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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:epialleleR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings epialleleR_1.7.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/epialleleR.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'epialleleR/DESCRIPTION' ... OK
* this is package 'epialleleR' version '1.7.0'
* 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 whether package 'epialleleR' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... NOTE
  installed size is 11.1Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      9.3Mb
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/epialleleR/libs/x64/epialleleR.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
generateVcfReport 6.11   0.25    7.33
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/epialleleR.Rcheck/00check.log'
for details.

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###
### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL epialleleR
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'epialleleR' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++17
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rcpp_cx_report.cpp -o rcpp_cx_report.o
rcpp_cx_report.cpp:182:1: warning: multi-line comment [-Wcomment]
  182 | //  #define spit_results {                                                       \
      | ^
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:32,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
                 from rcpp_cx_report.cpp:3:
F:/biocbuild/bbs-3.17-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 = dtl::pair<long long unsigned int, std::array<int, 16> >*; F = dtl::pair<long long unsigned int, std::array<int, 16> >*; typename dtl::enable_if_memtransfer_copy_assignable<I, F, F>::type = dtl::pair<long long unsigned int, std::array<int, 16> >*]':
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:2983:41:   required from 'void boost::container::vector<T, Allocator, Options>::priv_insert_forward_range_expand_forward(T*, 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 long unsigned int, std::array<int, 16> > >, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, boost::container::try_emplace_t, const long long unsigned int&, std::array<int, 16>&>; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; size_type = long long unsigned int; boost::move_detail::true_type = boost::move_detail::integral_constant<bool, true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:2827:13:   required from 'boost::container::vector<T, Allocator, Options>::iterator boost::container::vector<T, Allocator, Options>::priv_insert_forward_range(const pointer&, size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_emplace_proxy<boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, boost::container::try_emplace_t, const long long unsigned int&, std::array<int, 16>&>; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, false>; pointer = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:1865:45:   required from 'boost::container::vector<T, Allocator, Options>::iterator boost::container::vector<T, Allocator, Options>::emplace(const_iterator, Args&& ...) [with Args = {boost::container::try_emplace_t, const long long unsigned int&, std::array<int, 16>&}; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, false>; const_iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1020:48:   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(const_iterator, KeyType&&, Args&& ...) [with KeyType = const long long unsigned int&; Args = {std::array<int, 16>&}; Value = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; KeyOfValue = boost::container::dtl::select1st<long long unsigned int>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<long 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 long unsigned int, std::array<int, 16> >*, false>; typename boost::container::dtl::select_container_type<Value, AllocatorOrContainer>::type = boost::container::vector<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >, boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, void>; const_iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/flat_map.hpp:968:10:   required from 'boost::container::flat_map<Key, T, Compare, Allocator>::iterator boost::container::flat_map<Key, T, Compare, Allocator>::try_emplace(const_iterator, const key_type&, Args&& ...) [with Args = {std::array<int, 16>&}; Key = long long unsigned int; T = std::array<int, 16>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = void; iterator = boost::container::vec_iterator<std::pair<long long unsigned int, std::array<int, 16> >*, false>; const_iterator = boost::container::vec_iterator<std::pair<long long unsigned int, std::array<int, 16> >*, true>; key_type = long long unsigned int]'
rcpp_cx_report.cpp:133:32:   required from here
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:912:19: 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 long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  912 |       std::memmove((boost::movelib::iterator_to_raw_pointer)(r), (boost::movelib::iterator_to_raw_pointer)(f), sizeof(value_type)*n);
      |       ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29:
F:/biocbuild/bbs-3.17-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 long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} declared here
  218 | struct pair
      |        ^~~~
