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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:epialleleR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings epialleleR_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/epialleleR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epialleleR/DESCRIPTION’ ... OK
* this is package ‘epialleleR’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘epialleleR’ can be installed ... WARNING
Found the following significant warnings:
  /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:909:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>::element_type’ {aka ‘struct boost::container::dtl::pair<long unsigned int, std::array<int, 16> >’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<long unsigned int, std::array<int, 16> >’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:212:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>::element_type’ {aka ‘struct boost::container::dtl::pair<long unsigned int, std::array<int, 16> >’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/biocbuild/bbs-3.13-bioc/meat/epialleleR.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
generateVcfReport 20.142  0.874  21.224
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/epialleleR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL epialleleR
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘epialleleR’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rcpp_apply_cigar.cpp -o rcpp_apply_cigar.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rcpp_char_to_context.cpp -o rcpp_char_to_context.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/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-3.13-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/vector.hpp:32,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
                 from rcpp_cx_report.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of ‘typename boost::container::dtl::enable_if_memtransfer_copy_assignable<I, F, F>::type boost::container::move_backward(I, I, F) [with I = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*; F = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*; typename boost::container::dtl::enable_if_memtransfer_copy_assignable<I, F, F>::type = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*]’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/vector.hpp:2932:41:   required from ‘void boost::container::vector<T, Allocator, Options>::priv_insert_forward_range_expand_forward(T*, boost::container::vector<T, Allocator, Options>::size_type, InsertionProxy, boost::move_detail::true_type) [with InsertionProxy = boost::container::dtl::insert_emplace_proxy<boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >, boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*, boost::container::try_emplace_t, const long unsigned int&, std::array<int, 16>&>; T = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = long unsigned int; boost::move_detail::true_type = boost::move_detail::integral_constant<bool, true>]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/vector.hpp:2777:10:   required from ‘boost::container::vector<T, Allocator, Options>::iterator boost::container::vector<T, Allocator, Options>::priv_insert_forward_range(const pointer&, boost::container::vector<T, Allocator, Options>::size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_emplace_proxy<boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >, boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*, boost::container::try_emplace_t, const long unsigned int&, std::array<int, 16>&>; T = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::iterator = boost::container::vec_iterator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*, false>; typename boost::container::allocator_traits<typename boost::container::real_allocator<T, A>::type>::pointer = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*; boost::container::vector<T, Allocator, Options>::pointer = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*; boost::container::vector<T, Allocator, Options>::size_type = long unsigned int]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/vector.hpp:1828:87:   required from ‘boost::container::vector<T, Allocator, Options>::iterator boost::container::vector<T, Allocator, Options>::emplace(boost::container::vector<T, Allocator, Options>::const_iterator, Args&& ...) [with Args = {boost::container::try_emplace_t, const long unsigned int&, std::array<int, 16>&}; T = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::iterator = boost::container::vec_iterator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*, false>; typename boost::container::allocator_traits<typename boost::container::real_allocator<T, A>::type>::pointer = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*; boost::container::vector<T, Allocator, Options>::const_iterator = boost::container::vec_iterator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*, true>]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:989:20:   required from ‘std::pair<typename boost::container::dtl::select_container_type<Value, AllocatorOrContainer>::type::iterator, bool> boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::try_emplace(boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::const_iterator, KeyType&&, Args&& ...) [with KeyType = const long unsigned int&; Args = {std::array<int, 16>&}; Value = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >; KeyOfValue = boost::container::dtl::select1st<long unsigned int>; Compare = std::less<long unsigned int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >; typename boost::container::dtl::select_container_type<Value, AllocatorOrContainer>::type::iterator = boost::container::vec_iterator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*, false>; boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::const_iterator = boost::container::vec_iterator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*, true>]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/flat_map.hpp:945:89:   required from ‘boost::container::flat_map<Key, T, Compare, Allocator>::iterator boost::container::flat_map<Key, T, Compare, Allocator>::try_emplace(boost::container::flat_map<Key, T, Compare, Allocator>::const_iterator, const key_type&, Args&& ...) [with Args = {std::array<int, 16>&}; Key = long unsigned int; T = std::array<int, 16>; Compare = std::less<long unsigned int>; AllocatorOrContainer = void; boost::container::flat_map<Key, T, Compare, Allocator>::iterator = boost::container::vec_iterator<std::pair<long unsigned int, std::array<int, 16> >*, false>; boost::container::flat_map<Key, T, Compare, Allocator>::const_iterator = boost::container::vec_iterator<std::pair<long unsigned int, std::array<int, 16> >*, true>; boost::container::flat_map<Key, T, Compare, Allocator>::key_type = long unsigned int]’
rcpp_cx_report.cpp:120:55:   required from here
