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###
### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL epialleleR
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘epialleleR’ ...
** this is package ‘epialleleR’ version ‘1.19.3’
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c rcpp_fep.cpp -o rcpp_fep.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/concepts.hpp:26,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/size_type.hpp:20,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/size.hpp:21,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/functions.hpp:20,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:41,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/concept/interval_associator.hpp:11,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/associative_interval_container.hpp:18,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval_base_set.hpp:24,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval_set.hpp:14,
from rcpp_read_bam.cpp:3:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
rcpp_read_bam.cpp: In function ‘T_granges load_intervals(Rcpp::DataFrame&, const bam_hdr_t*)’:
rcpp_read_bam.cpp:61:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
61 | for (int i=0; i<seqlevels.size(); i++) { // for every BED seqlevel
| ~^~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/assert.hpp:35,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/continuous_interval.hpp:13,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/type_traits/interval_type_default.hpp:13,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval.hpp:12,
from rcpp_read_bam.cpp:2:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp: In instantiation of ‘static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<boost::DefaultConstructible<int> >]’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:137:5: required from ‘struct boost::DefaultConstructible<int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:135:3: required from ‘struct boost::DefaultConstructibleConcept<int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of ‘template<class Model> boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints<Model, (& Model::constraints)>*) [with Model = boost::DefaultConstructibleConcept<int>]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from ‘const bool boost::concepts::not_satisfied<boost::DefaultConstructibleConcept<int> >::value’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:45:51: required from ‘struct boost::concepts::not_satisfied<boost::DefaultConstructibleConcept<int> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: required from ‘struct boost::concepts::requirement_<void (*)(boost::DefaultConstructibleConcept<int>)>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/continuous_interval.hpp:45:9: required from ‘boost::icl::discrete_interval<DomainT, Compare>::discrete_interval(const DomainT&, const DomainT&, boost::icl::interval_bounds, boost::icl::discrete_interval<DomainT, Compare>*) [with DomainT = int; Compare = std::less]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/discrete_interval.hpp:120:16: required from ‘static boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::interval_type boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::construct(const domain_type&, const domain_type&, boost::icl::interval_bounds) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>; domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/concept/interval.hpp:254:52: required from ‘typename boost::enable_if<boost::icl::has_dynamic_bounds<Type>, Type>::type boost::icl::construct(const typename interval_traits<Type>::domain_type&, const typename interval_traits<Type>::domain_type&, interval_bounds) [with Type = discrete_interval<int, std::less>; typename boost::enable_if<has_dynamic_bounds<Type>, Type>::type = discrete_interval<int, std::less>; typename interval_traits<Type>::domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval.hpp:91:47: required from ‘static boost::icl::interval<DomainT, Compare>::interval_type boost::icl::interval<DomainT, Compare>::closed(const DomainT&, const DomainT&) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>]’
rcpp_read_bam.cpp:73:58: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:50:47: warning: ‘this’ pointer is null [-Wnonnull]
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:31,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/detail/concept_check.hpp:11,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/continuous_interval.hpp:14:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/usage.hpp:20:5: note: in a call to non-static member function ‘boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = boost::DefaultConstructible<int>]’
20 | ~usage_requirements() { ((Model*)0)->~Model(); }
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp: In instantiation of ‘static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::DefaultConstructibleConcept<int>]’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/continuous_interval.hpp:45:9: required from ‘boost::icl::discrete_interval<DomainT, Compare>::discrete_interval(const DomainT&, const DomainT&, boost::icl::interval_bounds, boost::icl::discrete_interval<DomainT, Compare>*) [with DomainT = int; Compare = std::less]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/discrete_interval.hpp:120:16: required from ‘static boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::interval_type boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::construct(const domain_type&, const domain_type&, boost::icl::interval_bounds) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>; domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/concept/interval.hpp:254:52: required from ‘typename boost::enable_if<boost::icl::has_dynamic_bounds<Type>, Type>::type boost::icl::construct(const typename interval_traits<Type>::domain_type&, const typename interval_traits<Type>::domain_type&, interval_bounds) [with Type = discrete_interval<int, std::less>; typename boost::enable_if<has_dynamic_bounds<Type>, Type>::type = discrete_interval<int, std::less>; typename interval_traits<Type>::domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval.hpp:91:47: required from ‘static boost::icl::interval<DomainT, Compare>::interval_type boost::icl::interval<DomainT, Compare>::closed(const DomainT&, const DomainT&) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>]’
