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###
### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL epialleleR
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘epialleleR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcpp_call_methylation.cpp -o rcpp_call_methylation.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcpp_check_bam.cpp -o rcpp_check_bam.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcpp_cx_report.cpp -o rcpp_cx_report.o
In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/container/vector.hpp:32,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/container/detail/flat_tree.hpp:29,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/container/flat_map.hpp:29,
                 from rcpp_cx_report.cpp:3:
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int, std::array<int, 32> >*; F = std::pair<long unsigned int, std::array<int, 32> >*]’:
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int, std::array<int, 32> > >; I = std::pair<long unsigned int, std::array<int, 32> >*; F = std::pair<long unsigned int, std::array<int, 32> >*; typename dtl::enable_if_memtransfer_copy_constructible<I, F, F>::type = std::pair<long unsigned int, std::array<int, 32> >*]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int, std::array<int, 32> > >; F = std::pair<long unsigned int, std::array<int, 32> >*; O = std::pair<long unsigned int, std::array<int, 32> >*; InsertionProxy = dtl::insert_range_proxy<new_allocator<std::pair<long unsigned int, std::array<int, 32> > >, boost::move_iterator<std::pair<long unsigned int, std::array<int, 32> >*> >; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int, std::array<int, 32> > >, boost::move_iterator<std::pair<long unsigned int, std::array<int, 32> >*> >; T = std::pair<long unsigned int, std::array<int, 32> >; A = void; Options = void; size_type = long unsigned int]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int, std::array<int, 32> >; A = void; Options = void; size_type = long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int, std::array<int, 32> >; A = void; Options = void; size_type = long unsigned int]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int, std::array<int, 32> >, void, void>; typename SequenceContainer::size_type = long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int, std::array<int, 32> >; KeyOfValue = boost::container::dtl::select1st<long unsigned int>; Compare = std::less<long unsigned int>; AllocatorOrContainer = void; size_type = long unsigned int]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int; T = std::array<int, 32>; Compare = std::less<long unsigned int>; AllocatorOrContainer = void; size_type = long unsigned int]’
rcpp_cx_report.cpp:107:17:   required from here
/home/biocbuild/bbs-3.20-bioc/R/site-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 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 /usr/include/c++/13/bits/stl_algobase.h:64,
                 from /usr/include/c++/13/bits/specfun.h:43,
                 from /usr/include/c++/13/cmath:3699,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/Rcpp/platform/compiler.h:100,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/Rcpp/r/headers.h:66,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/RcppCommon.h:30,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/Rcpp.h:27,
                 from rcpp_cx_report.cpp:1:
/usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘value_type’ {aka ‘struct std::pair<long unsigned int, std::array<int, 32> >’} declared here
  187 |     struct pair
      |            ^~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcpp_extract_patterns.cpp -o rcpp_extract_patterns.o
In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/container/vector.hpp:32,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/container/detail/flat_tree.hpp:29,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/container/flat_map.hpp:29,
                 from rcpp_extract_patterns.cpp:5:
/home/biocbuild/bbs-3.20-bioc/R/site-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>*]’:
/home/biocbuild/bbs-3.20-bioc/R/site-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>*]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int]’
rcpp_extract_patterns.cpp:58:18:   required from here
/home/biocbuild/bbs-3.20-bioc/R/site-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 /usr/include/c++/13/bits/stl_algobase.h:64,
                 from /usr/include/c++/13/bits/specfun.h:43,
                 from /usr/include/c++/13/cmath:3699,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/Rcpp/platform/compiler.h:100,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/Rcpp/r/headers.h:66,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/RcppCommon.h:30,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/Rcpp.h:27,
                 from rcpp_extract_patterns.cpp:4:
/usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘value_type’ {aka ‘struct std::pair<int, int>’} declared here
  187 |     struct pair
      |            ^~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcpp_fep.cpp -o rcpp_fep.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcpp_get_base_freqs.cpp -o rcpp_get_base_freqs.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcpp_get_xm_beta.cpp -o rcpp_get_xm_beta.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcpp_match_target.cpp -o rcpp_match_target.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcpp_mhl_report.cpp -o rcpp_mhl_report.o
In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/container/vector.hpp:32,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/container/detail/flat_tree.hpp:29,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/container/flat_map.hpp:29,
                 from rcpp_mhl_report.cpp:3:
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int, std::array<long unsigned int, 32> >*; F = std::pair<long unsigned int, std::array<long unsigned int, 32> >*]’:
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int, std::array<long unsigned int, 32> > >; I = std::pair<long unsigned int, std::array<long unsigned int, 32> >*; F = std::pair<long unsigned int, std::array<long unsigned int, 32> >*; typename dtl::enable_if_memtransfer_copy_constructible<I, F, F>::type = std::pair<long unsigned int, std::array<long unsigned int, 32> >*]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int, std::array<long unsigned int, 32> > >; F = std::pair<long unsigned int, std::array<long unsigned int, 32> >*; O = std::pair<long unsigned int, std::array<long unsigned int, 32> >*; InsertionProxy = dtl::insert_range_proxy<new_allocator<std::pair<long unsigned int, std::array<long unsigned int, 32> > >, boost::move_iterator<std::pair<long unsigned int, std::array<long unsigned int, 32> >*> >; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int, std::array<long unsigned int, 32> > >, boost::move_iterator<std::pair<long unsigned int, std::array<long unsigned int, 32> >*> >; T = std::pair<long unsigned int, std::array<long unsigned int, 32> >; A = void; Options = void; size_type = long unsigned int]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int, std::array<long unsigned int, 32> >; A = void; Options = void; size_type = long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int, std::array<long unsigned int, 32> >; A = void; Options = void; size_type = long unsigned int]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int, std::array<long unsigned int, 32> >, void, void>; typename SequenceContainer::size_type = long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int, std::array<long unsigned int, 32> >; KeyOfValue = boost::container::dtl::select1st<long unsigned int>; Compare = std::less<long unsigned int>; AllocatorOrContainer = void; size_type = long unsigned int]’
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int; T = std::array<long unsigned int, 32>; Compare = std::less<long unsigned int>; AllocatorOrContainer = void; size_type = long unsigned int]’
rcpp_mhl_report.cpp:137:18:   required from here
/home/biocbuild/bbs-3.20-bioc/R/site-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 unsigned int, std::array<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 /usr/include/c++/13/bits/stl_algobase.h:64,
                 from /usr/include/c++/13/bits/specfun.h:43,
                 from /usr/include/c++/13/cmath:3699,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/Rcpp/platform/compiler.h:100,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/Rcpp/r/headers.h:66,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/RcppCommon.h:30,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/Rcpp.h:27,
                 from rcpp_mhl_report.cpp:1:
/usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘value_type’ {aka ‘struct std::pair<long unsigned int, std::array<long unsigned int, 32> >’} declared here
  187 |     struct pair
      |            ^~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcpp_read_bam.cpp -o rcpp_read_bam.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcpp_read_genome.cpp -o rcpp_read_genome.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcpp_simulate_bam.cpp -o rcpp_simulate_bam.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcpp_threshold_reads.cpp -o rcpp_threshold_reads.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o epialleleR.so 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 /home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-epialleleR/00new/epialleleR/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (epialleleR)