F:/biocbuild/bbs-3.17-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 = pair<long long unsigned int, std::array<int, 16> >*; F = pair<long long unsigned int, std::array<int, 16> >*]':
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:325:23:   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<dtl::pair<long long unsigned int, std::array<int, 16> > >; I = dtl::pair<long long unsigned int, std::array<int, 16> >*; F = dtl::pair<long long unsigned int, std::array<int, 16> >*; typename dtl::enable_if_memtransfer_copy_constructible<I, F, F>::type = dtl::pair<long long unsigned int, std::array<int, 16> >*]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:1205:59:   required from 'void boost::container::uninitialized_move_and_insert_alloc(Allocator&, F, F, F, O, std::size_t, InsertionProxy) [with Allocator = new_allocator<dtl::pair<long long unsigned int, std::array<int, 16> > >; F = dtl::pair<long long unsigned int, std::array<int, 16> >*; O = dtl::pair<long long unsigned int, std::array<int, 16> >*; InsertionProxy = dtl::insert_range_proxy<new_allocator<dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::move_iterator<dtl::pair<long long unsigned int, std::array<int, 16> >*>, dtl::pair<long long unsigned int, std::array<int, 16> >*>; std::size_t = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:3008:10:   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<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:2611:10:   required from 'void boost::container::vector<T, Allocator, Options>::priv_move_to_new_buffer(size_type, boost::container::version_1) [with T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; size_type = long long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:1570:39:   required from 'void boost::container::vector<T, Allocator, Options>::reserve(size_type) [with T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:380:16:   required from 'void boost::container::dtl::flat_tree_reserve(SequenceContainer&, typename SequenceContainer::size_type, boost::move_detail::true_) [with SequenceContainer = boost::container::vector<pair<long long unsigned int, std::array<int, 16> >, boost::container::new_allocator<pair<long long unsigned int, std::array<int, 16> > >, void>; typename SequenceContainer::size_type = long long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1393:26:   required from 'void boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::reserve(size_type) [with Value = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; KeyOfValue = boost::container::dtl::select1st<long long unsigned int>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/flat_map.hpp:712:28:   required from 'void boost::container::flat_map<Key, T, Compare, Allocator>::reserve(size_type) [with Key = long long unsigned int; T = std::array<int, 16>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = void; size_type = long long unsigned int]'
rcpp_cx_report.cpp:114:17:   required from here
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:184:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  184 |       std::memmove(dest_raw, beg_raw, sizeof(value_type)*n);
      |       ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'value_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} declared here
  218 | struct pair
      |        ^~~~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of 'I boost::container::dtl::memmove_n_source(I, std::size_t, F) [with I = boost::move_iterator<pair<long long unsigned int, std::array<int, 16> >*>; F = pair<long long unsigned int, std::array<int, 16> >*; std::size_t = long long unsigned int]':
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:553:32:   required from 'typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, I>::type boost::container::uninitialized_copy_alloc_n_source(Allocator&, I, std::size_t, F) [with Allocator = new_allocator<dtl::pair<long long unsigned int, std::array<int, 16> > >; I = boost::move_iterator<dtl::pair<long long unsigned int, std::array<int, 16> >*>; F = dtl::pair<long long unsigned int, std::array<int, 16> >*; typename dtl::enable_if_memtransfer_copy_constructible<I, F, I>::type = boost::move_iterator<dtl::pair<long long unsigned int, std::array<int, 16> >*>; std::size_t = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:81:75:   required from 'void boost::container::dtl::insert_range_proxy<Allocator, FwdIt, Iterator>::uninitialized_copy_n_and_update(Allocator&, Iterator, std::size_t) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; FwdIt = boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; Iterator = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; std::size_t = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:1208:54:   required from 'void boost::container::uninitialized_move_and_insert_alloc(Allocator&, F, F, F, O, std::size_t, InsertionProxy) [with Allocator = new_allocator<dtl::pair<long long unsigned int, std::array<int, 16> > >; F = dtl::pair<long long unsigned int, std::array<int, 16> >*; O = dtl::pair<long long unsigned int, std::array<int, 16> >*; InsertionProxy = dtl::insert_range_proxy<new_allocator<dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::move_iterator<dtl::pair<long long unsigned int, std::array<int, 16> >*>, dtl::pair<long long unsigned int, std::array<int, 16> >*>; std::size_t = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:3008:10:   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<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:2611:10:   