| Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 666/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| epialleleR 1.16.0 (landing page) Oleksii Nikolaienko
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: epialleleR |
| Version: 1.16.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL epialleleR |
| StartedAt: 2025-10-13 20:49:37 -0000 (Mon, 13 Oct 2025) |
| EndedAt: 2025-10-13 20:51:19 -0000 (Mon, 13 Oct 2025) |
| EllapsedTime: 102.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL epialleleR
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘epialleleR’ ...
** this is package ‘epialleleR’ version ‘1.16.0’
** 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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c rcpp_cx_report.cpp -o rcpp_cx_report.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include/boost/container/vector.hpp:32,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include/boost/container/detail/flat_tree.hpp:29,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_cx_report.cpp:3:
/home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/site-library/Rcpp/include/Rcpp/platform/compiler.h:100,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include/Rcpp/r/headers.h:66,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include/RcppCommon.h:30,
from /home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c rcpp_extract_patterns.cpp -o rcpp_extract_patterns.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include/boost/container/vector.hpp:32,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include/boost/container/detail/flat_tree.hpp:29,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_extract_patterns.cpp:5:
/home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/site-library/Rcpp/include/Rcpp/platform/compiler.h:100,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include/Rcpp/r/headers.h:66,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include/RcppCommon.h:30,
from /home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c rcpp_mhl_report.cpp -o rcpp_mhl_report.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include/boost/container/vector.hpp:32,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include/boost/container/detail/flat_tree.hpp:29,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_mhl_report.cpp:3:
/home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/site-library/Rcpp/include/Rcpp/platform/compiler.h:100,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include/Rcpp/r/headers.h:66,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include/RcppCommon.h:30,
from /home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-devel_2025-02-19/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/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)