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:909:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>::element_type’ {aka ‘struct boost::container::dtl::pair<long unsigned int, std::array<int, 16> >’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  909 |       std::memmove((boost::movelib::iterator_to_raw_pointer)(r), (boost::movelib::iterator_to_raw_pointer)(f), sizeof(value_type)*n);
      |       ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
                 from rcpp_cx_report.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>::element_type’ {aka ‘struct boost::container::dtl::pair<long unsigned int, std::array<int, 16> >’} declared here
  218 | struct pair
      |        ^~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/vector.hpp:32,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
                 from rcpp_cx_report.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of ‘F boost::container::dtl::memmove(I, I, F) [with I = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*; F = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*]’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:321:23:   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 = boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >; I = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*; F = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*; typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, F>::type = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:1209:59:   required from ‘void boost::container::uninitialized_move_and_insert_alloc(Allocator&, F, F, F, O, typename boost::container::allocator_traits<Allocator>::size_type, InsertionProxy) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >; F = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*; O = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*; InsertionProxy = boost::container::dtl::insert_range_proxy<boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >, boost::move_iterator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>, boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>; typename boost::container::allocator_traits<Allocator>::size_type = long unsigned int]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/vector.hpp:2957:10:   required from ‘void boost::container::vector<T, Allocator, Options>::priv_insert_forward_range_new_allocation(T*, boost::container::vector<T, Allocator, Options>::size_type, T*, boost::container::vector<T, Allocator, Options>::size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_range_proxy<boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >, boost::move_iterator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>, boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>; T = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = long unsigned int]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/vector.hpp:2561:7:   required from ‘void boost::container::vector<T, Allocator, Options>::priv_move_to_new_buffer(boost::container::vector<T, Allocator, Options>::size_type, boost::container::version_1) [with T = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/vector.hpp:1537:10:   required from ‘void boost::container::vector<T, Allocator, Options>::reserve(boost::container::vector<T, Allocator, Options>::size_type) [with T = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = long unsigned int]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:369:4:   required from ‘void boost::container::dtl::flat_tree_reserve(SequenceContainer&, typename SequenceContainer::size_type, boost::move_detail::true_) [with SequenceContainer = boost::container::vector<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >, boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >, void>; typename SequenceContainer::size_type = long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1334:26:   required from ‘void boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::reserve(boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::size_type) [with Value = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >; KeyOfValue = boost::container::dtl::select1st<long unsigned int>; Compare = std::less<long unsigned int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >; boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::size_type = long unsigned int]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/flat_map.hpp:693:9:   required from ‘void boost::container::flat_map<Key, T, Compare, Allocator>::reserve(boost::container::flat_map<Key, T, Compare, Allocator>::size_type) [with Key = long unsigned int; T = std::array<int, 16>; Compare = std::less<long unsigned int>; AllocatorOrContainer = void; boost::container::flat_map<Key, T, Compare, Allocator>::size_type = long unsigned int]’
rcpp_cx_report.cpp:104:24:   required from here
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<long unsigned int, std::array<int, 16> >’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  183 |       std::memmove(dest_raw, beg_raw, sizeof(value_type)*n);
      |       ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
                 from rcpp_cx_report.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: ‘value_type’ {aka ‘struct boost::container::dtl::pair<long unsigned int, std::array<int, 16> >’} declared here
  218 | struct pair
      |        ^~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/vector.hpp:32,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
                 from rcpp_cx_report.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of ‘I boost::container::dtl::memmove_n_source(I, U, F) [with I = boost::move_iterator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>; U = long unsigned int; F = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*]’:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:549:32:   required from ‘typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, I>::type boost::container::uninitialized_copy_alloc_n_source(Allocator&, I, typename boost::container::allocator_traits<Allocator>::size_type, F) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >; I = boost::move_iterator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>; F = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*; typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, I>::type = boost::move_iterator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>; typename boost::container::allocator_traits<Allocator>::size_type = long unsigned int]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:83:75:   required from ‘void boost::container::dtl::insert_range_proxy<Allocator, FwdIt, Iterator>::uninitialized_copy_n_and_update(Allocator&, Iterator, boost::container::dtl::insert_range_proxy<Allocator, FwdIt, Iterator>::size_type) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >; FwdIt = boost::move_iterator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>; Iterator = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*; boost::container::dtl::insert_range_proxy<Allocator, FwdIt, Iterator>::size_type = long unsigned int]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:1212:4:   