required from 'void boost::container::vector<T, Allocator, Options>::priv_move_to_new_buffer(size_type, boost::container::version_1) [with T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; size_type = long long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:1570:39:   required from 'void boost::container::vector<T, Allocator, Options>::reserve(size_type) [with T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:380:16:   required from 'void boost::container::dtl::flat_tree_reserve(SequenceContainer&, typename SequenceContainer::size_type, boost::move_detail::true_) [with SequenceContainer = boost::container::vector<pair<long long unsigned int, std::array<int, 16> >, boost::container::new_allocator<pair<long long unsigned int, std::array<int, 16> > >, void>; typename SequenceContainer::size_type = long long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1393:26:   required from 'void boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::reserve(size_type) [with Value = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; KeyOfValue = boost::container::dtl::select1st<long long unsigned int>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/flat_map.hpp:712:28:   required from 'void boost::container::flat_map<Key, T, Compare, Allocator>::reserve(size_type) [with Key = long long unsigned int; T = std::array<int, 16>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = void; size_type = long long unsigned int]'
rcpp_cx_report.cpp:114:17:   required from here
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:214:19: 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 long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  214 |       std::memmove(boost::movelib::iterator_to_raw_pointer(r), boost::movelib::iterator_to_raw_pointer(f), sizeof(value_type)*n);
      |       ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.17-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 long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} declared here
  218 | struct pair
      |        ^~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rcpp_extract_patterns.cpp -o rcpp_extract_patterns.o
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:32,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
                 from rcpp_extract_patterns.cpp:2:
F:/biocbuild/bbs-3.17-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 = dtl::pair<int, int>*; F = dtl::pair<int, int>*; typename dtl::enable_if_memtransfer_copy_assignable<I, F, F>::type = dtl::pair<int, int>*]':
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:2983:41:   required from 'void boost::container::vector<T, Allocator, Options>::priv_insert_forward_range_expand_forward(T*, size_type, InsertionProxy, boost::move_detail::true_type) [with InsertionProxy = boost::container::dtl::insert_emplace_proxy<boost::container::new_allocator<boost::container::dtl::pair<int, int> >, boost::container::dtl::pair<int, int>*, boost::container::try_emplace_t, int, int>; T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; size_type = long long unsigned int; boost::move_detail::true_type = boost::move_detail::integral_constant<bool, true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:2827:13:   required from 'boost::container::vector<T, Allocator, Options>::iterator boost::container::vector<T, Allocator, Options>::priv_insert_forward_range(const pointer&, size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_emplace_proxy<boost::container::new_allocator<boost::container::dtl::pair<int, int> >, boost::container::dtl::pair<int, int>*, boost::container::try_emplace_t, int, int>; T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; iterator = boost::container::vec_iterator<boost::container::dtl::pair<int, int>*, false>; pointer = boost::container::dtl::pair<int, int>*; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:1865:45:   required from 'boost::container::vector<T, Allocator, Options>::iterator boost::container::vector<T, Allocator, Options>::emplace(const_iterator, Args&& ...) [with Args = {boost::container::try_emplace_t, int, int}; T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; iterator = boost::container::vec_iterator<boost::container::dtl::pair<int, int>*, false>; const_iterator = boost::container::vec_iterator<boost::container::dtl::pair<int, int>*, true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1020:48:   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(const_iterator, KeyType&&, Args&& ...) [with KeyType = int; Args = {int}; Value = boost::container::dtl::pair<int, int>; KeyOfValue = boost::container::dtl::select1st<int>; Compare = std::less<int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; typename boost::container::dtl::select_container_type<Value, AllocatorOrContainer>::type::iterator = boost::container::vec_iterator<boost::container::dtl::pair<int, int>*, false>; typename boost::container::dtl::select_container_type<Value, AllocatorOrContainer>::type = boost::container::vector<boost::container::dtl::pair<int, int>, boost::container::new_allocator<boost::container::dtl::pair<int, int> >, void>; const_iterator = boost::container::vec_iterator<boost::container::dtl::pair<int, int>*, true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/flat_map.hpp:1004:34:   required from 'boost::container::flat_map<Key, T, Compare, Allocator>::iterator boost::container::flat_map<Key, T, Compare, Allocator>::try_emplace(const_iterator, key_type&&, Args&& ...) [with Args = {int}; Key = int; T = int; Compare = std::less<int>; AllocatorOrContainer = void; iterator = boost::container::vec_iterator<std::pair<int, int>*, false>; const_iterator = boost::container::vec_iterator<std::pair<int, int>*, true>; key_type = int]'