rcpp_read_bam.cpp:73:58: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:50:47: warning: ‘this’ pointer is null [-Wnonnull]
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/aux_/integral_wrapper.hpp:22,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/int.hpp:20,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/lambda_fwd.hpp:23,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/aux_/na_spec.hpp:18,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/if.hpp:19,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/type_traits/interval_type_default.hpp:11:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:135:17: note: in a call to non-static member function ‘boost::DefaultConstructibleConcept<int>::~DefaultConstructibleConcept()’
135 | BOOST_concept(DefaultConstructible,(TT))
| ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
29 | # define BOOST_PP_CAT_I(a, b) a ## b
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/concept_def.hpp:23:12: note: in expansion of macro ‘BOOST_PP_CAT’
23 | struct BOOST_PP_CAT(name,Concept) \
| ^~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:135:3: note: in expansion of macro ‘BOOST_concept’
135 | BOOST_concept(DefaultConstructible,(TT))
| ^~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp: In instantiation of ‘static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<boost::LessThanComparable<int> >]’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:243:5: required from ‘struct boost::LessThanComparable<int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:241:3: required from ‘struct boost::LessThanComparableConcept<int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of ‘template<class Model> boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints<Model, (& Model::constraints)>*) [with Model = boost::LessThanComparableConcept<int>]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from ‘const bool boost::concepts::not_satisfied<boost::LessThanComparableConcept<int> >::value’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:45:51: required from ‘struct boost::concepts::not_satisfied<boost::LessThanComparableConcept<int> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: required from ‘struct boost::concepts::requirement_<void (*)(boost::LessThanComparableConcept<int>)>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/continuous_interval.hpp:46:9: required from ‘boost::icl::discrete_interval<DomainT, Compare>::discrete_interval(const DomainT&, const DomainT&, boost::icl::interval_bounds, boost::icl::discrete_interval<DomainT, Compare>*) [with DomainT = int; Compare = std::less]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/discrete_interval.hpp:120:16: required from ‘static boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::interval_type boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::construct(const domain_type&, const domain_type&, boost::icl::interval_bounds) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>; domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/concept/interval.hpp:254:52: required from ‘typename boost::enable_if<boost::icl::has_dynamic_bounds<Type>, Type>::type boost::icl::construct(const typename interval_traits<Type>::domain_type&, const typename interval_traits<Type>::domain_type&, interval_bounds) [with Type = discrete_interval<int, std::less>; typename boost::enable_if<has_dynamic_bounds<Type>, Type>::type = discrete_interval<int, std::less>; typename interval_traits<Type>::domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval.hpp:91:47: required from ‘static boost::icl::interval<DomainT, Compare>::interval_type boost::icl::interval<DomainT, Compare>::closed(const DomainT&, const DomainT&) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>]’
rcpp_read_bam.cpp:73:58: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:50:47: warning: ‘this’ pointer is null [-Wnonnull]
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/usage.hpp:20:5: note: in a call to non-static member function ‘boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = boost::LessThanComparable<int>]’
20 | ~usage_requirements() { ((Model*)0)->~Model(); }
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp: In instantiation of ‘static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::LessThanComparableConcept<int>]’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/continuous_interval.hpp:46:9: required from ‘boost::icl::discrete_interval<DomainT, Compare>::discrete_interval(const DomainT&, const DomainT&, boost::icl::interval_bounds, boost::icl::discrete_interval<DomainT, Compare>*) [with DomainT = int; Compare = std::less]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/discrete_interval.hpp:120:16: required from ‘static boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::interval_type boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::construct(const domain_type&, const domain_type&, boost::icl::interval_bounds) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>; domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/concept/interval.hpp:254:52: required from ‘typename boost::enable_if<boost::icl::has_dynamic_bounds<Type>, Type>::type boost::icl::construct(const typename interval_traits<Type>::domain_type&, const typename interval_traits<Type>::domain_type&, interval_bounds) [with Type = discrete_interval<int, std::less>; typename boost::enable_if<has_dynamic_bounds<Type>, Type>::type = discrete_interval<int, std::less>; typename interval_traits<Type>::domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval.hpp:91:47: required from ‘static boost::icl::interval<DomainT, Compare>::interval_type boost::icl::interval<DomainT, Compare>::closed(const DomainT&, const DomainT&) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>]’
rcpp_read_bam.cpp:73:58: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:50:47: warning: ‘this’ pointer is null [-Wnonnull]
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:241:17: note: in a call to non-static member function ‘boost::LessThanComparableConcept<int>::~LessThanComparableConcept()’
241 | BOOST_concept(LessThanComparable,(TT))
| ^~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
29 | # define BOOST_PP_CAT_I(a, b) a ## b
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/concept_def.hpp:23:12: note: in expansion of macro ‘BOOST_PP_CAT’
23 | struct BOOST_PP_CAT(name,Concept) \
| ^~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:241:3: note: in expansion of macro ‘BOOST_concept’
241 | BOOST_concept(LessThanComparable,(TT))
