long unsigned int, std::array<long long unsigned int, 32> >; A = void; Options = void; size_type = long long unsigned int]'
1657 | this->priv_move_to_new_buffer(new_cap, alloc_version());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:410:16: required from 'void boost::container::dtl::flat_tree_reserve(SequenceContainer&, typename SequenceContainer::size_type, boost::move_detail::true_) [with SequenceContainer = boost::container::vector<std::pair<long long unsigned int, std::array<long long unsigned int, 32> >, void, void>; typename SequenceContainer::size_type = long long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]'
410 | tseq.reserve(cap);
| ~~~~~~~~~~~~^~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1462:26: required from 'void boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::reserve(size_type) [with Value = std::pair<long long unsigned int, std::array<long long unsigned int, 32> >; KeyOfValue = boost::container::dtl::select1st<long long unsigned int>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = void; size_type = long long unsigned int]'
1462 | (flat_tree_reserve)(this->m_data.m_seq, cnt, dtl::bool_<value>());
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/flat_map.hpp:756:28: required from 'void boost::container::flat_map<Key, T, Compare, Allocator>::reserve(size_type) [with Key = long long unsigned int; T = std::array<long long unsigned int, 32>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = void; size_type = long long unsigned int]'
756 | { m_flat_tree.reserve(cnt); }
| ~~~~~~~~~~~~~~~~~~~^~~~~
rcpp_mhl_report.cpp:137:18: required from here
137 | mhl_map.reserve(100000); // reserving helps?
| ~~~~~~~~~~~~~~~^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:231:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct std::pair<long long unsigned int, std::array<long long unsigned int, 32> >'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
231 | std::memmove(dest_raw, beg_raw, sizeof(value_type)*n);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/stl_algobase.h:64,
from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/specfun.h:43,
from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/cmath:3898,
from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:100,
from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:66,
from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/RcppCommon.h:30,
from E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include/Rcpp.h:27,
from rcpp_mhl_report.cpp:1:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/stl_pair.h:284:12: note: 'value_type' {aka 'struct std::pair<long long unsigned int, std::array<long long unsigned int, 32> >'} declared here
284 | struct pair
| ^~~~
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools45/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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_read_genome.cpp -o rcpp_read_genome.o
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_simulate_bam.cpp -o rcpp_simulate_bam.o
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools45/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_call_methylation.o rcpp_check_bam.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_mhl_report.o rcpp_read_bam.o rcpp_read_genome.o rcpp_simulate_bam.o rcpp_threshold_reads.o E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lnghttp2 -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/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_1.15.3.zip
* DONE (epialleleR)