rcpp_extract_patterns.cpp:103:43:   required from here
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:912:19: 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<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  912 |       std::memmove((boost::movelib::iterator_to_raw_pointer)(r), (boost::movelib::iterator_to_raw_pointer)(f), sizeof(value_type)*n);
      |       ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} declared here
  218 | struct pair
      |        ^~~~
F:/biocbuild/bbs-3.17-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 = pair<int, int>*; F = pair<int, int>*]':
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:325:23:   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<dtl::pair<int, int> >; I = dtl::pair<int, int>*; F = dtl::pair<int, int>*; typename dtl::enable_if_memtransfer_copy_constructible<I, F, F>::type = dtl::pair<int, int>*]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:1205:59:   required from 'void boost::container::uninitialized_move_and_insert_alloc(Allocator&, F, F, F, O, std::size_t, InsertionProxy) [with Allocator = new_allocator<dtl::pair<int, int> >; F = dtl::pair<int, int>*; O = dtl::pair<int, int>*; InsertionProxy = dtl::insert_range_proxy<new_allocator<dtl::pair<int, int> >, boost::move_iterator<dtl::pair<int, int>*>, dtl::pair<int, int>*>; std::size_t = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:3008:10:   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<boost::container::dtl::pair<int, int> >, boost::move_iterator<boost::container::dtl::pair<int, int>*>, boost::container::dtl::pair<int, int>*>; T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:2611:10:   required from 'void boost::container::vector<T, Allocator, Options>::priv_move_to_new_buffer(size_type, boost::container::version_1) [with T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; size_type = long long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:1570:39:   required from 'void boost::container::vector<T, Allocator, Options>::reserve(size_type) [with T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:380:16:   required from 'void boost::container::dtl::flat_tree_reserve(SequenceContainer&, typename SequenceContainer::size_type, boost::move_detail::true_) [with SequenceContainer = boost::container::vector<pair<int, int>, boost::container::new_allocator<pair<int, int> >, void>; typename SequenceContainer::size_type = long long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1393:26:   required from 'void boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::reserve(size_type) [with Value = boost::container::dtl::pair<int, int>; KeyOfValue = boost::container::dtl::select1st<int>; Compare = std::less<int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/flat_map.hpp:712:28:   required from 'void boost::container::flat_map<Key, T, Compare, Allocator>::reserve(size_type) [with Key = int; T = int; Compare = std::less<int>; AllocatorOrContainer = void; size_type = long long unsigned int]'
rcpp_extract_patterns.cpp:68:18:   required from here
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:184:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  184 |       std::memmove(dest_raw, beg_raw, sizeof(value_type)*n);
      |       ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'value_type' {aka 'struct boost::container::dtl::pair<int, int>'} declared here
  218 | struct pair
      |        ^~~~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of 'I boost::container::dtl::memmove_n_source(I, std::size_t, F) [with I = boost::move_iterator<pair<int, int>*>; F = pair<int, int>*; std::size_t = long long unsigned int]':
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:553:32:   required from 'typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, I>::type boost::container::uninitialized_copy_alloc_n_source(Allocator&, I, std::size_t, F) [with Allocator = new_allocator<dtl::pair<int, int> >; I = boost::move_iterator<dtl::pair<int, int>*>; F = dtl::pair<int, int>*; typename dtl::enable_if_memtransfer_copy_constructible<I, F, I>::type = boost::move_iterator<dtl::pair<int, int>*>; std::size_t = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:81:75:   required from 'void boost::container::dtl::insert_range_proxy<Allocator, FwdIt, Iterator>::uninitialized_copy_n_and_update(Allocator&, Iterator, std::size_t) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; FwdIt = boost::move_iterator<boost::container::dtl::pair<int, int>*>; Iterator = boost::container::dtl::pair<int, int>*; std::size_t = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:1208:54:   required from 'void boost::container::uninitialized_move_and_insert_alloc(Allocator&, F, F, F, O, std::size_t, InsertionProxy) [with Allocator = new_allocator<dtl::pair<int, int> >; F = dtl::pair<int, int>*; O = dtl::pair<int, int>*; InsertionProxy = dtl::insert_range_proxy<new_allocator<dtl::pair<int, int> >, boost::move_iterator<dtl::pair<int, int>*>, dtl::pair<int, int>*>; std::size_t = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:3008:10:   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<boost::container::dtl::pair<int, int> >, boost::move_iterator<boost::container::dtl::pair<int, int>*>, boost::container::dtl::pair<int, int>*>; T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:2611:10:   