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This page was generated on 2025-01-04 11:46 -0500 (Sat, 04 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4756
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4475
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4435
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4390
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4383
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 646/2275HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epialleleR 1.15.1  (landing page)
Oleksii Nikolaienko
Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025)
git_url: https://git.bioconductor.org/packages/epialleleR
git_branch: devel
git_last_commit: c786e6e
git_last_commit_date: 2024-11-16 10:47:56 -0500 (Sat, 16 Nov 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

INSTALL results for epialleleR on kunpeng2

To the developers/maintainers of the epialleleR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epialleleR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: epialleleR
Version: 1.15.1
Command: /home/biocbuild/R/R/bin/R CMD INSTALL epialleleR
StartedAt: 2025-01-03 19:34:10 -0000 (Fri, 03 Jan 2025)
EndedAt: 2025-01-03 19:35:52 -0000 (Fri, 03 Jan 2025)
EllapsedTime: 102.0 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL epialleleR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘epialleleR’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++17
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c rcpp_call_methylation.cpp -o rcpp_call_methylation.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c rcpp_check_bam.cpp -o rcpp_check_bam.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c rcpp_cx_report.cpp -o rcpp_cx_report.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/container/vector.hpp:32,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/container/detail/flat_tree.hpp:29,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/container/flat_map.hpp:29,
                 from rcpp_cx_report.cpp:3:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/R/R-4.5.0-devel_2024-11-24/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> >*]’
  377 | {  return dtl::memmove(f, l, r); }
      |           ~~~~~~~~~~~~^~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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]’
 1306 |    O d_last = ::boost::container::uninitialized_move_alloc(a, first, pos, d_first);
      |               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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]’
 3276 |       boost::container::uninitialized_move_and_insert_alloc
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3277 |          (a, raw_old_buffer, pos, this->priv_raw_end(), new_start, n, insert_range_proxy);
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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>]’
 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());
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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]’
 1657 |          this->priv_move_to_new_buffer(new_cap, alloc_version());
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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>]’
  410 |    tseq.reserve(cap);
      |    ~~~~~~~~~~~~^~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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]’
 1462 |       (flat_tree_reserve)(this->m_data.m_seq, cnt, dtl::bool_<value>());
      |       ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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]’
  756 |       { m_flat_tree.reserve(cnt);   }
      |         ~~~~~~~~~~~~~~~~~~~^~~~~
rcpp_cx_report.cpp:107:17:   required from here
  107 |   cx_map.reserve(100000);                                                       // reserving helps?
      |   ~~~~~~~~~~~~~~^~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_algobase.h:64,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/specfun.h:43,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/cmath:3898,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include/Rcpp/platform/compiler.h:100,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include/Rcpp/r/headers.h:66,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include/RcppCommon.h:30,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include/Rcpp.h:27,
                 from rcpp_cx_report.cpp:1:
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_pair.h:284:12: note: ‘value_type’ {aka ‘struct std::pair<long unsigned int, std::array<int, 32> >’} declared here
  284 |     struct pair
      |            ^~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c rcpp_extract_patterns.cpp -o rcpp_extract_patterns.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/container/vector.hpp:32,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/container/detail/flat_tree.hpp:29,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/container/flat_map.hpp:29,
                 from rcpp_extract_patterns.cpp:5:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/R/R-4.5.0-devel_2024-11-24/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>*]’
  377 | {  return dtl::memmove(f, l, r); }
      |           ~~~~~~~~~~~~^~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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]’
 1306 |    O d_last = ::boost::container::uninitialized_move_alloc(a, first, pos, d_first);
      |               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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]’
 3276 |       boost::container::uninitialized_move_and_insert_alloc
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3277 |          (a, raw_old_buffer, pos, this->priv_raw_end(), new_start, n, insert_range_proxy);
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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>]’
 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());
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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]’
 1657 |          this->priv_move_to_new_buffer(new_cap, alloc_version());
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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>]’
  410 |    tseq.reserve(cap);
      |    ~~~~~~~~~~~~^~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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]’
 1462 |       (flat_tree_reserve)(this->m_data.m_seq, cnt, dtl::bool_<value>());
      |       ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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]’
  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));
      |   ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_algobase.h:64,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/specfun.h:43,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/cmath:3898,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include/Rcpp/platform/compiler.h:100,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include/Rcpp/r/headers.h:66,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include/RcppCommon.h:30,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include/Rcpp.h:27,
                 from rcpp_extract_patterns.cpp:4:
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_pair.h:284:12: note: ‘value_type’ {aka ‘struct std::pair<int, int>’} declared here
  284 |     struct pair
      |            ^~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c rcpp_fep.cpp -o rcpp_fep.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c rcpp_get_base_freqs.cpp -o rcpp_get_base_freqs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c rcpp_get_xm_beta.cpp -o rcpp_get_xm_beta.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c rcpp_match_target.cpp -o rcpp_match_target.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c rcpp_mhl_report.cpp -o rcpp_mhl_report.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/container/vector.hpp:32,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/container/detail/flat_tree.hpp:29,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/container/flat_map.hpp:29,
                 from rcpp_mhl_report.cpp:3:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/R/R-4.5.0-devel_2024-11-24/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> >*]’
  377 | {  return dtl::memmove(f, l, r); }
      |           ~~~~~~~~~~~~^~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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]’
 1306 |    O d_last = ::boost::container::uninitialized_move_alloc(a, first, pos, d_first);
      |               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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]’
 3276 |       boost::container::uninitialized_move_and_insert_alloc
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3277 |          (a, raw_old_buffer, pos, this->priv_raw_end(), new_start, n, insert_range_proxy);
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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>]’
 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());
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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]’
 1657 |          this->priv_move_to_new_buffer(new_cap, alloc_version());
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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>]’
  410 |    tseq.reserve(cap);
      |    ~~~~~~~~~~~~^~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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]’
 1462 |       (flat_tree_reserve)(this->m_data.m_seq, cnt, dtl::bool_<value>());
      |       ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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]’
  756 |       { m_flat_tree.reserve(cnt);   }
      |         ~~~~~~~~~~~~~~~~~~~^~~~~
rcpp_mhl_report.cpp:137:18:   required from here
  137 |   mhl_map.reserve(100000);                                                      // reserving helps?
      |   ~~~~~~~~~~~~~~~^~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_algobase.h:64,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/specfun.h:43,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/cmath:3898,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include/Rcpp/platform/compiler.h:100,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include/Rcpp/r/headers.h:66,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include/RcppCommon.h:30,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include/Rcpp.h:27,
                 from rcpp_mhl_report.cpp:1:
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_pair.h:284:12: note: ‘value_type’ {aka ‘struct std::pair<long unsigned int, std::array<long unsigned int, 32> >’} declared here
  284 |     struct pair
      |            ^~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c rcpp_read_bam.cpp -o rcpp_read_bam.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c rcpp_read_genome.cpp -o rcpp_read_genome.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c rcpp_simulate_bam.cpp -o rcpp_simulate_bam.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c rcpp_threshold_reads.cpp -o rcpp_threshold_reads.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/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/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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)