| ^~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/usage.hpp: In instantiation of ‘boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = boost::DefaultConstructible<int>]’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:50:47: required from ‘static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<boost::DefaultConstructible<int> >]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:137:5: required from ‘struct boost::DefaultConstructible<int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:135:3: required from ‘struct boost::DefaultConstructibleConcept<int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of ‘template<class Model> boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints<Model, (& Model::constraints)>*) [with Model = boost::DefaultConstructibleConcept<int>]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:42:5: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: required from ‘struct boost::concepts::requirement_<void (*)(boost::DefaultConstructibleConcept<int>)>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/continuous_interval.hpp:45:9: required from ‘boost::icl::discrete_interval<DomainT, Compare>::discrete_interval(const DomainT&, const DomainT&, boost::icl::interval_bounds, boost::icl::discrete_interval<DomainT, Compare>*) [with DomainT = int; Compare = std::less]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/discrete_interval.hpp:120:16: required from ‘static boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::interval_type boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::construct(const domain_type&, const domain_type&, boost::icl::interval_bounds) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>; domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/concept/interval.hpp:254:52: required from ‘typename boost::enable_if<boost::icl::has_dynamic_bounds<Type>, Type>::type boost::icl::construct(const typename interval_traits<Type>::domain_type&, const typename interval_traits<Type>::domain_type&, interval_bounds) [with Type = discrete_interval<int, std::less>; typename boost::enable_if<has_dynamic_bounds<Type>, Type>::type = discrete_interval<int, std::less>; typename interval_traits<Type>::domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval.hpp:91:47: required from ‘static boost::icl::interval<DomainT, Compare>::interval_type boost::icl::interval<DomainT, Compare>::closed(const DomainT&, const DomainT&) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>]’
rcpp_read_bam.cpp:73:58: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/usage.hpp:20:48: warning: ‘this’ pointer is null [-Wnonnull]
20 | ~usage_requirements() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/usage.hpp:37:7: note: in a call to non-static member function ‘boost::DefaultConstructible<TT>::~DefaultConstructible() [with TT = int]’
37 | ~model()
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:137:5: note: in expansion of macro ‘BOOST_CONCEPT_USAGE’
137 | BOOST_CONCEPT_USAGE(DefaultConstructible) {
| ^~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/usage.hpp: In instantiation of ‘boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = boost::LessThanComparable<int>]’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:50:47: required from ‘static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<boost::LessThanComparable<int> >]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:243:5: required from ‘struct boost::LessThanComparable<int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:241:3: required from ‘struct boost::LessThanComparableConcept<int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of ‘template<class Model> boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints<Model, (& Model::constraints)>*) [with Model = boost::LessThanComparableConcept<int>]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:42:5: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: required from ‘struct boost::concepts::requirement_<void (*)(boost::LessThanComparableConcept<int>)>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/continuous_interval.hpp:46:9: required from ‘boost::icl::discrete_interval<DomainT, Compare>::discrete_interval(const DomainT&, const DomainT&, boost::icl::interval_bounds, boost::icl::discrete_interval<DomainT, Compare>*) [with DomainT = int; Compare = std::less]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/discrete_interval.hpp:120:16: required from ‘static boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::interval_type boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::construct(const domain_type&, const domain_type&, boost::icl::interval_bounds) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>; domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/concept/interval.hpp:254:52: required from ‘typename boost::enable_if<boost::icl::has_dynamic_bounds<Type>, Type>::type boost::icl::construct(const typename interval_traits<Type>::domain_type&, const typename interval_traits<Type>::domain_type&, interval_bounds) [with Type = discrete_interval<int, std::less>; typename boost::enable_if<has_dynamic_bounds<Type>, Type>::type = discrete_interval<int, std::less>; typename interval_traits<Type>::domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval.hpp:91:47: required from ‘static boost::icl::interval<DomainT, Compare>::interval_type boost::icl::interval<DomainT, Compare>::closed(const DomainT&, const DomainT&) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>]’
rcpp_read_bam.cpp:73:58: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/usage.hpp:20:48: warning: ‘this’ pointer is null [-Wnonnull]
20 | ~usage_requirements() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/usage.hpp:37:7: note: in a call to non-static member function ‘boost::LessThanComparable<TT>::~LessThanComparable() [with TT = int]’
37 | ~model()
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:243:5: note: in expansion of macro ‘BOOST_CONCEPT_USAGE’
243 | BOOST_CONCEPT_USAGE(LessThanComparable) {
| ^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o epialleleR.so RcppExports.o rcpp_call_methylation.o rcpp_check_bam.o rcpp_cx_report.o rcpp_extract_patterns.o rcpp_fep.o rcpp_get_base_freqs.o rcpp_get_xm_beta.o rcpp_match_target.o rcpp_mhl_report.o rcpp_read_bam.o rcpp_read_genome.o rcpp_simulate_bam.o rcpp_threshold_reads.o /home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-epialleleR/00new/epialleleR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (epialleleR)