required from 'void boost::container::vector<T, Allocator, Options>::priv_move_to_new_buffer(size_type, boost::container::version_1) [with T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; size_type = long long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/vector.hpp:1570:39:   required from 'void boost::container::vector<T, Allocator, Options>::reserve(size_type) [with T = boost::container::dtl::pair<int, int>; A = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; Options = void; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:380:16:   required from 'void boost::container::dtl::flat_tree_reserve(SequenceContainer&, typename SequenceContainer::size_type, boost::move_detail::true_) [with SequenceContainer = boost::container::vector<pair<int, int>, boost::container::new_allocator<pair<int, int> >, void>; typename SequenceContainer::size_type = long long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1393:26:   required from 'void boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::reserve(size_type) [with Value = boost::container::dtl::pair<int, int>; KeyOfValue = boost::container::dtl::select1st<int>; Compare = std::less<int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<int, int> >; size_type = long long unsigned int]'
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/flat_map.hpp:712:28:   required from 'void boost::container::flat_map<Key, T, Compare, Allocator>::reserve(size_type) [with Key = int; T = int; Compare = std::less<int>; AllocatorOrContainer = void; size_type = long long unsigned int]'
rcpp_extract_patterns.cpp:68:18:   required from here
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:214:19: 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<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  214 |       std::memmove(boost::movelib::iterator_to_raw_pointer(r), boost::movelib::iterator_to_raw_pointer(f), sizeof(value_type)*n);
      |       ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} declared here
  218 | struct pair
      |        ^~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rcpp_fep.cpp -o rcpp_fep.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rcpp_get_base_freqs.cpp -o rcpp_get_base_freqs.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rcpp_get_xm_beta.cpp -o rcpp_get_xm_beta.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rcpp_match_target.cpp -o rcpp_match_target.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rcpp_read_bam.cpp -o rcpp_read_bam.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rcpp_threshold_reads.cpp -o rcpp_threshold_reads.o
g++ -shared -s -static-libgcc -o epialleleR.dll tmp.def RcppExports.o rcpp_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_read_bam.o rcpp_threshold_reads.o F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-epialleleR/00new/epialleleR/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (epialleleR)

R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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> BiocGenerics:::testPackage("epialleleR")
Reading BED file [0.050s]
Reading BAM file [0.010s]
Extracting methylation patterns [0.050s]
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
Reading BED file [0.050s]
Reading BAM file [0.000s]
Extracting methylation patterns [0.040s]
Reading BAM file [0.000s]
Extracting methylation patterns [0.050s]
Reading BAM file [0.000s]
Extracting methylation patterns [0.040s]
Reading BED file [0.020s]
Reading BAM file [0.000s]
Computing ECDFs for within- and out-of-context per-read beta values [0.030s]
Reading BED file [0.010s]
Reading BAM file [0.020s]
Computing ECDFs for within- and out-of-context per-read beta values [0.000s]
Reading BED file [0.000s]
Reading BAM file [0.000s]
Preparing amplicon report [0.010s]
Reading BED file [0.020s]
Reading BAM file [0.000s]
Thresholding reads [0.000s]
Preparing amplicon report [0.030s]
Writing the report [0.000s]
Reading BED file [0.020s]
Reading BAM file [0.000s]
Thresholding reads [0.000s]
Preparing amplicon report [0.010s]
Reading BAM file [0.010s]
Thresholding reads [0.000s]
Preparing cytosine report [0.030s]
Reading BAM file [0.020s]
Thresholding reads [0.010s]
Preparing cytosine report [0.020s]
Writing the report [0.000s]
Reading BAM file [0.010s]
Thresholding reads [0.000s]
Preparing cytosine report [0.020s]
Reading BED file [0.010s]
Reading VCF file [1.240s]
Reading BAM file [0.020s]
Extracting base frequences [0.040s]
Reading VCF file [0.170s]
Reading BAM file [0.000s]
Extracting base frequencesAlready preprocessed VCF supplied as an input. Options 'bed' and 'zero.based.bed' will have no effect.
Reading BAM file [0.010s]
Thresholding reads [0.000s]
Extracting base frequences [0.110s]
Writing the report [0.000s]
Reading BED file [0.000s]
Reading VCF file [0.590s]
Reading BAM file [0.000s]
Extracting base frequences [0.060s]
Already preprocessed BAM supplied as an input. Options 'min.mapq', 'min.baseq', 'skip.duplicates' and 'nthreads' will have no effect.

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit



RUNIT TEST PROTOCOL -- Wed Dec 28 23:39:42 2022 
*********************************************** 
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
epialleleR RUnit Tests - 7 test functions, 0 errors, 0 failures
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  16.90    1.12   18.51