required from ‘void boost::container::uninitialized_move_and_insert_alloc(Allocator&, F, F, F, O, typename boost::container::allocator_traits<Allocator>::size_type, InsertionProxy) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >; F = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*; O = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*; InsertionProxy = boost::container::dtl::insert_range_proxy<boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >, boost::move_iterator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>, boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>; typename boost::container::allocator_traits<Allocator>::size_type = long unsigned int]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/vector.hpp:2957:10:   required from ‘void boost::container::vector<T, Allocator, Options>::priv_insert_forward_range_new_allocation(T*, boost::container::vector<T, Allocator, Options>::size_type, T*, boost::container::vector<T, Allocator, Options>::size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_range_proxy<boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >, boost::move_iterator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>, boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>; T = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = long unsigned int]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/vector.hpp:2561:7:   required from ‘void boost::container::vector<T, Allocator, Options>::priv_move_to_new_buffer(boost::container::vector<T, Allocator, Options>::size_type, boost::container::version_1) [with T = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/vector.hpp:1537:10:   required from ‘void boost::container::vector<T, Allocator, Options>::reserve(boost::container::vector<T, Allocator, Options>::size_type) [with T = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = long unsigned int]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:369:4:   required from ‘void boost::container::dtl::flat_tree_reserve(SequenceContainer&, typename SequenceContainer::size_type, boost::move_detail::true_) [with SequenceContainer = boost::container::vector<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >, boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >, void>; typename SequenceContainer::size_type = long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1334:26:   required from ‘void boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::reserve(boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::size_type) [with Value = boost::container::dtl::pair<long unsigned int, std::array<int, 16> >; KeyOfValue = boost::container::dtl::select1st<long unsigned int>; Compare = std::less<long unsigned int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<long unsigned int, std::array<int, 16> > >; boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::size_type = long unsigned int]’
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/flat_map.hpp:693:9:   required from ‘void boost::container::flat_map<Key, T, Compare, Allocator>::reserve(boost::container::flat_map<Key, T, Compare, Allocator>::size_type) [with Key = long unsigned int; T = std::array<int, 16>; Compare = std::less<long unsigned int>; AllocatorOrContainer = void; boost::container::flat_map<Key, T, Compare, Allocator>::size_type = long unsigned int]’
rcpp_cx_report.cpp:104:24:   required from here
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:212:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>::element_type’ {aka ‘struct boost::container::dtl::pair<long unsigned int, std::array<int, 16> >’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  212 |       std::memmove(boost::movelib::iterator_to_raw_pointer(r), boost::movelib::iterator_to_raw_pointer(f), sizeof(value_type)*n);
      |       ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
                 from rcpp_cx_report.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long unsigned int, std::array<int, 16> >*>::element_type’ {aka ‘struct boost::container::dtl::pair<long unsigned int, std::array<int, 16> >’} declared here
  218 | struct pair
      |        ^~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rcpp_get_base_freqs.cpp -o rcpp_get_base_freqs.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rcpp_get_xm_beta.cpp -o rcpp_get_xm_beta.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rcpp_match_target.cpp -o rcpp_match_target.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rcpp_merge_ends.cpp -o rcpp_merge_ends.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rcpp_threshold_reads.cpp -o rcpp_threshold_reads.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o epialleleR.so RcppExports.o rcpp_apply_cigar.o rcpp_char_to_context.o rcpp_cx_report.o rcpp_get_base_freqs.o rcpp_get_xm_beta.o rcpp_match_target.o rcpp_merge_ends.o rcpp_threshold_reads.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/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)

R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("epialleleR")
Reading BED file [0.110s]
Reading BAM file [1.167s]
Preprocessing BAM data:
  Transforming sequences [0.019s]
  Merging pairs [0.012s]
Computing ECDFs for within- and out-of-context per-read beta values [0.034s]
Reading BED file [0.016s]
Reading BAM file [0.144s]
Preprocessing BAM data:
  Transforming sequences [0.007s]
  Merging pairs [0.007s]
Computing ECDFs for within- and out-of-context per-read beta values [0.006s]
Reading BED file [0.017s]
Reading BAM file [0.142s]
Preprocessing BAM data:
  Transforming sequences [0.007s]
  Merging pairs [0.007s]
Preparing amplicon report [0.038s]
Reading BED file [0.016s]
Reading BAM file [0.178s]
Preprocessing BAM data:
  Transforming sequences [0.010s]
  Merging pairs [0.010s]
Thresholding reads [0.001s]
Preparing amplicon report [0.024s]
Writing the report [0.001s]
Reading BAM file [1.060s]
Preprocessing BAM data:
  Transforming sequences [0.019s]
  Merging pairs [0.016s]
Thresholding reads [0.002s]
Preparing cytosine report [0.021s]
Reading BAM file [0.190s]
Preprocessing BAM data:
  Transforming sequences [0.018s]
  Merging pairs [0.016s]
Thresholding reads [0.003s]
Preparing cytosine report [0.022s]
Writing the report [0.001s]
Reading BED file [0.018s]
Reading VCF file [0.636s]
Reading BAM file [0.156s]
Preprocessing BAM data:
  Transforming sequences [0.008s]
  Merging pairs [0.007s]
Extracting base frequences [0.080s]
Already preprocessed VCF supplied as an input. Options 'bed' and 'zero.based.bed' will have no effect.
Reading BAM file [1.356s]
Preprocessing BAM data:
  Transforming sequences [0.024s]
  Merging pairs [0.019s]
Thresholding reads [0.003s]
Extracting base frequences [9.843s]
Writing the report [0.007s]
Already preprocessed BAM supplied as an input. Options 'min.mapq' and 'skip.duplicates' will have no effect.


RUNIT TEST PROTOCOL -- Thu Oct 14 09:48:34 2021 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
epialleleR RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 39.476   2.008  41.593